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Aguilera-Toro M, Kragh ML, Thomasen AV, Piccini V, Rauh V, Xiao Y, Wiking L, Poulsen NA, Hansen LT, Larsen LB. Proteolytic activity and heat resistance of the protease AprX from Pseudomonas in relation to genotypic characteristics. Int J Food Microbiol 2023; 391-393:110147. [PMID: 36848797 DOI: 10.1016/j.ijfoodmicro.2023.110147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
AprX is an alkaline metalloprotease produced by Pseudomonas spp. and encoded by its initial gene of the aprX-lipA operon. The intrinsic diversity among Pseudomonas spp. regarding their proteolytic activity is the main challenge for the development of accurate methods for spoilage prediction of ultra-high temperature (UHT) treated milk in the dairy industry. In the present study, 56 Pseudomonas strains were characterized by assessing their proteolytic activity in milk before and after lab-scale UHT treatment. From these, 24 strains were selected based on their proteolytic activity for whole genome sequencing (WGS) to identify common genotypic characteristics that correlated with the observed variations in proteolytic activity. Four groups (A1, A2, B and N) were determined based on operon aprX-lipA sequence similarities. These alignment groups were observed to significantly influence the proteolytic activity of the strains, with an average proteolytic activity of A1 > A2 > B > N. The lab-scale UHT treatment did not significantly influence their proteolytic activity, indicating a high thermal stability of proteases among strains. Amino acid sequence variation of biologically-relevant motifs in the AprX sequence, namely the Zn2+-binding motif at the catalytic domain and the C-terminal type I secretion signaling mechanism, were found to be highly conserved within alignment groups. These motifs could serve as future potential genetic biomarkers for determination of alignment groups and thereby strain spoilage potential.
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Affiliation(s)
| | - Martin Laage Kragh
- Technical University of Denmark, Food Microbiology and Hygiene Research Group, Denmark
| | | | | | | | - Yinghua Xiao
- Arla Innovation Center, Arla Foods Amba, Denmark
| | - Lars Wiking
- Department of Food Science, Aarhus University, Denmark
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2
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Leader DP, Milner-White EJ. Identification and characterization of two classes of G1 β-bulge. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:217-223. [PMID: 33559610 PMCID: PMC7869896 DOI: 10.1107/s2059798320015533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/24/2020] [Indexed: 11/10/2022]
Abstract
In standard β-bulges, a residue in one strand of a β-sheet forms hydrogen bonds to two successive residues (`1' and `2') of a second strand. Two categories, `classic' and `G1' β-bulges, are distinguished by their dihedral angles: 1,2-αRβR (classic) or 1,2-αLβR (G1). It had previously been observed that G1 β-bulges are most often found as components of two quite distinct composite structures, suggesting that a basis for further differentiation might exist. Here, it is shown that two subtypes of G1 β-bulges, G1α and G1β, may be distinguished by their conformation (αR or βR) at residue `0' of the second strand. β-Bulges that are constituents of the composite structure named the β-bulge loop are of the G1α type, whereas those that are constituents of the composite structure named β-link here are of the G1β type. A small proportion of G1β β-bulges, but not G1α β-bulges, occur in other contexts. There are distinctive differences in amino-acid composition and sequence pattern between these two types of G1 β-bulge which may have practical application in protein design.
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Affiliation(s)
- David P Leader
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - E James Milner-White
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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3
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Baumann U. Structure-Function Relationships of the Repeat Domains of RTX Toxins. Toxins (Basel) 2019; 11:toxins11110657. [PMID: 31718085 PMCID: PMC6891781 DOI: 10.3390/toxins11110657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/07/2019] [Accepted: 11/09/2019] [Indexed: 01/08/2023] Open
Abstract
RTX proteins are a large family of polypeptides of mainly Gram-negative origin that are secreted into the extracellular medium by a type I secretion system featuring a non-cleavable C-terminal secretion signal, which is preceded by a variable number of nine-residue tandem repeats. The three-dimensional structure forms a parallel β-roll, where β-strands of two parallel sheets are connected by calcium-binding linkers in such a way that a right-handed spiral is built. The Ca2+ ions are an integral part of the structure, which cannot form without them. The structural determinants of this unique architecture will be reviewed with its conservations and variations together with the implication for secretion and folding of these proteins. The general purpose of the RTX domains appears to act as an internal chaperone that keeps the polypeptide unfolded in the calcium-deprived cytosol and triggers folding in the calcium-rich extracellular medium. A rather recent addition to the structural biology of the RTX toxin is a variant occurring in a large RTX adhesin, where this non-canonical β-roll binds to ice and diatoms.
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Affiliation(s)
- Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Zülpicherstrasse 47, D-50674 Cologne, Germany
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4
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Role of structural ions on the dynamics of the Pseudomonas fluorescens 07A metalloprotease. Food Chem 2019; 286:309-315. [DOI: 10.1016/j.foodchem.2019.01.204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/24/2019] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
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5
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Matéos A, Guyard-Nicodème M, Baglinière F, Jardin J, Gaucheron F, Dary A, Humbert G, Gaillard JL. Proteolysis of milk proteins by AprX, an extracellular protease identified in Pseudomonas LBSA1 isolated from bulk raw milk, and implications for the stability of UHT milk. Int Dairy J 2015. [DOI: 10.1016/j.idairyj.2015.04.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Zhang L, Morrison AJ, Thibodeau PH. Interdomain Contacts and the Stability of Serralysin Protease from Serratia marcescens. PLoS One 2015; 10:e0138419. [PMID: 26378460 PMCID: PMC4574703 DOI: 10.1371/journal.pone.0138419] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 08/30/2015] [Indexed: 11/20/2022] Open
Abstract
The serralysin family of bacterial metalloproteases is associated with virulence in multiple modes of infection. These extracellular proteases are members of the Repeats-in-ToXin (RTX) family of toxins and virulence factors, which mediated virulence in E. coli, B. pertussis, and P. aeruginosa, as well as other animal and plant pathogens. The serralysin proteases are structurally dynamic and their folding is regulated by calcium binding to a C-terminal domain that defines the RTX family of proteins. Previous studies have suggested that interactions between N-terminal sequences and this C-terminal domain are important for the high thermal and chemical stabilities of the RTX proteases. Extending from this, stabilization of these interactions in the native structure may lead to hyperstabilization of the folded protein. To test this hypothesis, cysteine pairs were introduced into the N-terminal helix and the RTX domain and protease folding and activity were assessed. Under stringent pH and temperature conditions, the disulfide-bonded mutant showed increased protease activity and stability. This activity was dependent on the redox environment of the refolding reaction and could be blocked by selective modification of the cysteine residues before protease refolding. These data demonstrate that the thermal and chemical stability of these proteases is, in part, mediated by binding between the RTX domain and the N-terminal helix and demonstrate that stabilization of this interaction can further stabilize the active protease, leading to additional pH and thermal tolerance.
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Affiliation(s)
- Liang Zhang
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, United States of America
| | - Anneliese J. Morrison
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, United States of America
| | - Patrick H. Thibodeau
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, United States of America
- * E-mail:
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7
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Schacherl M, Pichlo C, Neundorf I, Baumann U. Structural Basis of Proline-Proline Peptide Bond Specificity of the Metalloprotease Zmp1 Implicated in Motility of Clostridium difficile. Structure 2015. [DOI: 10.1016/j.str.2015.06.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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8
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Cerdà-Costa N, Gomis-Rüth FX. Architecture and function of metallopeptidase catalytic domains. Protein Sci 2014; 23:123-44. [PMID: 24596965 DOI: 10.1002/pro.2400] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The cleavage of peptide bonds by metallopeptidases (MPs) is essential for life. These ubiquitous enzymes participate in all major physiological processes, and so their deregulation leads to diseases ranging from cancer and metastasis, inflammation, and microbial infection to neurological insults and cardiovascular disorders. MPs cleave their substrates without a covalent intermediate in a single-step reaction involving a solvent molecule, a general base/acid, and a mono- or dinuclear catalytic metal site. Most monometallic MPs comprise a short metal-binding motif (HEXXH), which includes two metal-binding histidines and a general base/acid glutamate, and they are grouped into the zincin tribe of MPs. The latter divides mainly into the gluzincin and metzincin clans. Metzincins consist of globular ∼ 130-270-residue catalytic domains, which are usually preceded by N-terminal pro-segments, typically required for folding and latency maintenance. The catalytic domains are often followed by C-terminal domains for substrate recognition and other protein-protein interactions, anchoring to membranes, oligomerization, and compartmentalization. Metzincin catalytic domains consist of a structurally conserved N-terminal subdomain spanning a five-stranded β-sheet, a backing helix, and an active-site helix. The latter contains most of the metal-binding motif, which is here characteristically extended to HEXXHXXGXX(H,D). Downstream C-terminal subdomains are generally shorter, differ more among metzincins, and mainly share a conserved loop--the Met-turn--and a C-terminal helix. The accumulated structural data from more than 300 deposited structures of the 12 currently characterized metzincin families reviewed here provide detailed knowledge of the molecular features of their catalytic domains, help in our understanding of their working mechanisms, and form the basis for the design of novel drugs.
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9
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Thomas S, Bakkes PJ, Smits SHJ, Schmitt L. Equilibrium folding of pro-HlyA from Escherichia coli reveals a stable calcium ion dependent folding intermediate. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1500-10. [PMID: 24865936 DOI: 10.1016/j.bbapap.2014.05.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/13/2014] [Accepted: 05/16/2014] [Indexed: 11/17/2022]
Abstract
HlyA from Escherichia coli is a member of the repeats in toxin (RTX) protein family, produced by a wide range of Gram-negative bacteria and secreted by a dedicated Type 1 Secretion System (T1SS). RTX proteins are thought to be secreted in an unfolded conformation and to fold upon secretion by Ca(2+) binding. However, the exact mechanism of secretion, ion binding and folding to the correct native state remains largely unknown. In this study we provide an easy protocol for high-level pro-HlyA purification from E. coli. Equilibrium folding studies, using intrinsic tryptophan fluorescence, revealed the well-known fact that Ca(2+) is essential for stability as well as correct folding of the whole protein. In the absence of Ca(2+), pro-HlyA adopts a non-native conformation. Such molecules could however be rescued by Ca(2+) addition, indicating that these are not dead-end species and that Ca(2+) drives pro-HlyA folding. More importantly, pro-HlyA unfolded via a two-state mechanism, whereas folding was a three-state process. The latter is indicative of the presence of a stable folding intermediate. Analysis of deletion and Trp mutants revealed that the first folding transition, at 6-7M urea, relates to Ca(2+) dependent structural changes at the extreme C-terminus of pro-HlyA, sensed exclusively by Trp914. Since all Trp residues of HlyA are located outside the RTX domain, our results demonstrate that Ca(2+) induced folding is not restricted to the RTX domain. Taken together, Ca(2+) binding to the pro-HlyA RTX domain is required to drive the folding of the entire protein to its native conformation.
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Affiliation(s)
- Sabrina Thomas
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr 1, 40225 Düsseldorf, Germany
| | - Patrick J Bakkes
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr 1, 40225 Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr 1, 40225 Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr 1, 40225 Düsseldorf, Germany.
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10
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Balaban NP, Rudakova NL, Sharipova MR. Structural and functional characteristics and properties of metzincins. BIOCHEMISTRY (MOSCOW) 2012; 77:119-27. [PMID: 22348470 DOI: 10.1134/s0006297912020010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this review the main families of endopeptidases belonging to the clan of metzincins of zinc-dependent metalloproteinases in organisms of wide evolutional range from bacteria to mammals are considered. The data on classification, physicochemical properties, substrate specificity, and structural features of this group of enzymes are given. The activation mechanisms of metzincins, the role of these proteins in organisms, and their participation in various physiological processes are discussed.
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11
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Massaoud MK, Marokházi J, Venekei I. Enzymatic characterization of a serralysin-like metalloprotease from the entomopathogen bacterium, Xenorhabdus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1333-9. [PMID: 21635975 DOI: 10.1016/j.bbapap.2011.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/27/2011] [Accepted: 05/11/2011] [Indexed: 11/19/2022]
Abstract
We investigated the enzymatic properties of a serralysin-type metalloenzyme, provisionally named as protease B, which is secreted by Xenorhabdus bacterium, and probably is the ortholog of PrA peptidase of Photorhabdus bacterium. Testing the activity on twenty-two oligopeptide substrates we found that protease B requires at least three amino acids N-terminal to the scissile bond for detectable hydrolysis. On such substrate protease B was clearly specific for positively charged residues (Arg and Lys) at the P1 substrate position and was rather permissive in the others. Interestingly however, it preferred Ser at P1 in the oligopeptide substrate which contained amino acids also C-terminal to the scissile bond, and was cleaved with the highest k(cat)/K(M) value. The pH profile of activity, similarly to other serralysins, has a wide peak with high values between pH 6.5 and 8.0. The activity was slightly increased by Cu(2+) and Co(2+) ions, it was not sensitive for serine protease inhibitors, but it was inhibited by 1,10-phenanthroline, features shared by many Zn-metalloproteases. At the same time, EDTA inhibited the activity only partially even either after long incubation or in excess amount, and Zn(2+) was inhibitory (both are unusual among serralysins). The 1,10-phenanthroline inhibited activity could be restored with the addition of Mn(2+), Cu(2+) and Co(2+) up to 90-200% of its original value, while Zn(2+) was inefficient. We propose that both the Zn inhibition of protease B activity and its resistance to EDTA inhibition might be caused by an Asp in position 191 where most of the serralysins contain Asn.
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Affiliation(s)
- Mustafa K Massaoud
- Department of Biochemistry, Eotovos Lorand University, Budapest, Hungary.
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12
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A novel secreted metzincin metalloproteinase from Bacillus intermedius. FEBS Lett 2010; 584:4419-25. [DOI: 10.1016/j.febslet.2010.09.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 09/16/2010] [Accepted: 09/18/2010] [Indexed: 01/03/2023]
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13
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Pojanapotha P, Thamwiriyasati N, Powthongchin B, Katzenmeier G, Angsuthanasombat C. Bordetella pertussis CyaA-RTX subdomain requires calcium ions for structural stability against proteolytic degradation. Protein Expr Purif 2010; 75:127-32. [PMID: 20691271 DOI: 10.1016/j.pep.2010.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 07/25/2010] [Accepted: 07/30/2010] [Indexed: 10/19/2022]
Abstract
Previously, the 126-kDa Bordetella pertussis CyaA pore-forming (CyaA-PF) domain expressed in Escherichia coli was shown to retain its hemolytic activity. Here, a 100-kDa RTX (Repeat-in-ToXin) subcloned fragment (CyaA-RTX) containing a number of putative calcium-binding repeats was further investigated. The recombinant CyaA-RTX protein, although expressed as a soluble form in a protease-deficient E. coli strain BL21(DE3)pLysS, was found to be highly sensitive to proteolytic degradation. Interestingly, the addition of calcium ions in a millimolar range into the CyaA-RTX preparation significantly prevented the degradation. Moreover, levels of proteolytic degradation were dependent on calcium concentrations, implying an important role for calcium-binding sites in the RTX subdomain for structural stability. Homology-based modeling of the repetitive blocks in the CyaA-RTX subdomain supports that this calcium-bound protein folds into a parallel β-roll structure with calcium ions acting as a structural stabilizing bridge.
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Affiliation(s)
- Pichaya Pojanapotha
- Laboratory of Molecular Biophysics and Structural Biochemistry, Bacterial Protein Toxin Research Cluster, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom 73170, Thailand
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14
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Sánchez-Magraner L, Cortajarena AL, García-Pacios M, Arrondo JLR, Agirre J, Guérin DMA, Goñi FM, Ostolaza H. Interdomain Ca(2+) effects in Escherichia coli alpha-haemolysin: Ca(2+) binding to the C-terminal domain stabilizes both C- and N-terminal domains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1225-33. [PMID: 20223223 DOI: 10.1016/j.bbamem.2010.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 02/08/2010] [Accepted: 03/03/2010] [Indexed: 11/17/2022]
Abstract
alpha-Haemolysin (HlyA) is a toxin secreted by pathogenic Escherichia coli, whose lytic activity requires submillimolar Ca(2+) concentrations. Previous studies have shown that Ca(2+) binds within the Asp and Gly rich C-terminal nonapeptide repeat domain (NRD) in HlyA. The presence of the NRD puts HlyA in the RTX (Repeats in Toxin) family of proteins. We tested the stability of the whole protein, the amphipathic helix domain and the NRD, in both the presence and absence of Ca(2+) using native HlyA, a truncated form of HlyADeltaN601 representing the C-terminal domain, and a novel mutant HlyA W914A whose intrinsic fluorescence indicates changes in the N-terminal domain. Fluorescence and infrared spectroscopy, tryptic digestion, and urea denaturation techniques concur in showing that calcium binding to the repeat domain of alpha-haemolysin stabilizes and compacts both the NRD and the N-terminal domains of HlyA. The stabilization of the N-terminus through Ca(2+) binding to the C-terminus reveals long-range inter-domain structural effects. Considering that RTX proteins consist, in general, of a Ca(2+)-binding NRD and separate function-specific domains, the long-range stabilizing effects of Ca(2+) in HlyA may well be common to other members of this family.
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Affiliation(s)
- Lissete Sánchez-Magraner
- Unidad de Biofísica (Centro Mixto CSIC-UPV/EHU), and the Departamento de Bioquímica, Universidad del País Vasco, Aptdo. 644, 48080 Bilbao, Spain
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15
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Tallant C, García-Castellanos R, Baumann U, Gomis-Rüth FX. On the relevance of the Met-turn methionine in metzincins. J Biol Chem 2010; 285:13951-7. [PMID: 20202937 DOI: 10.1074/jbc.m109.083378] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The metzincins are a clan of metallopeptidases consisting of families that share a series of structural elements. Among them is the Met-turn, a tight 1,4-turn found directly below the zinc-binding site, which is structurally and spatially conserved and invariantly shows a methionine at position 3 in all metzincins identified. The reason for this conservation has been a matter of debate since its discovery. We have studied this structural element in Methanosarcina acetivorans ulilysin, the structural prototype of the pappalysin family, by generating 10 mutants that replaced methionine with proteogenic amino acids. We compared recombinant overexpression yields, autolytic and tryptic activation, proteolytic activity, thermal stability, and three-dimensional structure with those of the wild type. All forms were soluble and could be purified, although with varying yields, and three variants underwent autolysis, could be activated by trypsin, and displayed significant proteolytic activity. All variants were analyzed for the thermal stability of their zymogens. None of the mutants analyzed proved more stable or active than the wild type. Both bulky and small side chains, as well as hydrophilic ones, showed diminished thermal stability. Two mutants, leucine and cysteine, crystallized and showed three-dimensional structures that were indistinguishable from the wild type. These studies reveal that the Met-turn acts as a plug that snugly inserts laterally into a core structure created by the protein segment engaged in zinc binding and thus contributes to its structural integrity, which is indispensable for function. Replacement of the methionine with residues that deviate in size, side-chain conformation, and chemical properties impairs the plug-core interaction and prejudices molecular stability and activity.
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Affiliation(s)
- Cynthia Tallant
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona Science Park, Helix Building, c/Baldiri Reixac, 15-21, E-08028 Barcelona, Spain
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16
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Chufán EE, De M, Eipper BA, Mains RE, Amzel LM. Amidation of bioactive peptides: the structure of the lyase domain of the amidating enzyme. Structure 2009; 17:965-73. [PMID: 19604476 DOI: 10.1016/j.str.2009.05.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 04/29/2009] [Accepted: 05/01/2009] [Indexed: 11/26/2022]
Abstract
Many neuropeptides and peptide hormones require amidation of their carboxy terminal for full biological activity. The enzyme peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL; EC 4.3.2.5) catalyzes the second and last step of this reaction, N-dealkylation of the peptidyl-alpha-hydroxyglycine to generate the alpha-amidated peptide and glyoxylate. Here we report the X-ray crystal structure of the PAL catalytic core (PALcc) alone and in complex with the nonpeptidic substrate alpha-hydroxyhippuric acid. The structures show that PAL folds as a six-bladed beta-propeller. The active site is formed by a Zn(II) ion coordinated by three histidine residues; the substrate binds to this site with its alpha-hydroxyl group coordinated to the Zn(II) ion. The structures also reveal a tyrosine residue (Tyr(654)) at the active site as the catalytic base for hydroxyl deprotonation, an unusual role for tyrosine. A reaction mechanism is proposed based on this structural data and validated by biochemical analysis of site-directed PALcc mutants.
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Affiliation(s)
- Eduardo E Chufán
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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17
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Oberholzer AE, Bumann M, Hege T, Russo S, Baumann U. Metzincin's canonical methionine is responsible for the structural integrity of the zinc-binding site. Biol Chem 2009; 390:875-81. [DOI: 10.1515/bc.2009.100] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The metzincins constitute a subclan of metalloproteases possessing a HEXXHXXGXXH/D zinc-binding consensus sequence where the three histidines are zinc ligands and the glutamic acid is the catalytic base. A completely conserved methionine is located downstream of this motif. Families of the metzincin clan comprise, besides others, astacins, adamalysins proteases, matrix metallo-proteases, and serralysins. The latter are extracellular 50 kDa proteases secreted by Gram-negative bacteria via a type I secretion system. While there is a large body of structural and biochemical information available, the function of the conserved methionine has not been convincingly clarified yet. Here, we present the crystal structures of a number of mutants of the serralysin member protease C with the conserved methionine being replaced by Ile, Ala, and His. Together with our former report on the leucine and cysteine mutants, we demonstrate here that replacement of the methionine side chain results in an increasing distortion of the zinc-binding geometry, especially pronounced in the χ2 angles of the first and third histidine of the consensus sequence. This is correlated with an increasing loss of proteolytic activity and a sharp increase of flexibility of large segments of the polypeptide chain.
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18
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Abstract
Metalloproteases cleave proteins and peptides, and deregulation of their function leads to pathology. An understanding of their structure and mechanisms of action is necessary to the development of strategies for their regulation. Among metallopeptidases are the metzincins, which are mostly multidomain proteins with approximately 130-260-residue globular catalytic domains showing a common core architecture characterized by a long zinc-binding consensus motif, HEXXHXXGXX(H/D), and a methionine-containing Met-turn. Metzincins participate in unspecific protein degradation such as digestion of intake proteins and tissue development, maintenance, and remodeling, but they are also involved in highly specific cleavage events to activate or inactivate themselves or other (pro)enzymes and bioactive peptides. Metzincins are subdivided into families, and seven such families have been analyzed at the structural level: the astacins, ADAMs/adamalysins/reprolysins, serralysins, matrix metalloproteinases, snapalysins, leishmanolysins, and pappalysins. These families are reviewed from a structural point of view.
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Affiliation(s)
- F Xavier Gomis-Rüth
- Proteolysis Lab, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona Science Park, Helix Building, c/Baldiri Reixac, 15-21, E-08028 Barcelona, Spain.
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Chung CW, You J, Kim K, Moon Y, Kim H, Ahn JH. Export of recombinant proteins in Escherichia coli using ABC transporter with an attached lipase ABC transporter recognition domain (LARD). Microb Cell Fact 2009; 8:11. [PMID: 19178697 PMCID: PMC2642768 DOI: 10.1186/1475-2859-8-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 01/29/2009] [Indexed: 11/21/2022] Open
Abstract
Background ATP binding cassette (ABC) transporter secretes the protein through inner and outer membranes simultaneously in gram negative bacteria. Thermostable lipase (TliA) of Pseudomonas fluorescens SIK W1 is secreted through the ABC transporter. TliA has four glycine-rich repeats (GGXGXD) in its C-terminus, which appear in many ABC transporter-secreted proteins. From a homology model of TliA derived from the structure of P. aeruginosa alkaline protease (AprA), lipase ABC transporter domains (LARDs) were designed for the secretion of fusion proteins. Results The LARDs included four glycine-rich repeats comprising a β-roll structure, and were added to the C-terminus of test proteins. Either Pro-Gly linker or Factor Xa site was added between fusion proteins and LARDs. We attached different length of LARDs such as LARD0, LARD1 or whole TliA (the longest LARD) to three types of proteins; green fluorescent protein (GFP), epidermal growth factor (EGF) and cytoplasmic transduction peptide (CTP). These fusion proteins were expressed in Escherichia coli together with ABC transporter of either P. fluorescens or Erwinia chrysanthemi. Export of fusion proteins with the whole TliA through the ABC transporter was evident on the basis of lipase enzymatic activity. Upon supplementation of E. coli with ABC transporter, GFP-LARDs and EGF-LARDs were excreted into the culture supernatant. Conclusion The LARDs or whole TliA were attached to C-termini of model proteins and enabled the export of the model proteins such as GFP and EGF in E. coli supplemented with ABC transporter. These results open the possibility for the extracellular production of recombinant proteins in Pseudomonas using LARDs or TliA as a C-terminal signal sequence.
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Affiliation(s)
- Chan Woo Chung
- Korea Science Academy, #899, Tanggam 3-Dong, Busanjin-Gu, Busan, 614-822, Korea.
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20
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Meier R, Drepper T, Svensson V, Jaeger KE, Baumann U. A Calcium-gated Lid and a Large β-Roll Sandwich Are Revealed by the Crystal Structure of Extracellular Lipase from Serratia marcescens. J Biol Chem 2007; 282:31477-83. [PMID: 17728256 DOI: 10.1074/jbc.m704942200] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lipase LipA from Serratia marcescens is a 613-amino acid enzyme belonging to family I.3 of lipolytic enzymes that has an important biotechnological application in the production of a chiral precursor for the coronary vasodilator diltiazem. Like other family I.3 lipases, LipA is secreted by Gram-negative bacteria via a type I secretion system and possesses 13 copies of a calcium binding tandem repeat motif, GGXGXDXUX (U, hydrophobic amino acids), in the C-terminal part of the polypeptide chain. The 1.8-A crystal structure of LipA reveals a close relation to eukaryotic lipases, whereas family I.1 and I.2 enzymes appear to be more distantly related. Interestingly, the structure shows for the N-terminal lipase domain a variation on the canonical alpha/beta hydrolase fold in an open conformation, where the putative lid helix is anchored by a Ca(2+) ion essential for activity. Another novel feature observed in this lipase structure is the presence of a helical hairpin additional to the putative lid helix that exposes a hydrophobic surface to the aqueous medium and might function as an additional lid. The tandem repeats form two separated parallel beta-roll domains that pack tightly against each other. Variations of the consensus sequence of the tandem repeats within the second beta-roll result in an asymmetric Ca(2+) binding on only one side of the roll. The analysis of the properties of the beta-roll domains suggests an intramolecular chaperone function.
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Affiliation(s)
- Reto Meier
- Department of Chemistry and Biochemistry, University Bern Freiestrasse 3, CH-3012 Bern, Switzerland
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21
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Scotter AJ, Guo M, Tomczak MM, Daley ME, Campbell RL, Oko RJ, Bateman DA, Chakrabartty A, Sykes BD, Davies PL. Metal ion-dependent, reversible, protein filament formation by designed beta-roll polypeptides. BMC STRUCTURAL BIOLOGY 2007; 7:63. [PMID: 17908326 PMCID: PMC2174480 DOI: 10.1186/1472-6807-7-63] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 10/01/2007] [Indexed: 12/28/2022]
Abstract
BACKGROUND A right-handed, calcium-dependent beta-roll structure found in secreted proteases and repeat-in-toxin proteins was used as a template for the design of minimal, soluble, monomeric polypeptides that would fold in the presence of Ca2+. Two polypeptides were synthesised to contain two and four metal-binding sites, respectively, and exploit stacked tryptophan pairs to stabilise the fold and report on the conformational state of the polypeptide. RESULTS Initial analysis of the two polypeptides in the presence of calcium suggested the polypeptides were disordered. The addition of lanthanum to these peptides caused aggregation. Upon further study by right angle light scattering and electron microscopy, the aggregates were identified as ordered protein filaments that required lanthanum to polymerize. These filaments could be disassembled by the addition of a chelating agent. A simple head-to-tail model is proposed for filament formation that explains the metal ion-dependency. The model is supported by the capping of one of the polypeptides with biotin, which disrupts filament formation and provides the ability to control the average length of the filaments. CONCLUSION Metal ion-dependent, reversible protein filament formation is demonstrated for two designed polypeptides. The polypeptides form filaments that are approximately 3 nm in diameter and several hundred nm in length. They are not amyloid-like in nature as demonstrated by their behaviour in the presence of congo red and thioflavin T. A capping strategy allows for the control of filament length and for potential applications including the "decoration" of a protein filament with various functional moieties.
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Affiliation(s)
- Andrew J Scotter
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Biochemistry, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Meng Guo
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Medical Biophysics, University of Toronto, ON, M5G 2M9, Canada
- Ontario Cancer Institute, University of Toronto, ON, M5G 2M9, Canada
| | - Melanie M Tomczak
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Biochemistry, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Margaret E Daley
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, 6G 2H7, Canada
| | - Robert L Campbell
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Biochemistry, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Richard J Oko
- Department of Anatomy and Cell Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| | - David A Bateman
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Medical Biophysics, University of Toronto, ON, M5G 2M9, Canada
- Ontario Cancer Institute, University of Toronto, ON, M5G 2M9, Canada
| | - Avijit Chakrabartty
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Medical Biophysics, University of Toronto, ON, M5G 2M9, Canada
- Ontario Cancer Institute, University of Toronto, ON, M5G 2M9, Canada
| | - Brian D Sykes
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, 6G 2H7, Canada
| | - Peter L Davies
- Protein Engineering Network Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB, T6G 2S2, Canada
- Department of Biochemistry, Queen's University, Kingston, ON, K7L 3N6, Canada
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22
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Marokházi J, Mihala N, Hudecz F, Fodor A, Gráf L, Venekei I. Cleavage site analysis of a serralysin-like protease, PrtA, from an insect pathogen Photorhabdus luminescens and development of a highly sensitive and specific substrate. FEBS J 2007; 274:1946-56. [PMID: 17355285 DOI: 10.1111/j.1742-4658.2007.05739.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aim of this study was the development of a sensitive and specific substrate for protease A (PrtA), a serralysin-like metzincin from the entomopathogenic microorganism, Photorhabdus. First, cleavage of three biological peptides, the A and B chains of insulin and beta-lipotropin, and of 15 synthetic peptides, was investigated. In the biological peptides, a preference for the hydrophobic residues Ala, Leu and Val was observed at three substrate positions, P2, P1' and P2'. At these positions in the synthetic peptides the preferred residues were Val, Ala and Val, respectively. They contributed to the efficiency of hydrolysis in the order P1' > P2 > P2'. Six amino acids of the synthetic peptides were sufficient to reach the maximum rate of hydrolysis, in accordance with the ability of PrtA to cleave three amino acids from both the N- and the C-terminus of some fragments of biological peptides. Using the best synthetic peptide, a fluorescence-quenched substrate, N-(4-[4'(dimethylamino)phenylazo]benzoyl-EVYAVES-5-[(2-aminoethyl)amino]naphthalene-1-sulfonic acid, was prepared. The approximately 4 x 10(6) M(-1) x s(-1) specificity constant of PrtA (at K(m) approximately 5 x 10(-5) M and k(cat) approximately 2 x 10(2) s(-1)) on this substrate was the highest activity for a serralysin-type enzyme, allowing precise measurement of the effects of several inhibitors and pH on PrtA activity. These showed the characteristics of a metalloenzyme and a wide range of optimum pH, similar to other serralysins. PrtA activity could be measured in biological samples (Photorhabdus-infected insect larvae) without interference from other enzymes, which indicates that substrate selectivity is high towards PrtA. The substrate sensitivity allowed early (14 h post infection) detection of PrtA, which might indicate PrtA's participation in the establishment of infection and not only, as it has been supposed, in bioconversion.
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Affiliation(s)
- Judit Marokházi
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
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Angkawidjaja C, You DJ, Matsumura H, Koga Y, Takano K, Kanaya S. Extracellular overproduction and preliminary crystallographic analysis of a family I.3 lipase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:187-9. [PMID: 17329810 PMCID: PMC2330184 DOI: 10.1107/s1744309107004575] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Accepted: 01/29/2007] [Indexed: 11/10/2022]
Abstract
A family I.3 lipase from Pseudomonas sp. MIS38 was secreted from Escherichia coli cells to the external medium, purified and crystallized and preliminary crystallographic studies were performed. The crystal was grown at 277 K by the hanging-drop vapour-diffusion method. Native X-ray diffraction data were collected to 1.7 A resolution using synchrotron radiation at station BL38B1, SPring-8. The crystal belongs to space group P2(1), with unit-cell parameters a = 48.79, b = 84.06, c = 87.04 A. Assuming the presence of one molecule per asymmetric unit, the Matthews coefficient V(M) was calculated to be 2.73 A3 Da(-1) and the solvent content was 55%.
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Affiliation(s)
- Clement Angkawidjaja
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Dong-Ju You
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroyoshi Matsumura
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- CREST (Sosho Project), JST, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuichi Koga
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazufumi Takano
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- CREST (Sosho Project), JST, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigenori Kanaya
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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24
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Abstract
Beta-rolls and beta-helices belong to a larger group of topologically similar proteins with solenoid folds: because their regular secondary structure elements are exclusively beta-strands, they are referred to as beta-solenoids. The number of beta-solenoids whose structures are known is now large enough to support a systematic analysis. Here we survey the distinguishing structural features of beta-solenoids, also documenting their notable diversity. Appraisal of these structures suggests a classification based on handedness, twist, oligomerization state, and coil shape. In addition, beta-solenoids are distinguished by the number of chains that wind around a common axis: the majority are single-stranded but there is a recently discovered subset of triple-stranded beta-solenoids. This survey has revealed some relationships of the amino acid sequences of beta-solenoids with their structures and functions-in particular, the repetitive character of the coil sequences and conformations that recur in tracts of tandem repeats. We have proposed the term beta-arc for the distinctive turns found in beta-solenoids and beta-arch for the corresponding strand-turn-strand motifs. The evolutionary mechanisms underlying these proteins are also discussed. This analysis has direct implications for sequence-based detection, structural prediction, and de novo design of other beta-solenoid proteins. The abundance of virulence factors, toxins and allergens among beta-solenoids, as well as commonalities of beta-solenoids with amyloid fibrils, imply that this class of folds may have a broader role in human diseases than was previously recognized. Thus, identification of genes with putative beta-solenoid domains promises to be a fertile direction in the search for viable targets in the development of new antibiotics and vaccines.
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Affiliation(s)
- Andrey V Kajava
- Centre de Recherches de Biochimie Macromoléculaire, CNRS FRE-2593, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
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25
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Sénèque O, Rager MN, Giorgi M, Prangé T, Tomas A, Reinaud O. Biomimetic Zinc Funnel Complexes Based on Calix[6]N3ArO Ligands: An Acid−Base Switch for Guest Binding. J Am Chem Soc 2005; 127:14833-40. [PMID: 16231937 DOI: 10.1021/ja053620e] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The coordination chemistry of Zn in an N(3)ArOH environment has been explored. The ligands are based on calix[6]arenes that present two imidazole arms and an amino phenol moiety at the narrow rim. Three different types of complexes have been characterized. One is dicationic with Zn(2+) coordinated to the three nitrogen atoms and to the oxygen of the phenol group of the calix[6]ligand. This complex is very sensitive to exogenous coordinating molecules and exists as a 5-coordinate species due to the endo-complexation of a guest. The second species is a monocationic complex for which the phenol group has been deprotonated. The resulting N(3)ArOZn complex can also bind a guest ligand albeit with a lower affinity than the dicationic complex. The third species is neutral. It can be obtained upon reaction with a base to yield a hydroxo complex or with an anion such as a chloride that coordinates the metal center from the outside of the calixarene cavity. The simultaneous binding of two anionic donors decreases the Zn Lewis acidity, allowing an impressive conformational reorganization of the system. One imidazole arm is released by the metal center. The other one undergoes self-inclusion into the pi-basic calixarene cavity because the low affinity of the metal center for neutral ligand does not allow the endo-coordination of an exogenous guest. Hence, the calix[6]N(3)ArOH-based Zn complexes act as an acid-base switch for guest binding. Several aspects of this system appear reminiscent of Zn-peptidases of the astacin and serralisin families.
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Affiliation(s)
- Olivier Sénèque
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Université René Descartes, 75270 Paris Cedex 06, France
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26
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Angkawidjaja C, Paul A, Koga Y, Takano K, Kanaya S. Importance of a repetitive nine-residue sequence motif for intracellular stability and functional structure of a family I.3 lipase. FEBS Lett 2005; 579:4707-12. [PMID: 16098975 DOI: 10.1016/j.febslet.2005.07.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Revised: 07/06/2005] [Accepted: 07/19/2005] [Indexed: 10/25/2022]
Abstract
PML5 is a functional derivative of a family I.3 lipase from Pseudomonas sp. MIS38 and contains five repeats of a nine-residue sequence motif. Two aspartate residues within the second and third repetitive sequences of PML5 were replaced by Ala. The secretion level, intracellular accumulation level, and stability of the resultant mutant protein were greatly reduced as compared to those of PML5. In addition, this mutant protein was inactive and did not bind Ca2+ ion. We propose that the repetitive sequences of PML5 form a beta-roll structure in the cells and thereby contribute to the intracellular stability and secretion efficiency of the protein.
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Affiliation(s)
- Clement Angkawidjaja
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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27
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Yongzheng Y, Reymond JL. Protease profiling using a fluorescent domino peptide cocktail. MOLECULAR BIOSYSTEMS 2005; 1:57-63. [PMID: 16880964 DOI: 10.1039/b419446b] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Five hexapeptides were prepared containing, in a domino-type arrangement, all 25 possible dipeptides between (1) aromatic, (2) hydrophobic, (3) positively charged, (4) negatively charged, and (5) small and polar amino acids. The peptides were fluorescence labeled at the N-terminus with a (7-coumaryl)oxyacetyl group, allowing the selective detection of N-terminal cleavage products. The five peptides were used as a cocktail reagent in an HPLC analysis. The cocktail produced specific cleavage patterns, or fingerprints, for a variety of proteases. This domino peptide cocktail can be used as a general reagent for protease identification and functional profiling.
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Affiliation(s)
- Yang Yongzheng
- Department of Chemistry & Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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28
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Belas R, Manos J, Suvanasuthi R. Proteus mirabilis ZapA metalloprotease degrades a broad spectrum of substrates, including antimicrobial peptides. Infect Immun 2004; 72:5159-67. [PMID: 15322010 PMCID: PMC517467 DOI: 10.1128/iai.72.9.5159-5167.2004] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Revised: 06/10/2004] [Accepted: 06/22/2004] [Indexed: 11/20/2022] Open
Abstract
The 54-kDa extracellular metalloprotease ZapA is an important virulence factor of uropathogenic Proteus mirabilis. While ZapA has the ability to degrade host immunoglobulins (Igs), the dramatic attenuation of virulence in ZapA mutants suggests that this enzyme may have a broader spectrum of activity. This hypothesis was tested by in vitro assays with purified ZapA and an array of purified protein or peptide substrates. The data reveal that many proteins found in the urinary tract are substrates of ZapA proteolysis, including complement (C1q and C3), cell matrix (collagen, fibronectin, and laminin), and cytoskeletal proteins (actin and tubulin). Proteolysis of IgA and IgG was significantly enhanced by conditions that denatured the Igs. It was discovered that the antimicrobial peptides human beta-defensin 1 (hBD1) and LL-37 are readily cleaved by the enzyme. To the best of our knowledge, this is the first report of a bacterial protease capable of cleaving hBD1, a component of the human renal tubule innate immune response. Proteolysis of hBD1 resulted in ca. six peptides, while proteolysis of LL-37 resulted in at least nine products. Matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis of the molecular masses of the reaction products indicated that ZapA preferred no distinct peptide bond. The antimicrobial activity of hBD1 and LL-37 was significantly reduced following ZapA treatment, suggesting that proteolysis results in inactivation of these peptides. The data suggest that a function of ZapA during urinary tract infections is the proteolysis of antimicrobial peptides associated with the innate immune response.
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Affiliation(s)
- Robert Belas
- Center of Marine Biotechnology, University of Maryland Biotechnology Institute, 710 East Pratt St., Baltimore, MD 21202, USA.
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29
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Abstract
Metalloendopeptidases are present across all kingdoms of living organisms; they are ubiquitous and widely involved in metabolism regulation through their ability either to extensively degrade proteins or to selectively hydrolyze specific peptide bonds. They must be subjected to exquisite spatial and temporal control to prevent this vast potential from becoming destructive. These enzymes are mostly zinc-dependent and the majority of them, named zincins, possess a short consensus sequence, HEXXH, with the two histidines acting as ligands of the catalytic zinc and the glutamate as the general base. A subclass of the zincins is characterized by a C-terminally elongated motif, HEXXHXXGXXH/D, with an additional strictly conserved glycine and a third zinc-binding histidine or aspartate. Currently, representative three-dimensional structures of six different proteinase families bearing this motif show, despite low sequence similarity, comparable overall topology. This includes a substrate-binding crevice, which subdivides the enzyme moiety into an upper and a lower subdomain. A common five-stranded beta-sheet and two alpha-helices are always found in the upper subdomain. The second of these helices encompasses the first half of the elongated consensus sequence and is therefore termed the active-site helix. Other shared characteristics are an invariant methionine-containing Met-turn beneath the catalytic metal and a further C-terminal helix in the lower subdomain. All these structural features identify the metzincin clan of metalloendopeptidases. This clan is reviewed from a structural point of view, based on the reported structures of representative members of the astacins, adamalysins, serralysins, matrixins, snapalysins, and leishmanolysins, and of inhibited forms, either by specific endogenous protein inhibitors or by zymogenic pro-domains. Moreover, newly available genomic sequences have unveiled novel putative metzincin families and new hypothetical members of existing ones.
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Affiliation(s)
- F Xavier Gomis-Rüth
- Institut de Biologia Molecular de Barcelona, CID-CSICC/ Jordi Girona, 18-26; 08034 Barcelona, Spain.
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30
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Hege T, Baumann U. The conserved methionine residue of the metzincins: a site-directed mutagenesis study. J Mol Biol 2001; 314:181-6. [PMID: 11718552 DOI: 10.1006/jmbi.2001.5125] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The metalloprotease clan of the metzincins derive their name from the presence of a conserved methionine residue that is located on the C-terminal side of the zinc-binding consensus sequence HEXXHXXGXXH. This methionine residue is located in a rather divergent part of the primary sequence but is structurally very well conserved. It is located under the pyramidal base of the three histidine residues that coordinate the catalytic zinc ion and is not involved in any direct contact with the metal nor the substrate. In order to clarify its role, this methionine residue (M226) of the protease C from Erwinia chrysanthemi has been mutated to various other amino acids. The mutants M226L, M226A, M226I were sufficiently stable to be isolated, while the mutants M226H, M226S and M226N could not be purified. The kinetic properties of these mutants were analysed. All mutants showed decreased activity, whereby increases in K(M) as well as decreases in k(cat) were observed. The M226L mutant and M226C-E189 K double mutant, which has the catalytic glutamic acid substituted as well, could be crystallised. The structure of the M226L mutant was determined to a resolution of 2.0 A and refined to R(free) of 0.20. The structure is isomorphous to the wild-type and does not show large differences, with the exception of a very small movement of the zinc-liganding histidine residues. The M226C-E189 K double mutant crystal structure has been refined to an R(free) of 0.20 at 2.1 A resolution. A small rearrangement of the zinc-liganding histidine residues can be detected, which leads to a slightly different zinc coordination and could explain the decrease in activity.
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Affiliation(s)
- T Hege
- Department of Chemistry and Biochemistry, University of Berne, Berne, CH-3012, Switzerland
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