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Hegedus L, Toth A, Harami GM, Palinkas J, Karatayeva N, Sajben-Nagy E, Bene S, Afzali Jaktajdinani S, Kovacs M, Juhasz S, Burkovics P. Werner helicase interacting protein 1 contributes to G-quadruplex processing in human cells. Sci Rep 2024; 14:15740. [PMID: 38977862 PMCID: PMC11231340 DOI: 10.1038/s41598-024-66425-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024] Open
Abstract
Genome replication is frequently impeded by highly stable DNA secondary structures, including G-quadruplex (G4) DNA, that can hinder the progression of the replication fork. Human WRNIP1 (Werner helicase Interacting Protein 1) associates with various components of the replication machinery and plays a crucial role in genome maintenance processes. However, its detailed function is still not fully understood. Here we show that human WRNIP1 interacts with G4 structures and provide evidence for its contribution to G4 processing. The absence of WRNIP1 results in elevated levels of G4 structures, DNA damage and chromosome aberrations following treatment with PhenDC3, a G4-stabilizing ligand. Additionally, we establish a functional and physical relationship between WRNIP1 and the PIF1 helicase in G4 processing. In summary, our results suggest that WRNIP1 aids genome replication and maintenance by regulating G4 processing and this activity relies on Pif1 DNA helicase.
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Affiliation(s)
- Lili Hegedus
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary
| | - Agnes Toth
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gabor M Harami
- ELTE-MTA Momentum Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Janos Palinkas
- ELTE-MTA Momentum Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Nargis Karatayeva
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Eniko Sajben-Nagy
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary
| | - Szabolcs Bene
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary
| | - Sara Afzali Jaktajdinani
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Mihaly Kovacs
- ELTE-MTA Momentum Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
- HUN-REN-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Szilvia Juhasz
- HCEMM Cancer Microbiome Core Group, Szeged, Hungary.
- Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary.
| | - Peter Burkovics
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary.
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2
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Tikhonova E, Mariasina S, Efimov S, Polshakov V, Maksimenko O, Georgiev P, Bonchuk A. Structural basis for interaction between CLAMP and MSL2 proteins involved in the specific recruitment of the dosage compensation complex in Drosophila. Nucleic Acids Res 2022; 50:6521-6531. [PMID: 35648444 PMCID: PMC9226498 DOI: 10.1093/nar/gkac455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 04/26/2022] [Accepted: 05/30/2022] [Indexed: 12/02/2022] Open
Abstract
Transcriptional regulators select their targets from a large pool of similar genomic sites. The binding of the Drosophila dosage compensation complex (DCC) exclusively to the male X chromosome provides insight into binding site selectivity rules. Previous studies showed that the male-specific organizer of the complex, MSL2, and ubiquitous DNA-binding protein CLAMP directly interact and play an important role in the specificity of X chromosome binding. Here, we studied the highly specific interaction between the intrinsically disordered region of MSL2 and the N-terminal zinc-finger C2H2-type (C2H2) domain of CLAMP. We obtained the NMR structure of the CLAMP N-terminal C2H2 zinc finger, which has a classic C2H2 zinc-finger fold with a rather unusual distribution of residues typically used in DNA recognition. Substitutions of residues in this C2H2 domain had the same effect on the viability of males and females, suggesting that it plays a general role in CLAMP activity. The N-terminal C2H2 domain of CLAMP is highly conserved in insects. However, the MSL2 region involved in the interaction is conserved only within the Drosophila genus, suggesting that this interaction emerged during the evolution of a mechanism for the specific recruitment of the DCC on the male X chromosome in Drosophilidae.
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Affiliation(s)
- Evgeniya Tikhonova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Moscow 119334, Russia
| | - Sofia Mariasina
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Sergey Efimov
- NMR Laboratory, Institute of Physics, Kazan Federal University, Kazan 420008, Russia
| | - Vladimir Polshakov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Oksana Maksimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Moscow 119334, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Moscow 119334, Russia
| | - Artem Bonchuk
- Department of the Control of Genetic Processes, Institute of Gene Biology, Moscow 119334, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Moscow 119334, Russia
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3
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Socha A, Yang D, Bulsiewicz A, Yaprianto K, Kupculak M, Liang CC, Hadjicharalambous A, Wu R, Gygi SP, Cohn MA. WRNIP1 Is Recruited to DNA Interstrand Crosslinks and Promotes Repair. Cell Rep 2020; 32:107850. [PMID: 32640220 PMCID: PMC7351111 DOI: 10.1016/j.celrep.2020.107850] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/15/2020] [Accepted: 06/11/2020] [Indexed: 12/22/2022] Open
Abstract
The Fanconi anemia (FA) pathway repairs DNA interstrand crosslinks (ICLs). Many FA proteins are recruited to ICLs in a timely fashion so that coordinated repair can occur. However, the mechanism of this process is poorly understood. Here, we report the purification of a FANCD2-containing protein complex with multiple subunits, including WRNIP1. Using live-cell imaging, we show that WRNIP1 is recruited to ICLs quickly after their appearance, promoting repair. The observed recruitment facilitates subsequent recruitment of the FANCD2/FANCI complex. Depletion of WRNIP1 sensitizes cells to ICL-forming drugs. We find that ubiquitination of WRNIP1 and the activity of its UBZ domain are required to facilitate recruitment of FANCD2/FANCI and promote repair. Altogether, we describe a mechanism by which WRNIP1 is recruited rapidly to ICLs, resulting in chromatin loading of the FANCD2/FANCI complex in an unusual process entailing ubiquitination of WRNIP1 and the activity of its integral UBZ domain. Multiple proteins are identified in a FANCD2 protein complex, including WRNIP1 WRNIP1 is recruited to DNA interstrand crosslinks and promotes DNA repair Recruitment of WRNIP1 facilitates loading of the FANCD2/FANCI complex onto DNA Ubiquitination of WRNIP1 and its UBZ domain are required for DNA repair
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Affiliation(s)
- Anna Socha
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Di Yang
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Alicja Bulsiewicz
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Kelvin Yaprianto
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Marian Kupculak
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Chih-Chao Liang
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | | | - Ronghu Wu
- Department of Cell Biology, Harvard Medical School, Boston, MA 01125, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 01125, USA
| | - Martin A Cohn
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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Park H, Kang JH, Lee S. Autophagy in Neurodegenerative Diseases: A Hunter for Aggregates. Int J Mol Sci 2020; 21:ijms21093369. [PMID: 32397599 PMCID: PMC7247013 DOI: 10.3390/ijms21093369] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
Cells have developed elaborate quality-control mechanisms for proteins and organelles to maintain cellular homeostasis. Such quality-control mechanisms are maintained by conformational folding via molecular chaperones and by degradation through the ubiquitin-proteasome or autophagy-lysosome system. Accumulating evidence suggests that impaired autophagy contributes to the accumulation of intracellular inclusion bodies consisting of misfolded proteins, which is a hallmark of most neurodegenerative diseases. In addition, genetic mutations in core autophagy-related genes have been reported to be linked to neurodegenerative diseases, such as Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease. Conversely, the pathogenic proteins, such as amyloid β and α-synuclein, are detrimental to the autophagy pathway. Here, we review the recent advances in understanding the relationship between autophagic defects and the pathogenesis of neurodegenerative diseases and suggest autophagy induction as a promising strategy for the treatment of these conditions.
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Affiliation(s)
- Hyungsun Park
- Department of Anatomy, College of Medicine, Inha University, Incheon 22212, Korea;
- Hypoxia-related Disease Research Center, College of Medicine, Inha University, Incheon 22212, Korea;
| | - Ju-Hee Kang
- Hypoxia-related Disease Research Center, College of Medicine, Inha University, Incheon 22212, Korea;
- Department of Pharmacology, College of Medicine, Inha University, Incheon 22212, Korea
| | - Seongju Lee
- Department of Anatomy, College of Medicine, Inha University, Incheon 22212, Korea;
- Hypoxia-related Disease Research Center, College of Medicine, Inha University, Incheon 22212, Korea;
- Correspondence: ; Tel.: +82-32-860-9891
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5
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Two NEMO-like Ubiquitin-Binding Domains in CEP55 Differently Regulate Cytokinesis. iScience 2019; 20:292-309. [PMID: 31605944 PMCID: PMC6817665 DOI: 10.1016/j.isci.2019.08.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/15/2019] [Accepted: 08/21/2019] [Indexed: 02/02/2023] Open
Abstract
CEP55 regulates the final critical step of cell division termed cytokinetic abscission. We report herein that CEP55 contains two NEMO-like ubiquitin-binding domains (UBDs), NOA and ZF, which regulate its function in a different manner. In vitro studies of isolated domains showed that NOA adopts a dimeric coiled-coil structure, whereas ZF is based on a UBZ scaffold. Strikingly, CEP55 knocked-down HeLa cells reconstituted with the full-length CEP55 ubiquitin-binding defective mutants, containing structure-guided mutations either in NOACEP55 or ZFCEP55 domains, display severe abscission defects. In addition, the ZFCEP55 can be functionally replaced by some ZF-based UBDs belonging to the UBZ family, indicating that the essential function of ZFCEP55 is to act as ubiquitin receptor. Our work reveals an unexpected role of CEP55 in non-degradative ubiquitin signaling during cytokinetic abscission and provides a molecular basis as to how CEP55 mutations can lead to neurological disorders such as the MARCH syndrome.
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Kluska K, Adamczyk J, Krężel A. Metal binding properties of zinc fingers with a naturally altered metal binding site. Metallomics 2019; 10:248-263. [PMID: 29230465 DOI: 10.1039/c7mt00256d] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Zinc fingers (ZFs) are among the most abundant motifs found in proteins, and are commonly known for their structural role. Classical ZFs (CCHH) are part of the transcription factors that participate in DNA binding. Although biochemical studies of classical ZFs have a long history, there is limited knowledge about the sequential and structural diversity of ZFs. We have found that classical ZFs, with metal binding sites consisting of amino acids other than conserved Cys or His residues, are frequently encoded in the human genome, and we refer to these peptides as ZFs with a naturally altered metal binding site. The biological role of the altered ZFs remains undiscovered. In this study, we characterized nine natural XCHH, CXHH, CCXH and CCHX ZFs in terms of their Zn(ii) and Co(ii) binding properties, such as complex stoichiometry, spectroscopic properties and metal-to-peptide affinity. We revealed that XCHH and CXHH ZFs form ML complexes that are 4-5 orders of magnitude weaker in comparison to CCHH ZFs. Nevertheless, spectroscopic studies demonstrate that, depending on the altered position, they may adopt an open coordination geometry with one or two water molecules bound to a central metal ion, which has not been demonstrated in natural ZFs before. Stability data show that both CCXH and CCHX peptides have high Zn(ii) affinity (with a Kd of 10-9 to 10-11 M), suggesting their potential biological function. This study is a comprehensive overview of the relationship between the sequence, structure, and stability of ZFs.
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Affiliation(s)
- Katarzyna Kluska
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
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Hu S, Wang Y, Gong Y, Liu J, Li Y, Pan L. Mechanistic Insights into Recognitions of Ubiquitin and Myosin VI by Autophagy Receptor TAX1BP1. J Mol Biol 2018; 430:3283-3296. [DOI: 10.1016/j.jmb.2018.06.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/01/2018] [Accepted: 06/18/2018] [Indexed: 12/29/2022]
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Godwin RC, Gmeiner WH, Salsbury FR. All-atom molecular dynamics comparison of disease-associated zinc fingers. J Biomol Struct Dyn 2018; 36:2581-2594. [PMID: 28814200 PMCID: PMC5882596 DOI: 10.1080/07391102.2017.1363662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 07/24/2017] [Indexed: 10/19/2022]
Abstract
An important regulatory domain of NF-[Formula: see text]B Essential Modulator (NEMO) is a ubiquitin-binding zinc finger, with a tetrahedral CYS3HIS1 zinc-coordinating binding site. Two variations of NEMO's zinc finger are implicated in various disease states including ectodermal dysplasia and adult-onset glaucoma. To discern structural and dynamical differences between these disease states, we present results of 48-[Formula: see text]s of molecular dynamics simulations for three zinc finger systems each in two states, with and without zinc-bound and correspondingly appropriate cysteine thiol/thiolate configurations. The wild-type protein, often studied for its role in cancer, maintains the most rigid and conformationally stable zinc-bound configuration compared with the diseased counterparts. The glaucoma-related protein has persistent loss of secondary structure except within the dominant conformation. Conformational overlap between wild-type and glaucoma isoforms indicate a competitive binding mechanism may be substantial in the malfunctioning configuration, while the alpha-helical disruption of the ectodermal dysplasia suggests a loss of binding selectivity is responsible for aberrant function.
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Affiliation(s)
- Ryan C. Godwin
- Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - William H. Gmeiner
- Department of Cancer Biology, WFU School of Medicine, Winston-Salem, NC, USA
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Powers KT, Elcock AH, Washington MT. The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility. Nucleic Acids Res 2018; 46:2107-2120. [PMID: 29385534 PMCID: PMC5829636 DOI: 10.1093/nar/gky031] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/10/2018] [Accepted: 01/22/2018] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic DNA polymerase η catalyzes translesion synthesis of thymine dimers and 8-oxoguanines. It is comprised of a polymerase domain and a C-terminal region, both of which are required for its biological function. The C-terminal region mediates interactions with proliferating cell nuclear antigen (PCNA) and other translesion synthesis proteins such as Rev1. This region contains a ubiquitin-binding/zinc-binding (UBZ) motif and a PCNA-interacting protein (PIP) motif. Currently little structural information is available for this region of polymerase η. Using a combination of approaches-including genetic complementation assays, X-ray crystallography, Langevin dynamics simulations, and small-angle X-ray scattering-we show that the C-terminal region is partially unstructured and has high conformational flexibility. This implies that the C-terminal region acts as a flexible tether linking the polymerase domain to PCNA thereby increasing its local concentration. Such tethering would facilitate the sampling of translesion synthesis polymerases to ensure that the most appropriate one is selected to bypass the lesion.
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Affiliation(s)
- Kyle T Powers
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, USA
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, USA
| | - M Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, USA
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Abstract
WRNIP1 interacts with WRN helicase, which is defective in the premature aging disease Werner syndrome. WRNIP1 belongs to the AAA+ ATPase family and is conserved from Escherichia coli to human. The protein contains an ubiquitin-binding zinc finger (UBZ) domain at the N terminus and an ATPase domain in the middle region. In addition to WRN, WRNIP1 interacts with proteins involved in multiple cellular pathways, including RAD18, monoubiquitylated PCNA, DNA polymerase δ, RAD51, and ATMIN. Mgs1, the yeast homolog of WRNIP1, may act downstream of ubiquitylation of PCNA to mobilize DNA polymerase δ. By contrast, the functions of WRNIP1 in higher eukaryotic cells remain obscure, although data regarding the roles of WRNIP1 in DNA transactions have emerged recently. Here, we first describe the functions of Mgs1 in DNA transaction. We then describe various features of WRNIP1 and discuss its possible roles based on recent studies of the function of WRNIP1.
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Affiliation(s)
- Akari Yoshimura
- a Molecular Cell Biology Laboratory , Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University , Nishitokyo-shi Tokyo , Japan
| | - Masayuki Seki
- b Laboratory of Biochemistry , Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University , Aoba-ku , Sendai , Japan
| | - Takemi Enomoto
- a Molecular Cell Biology Laboratory , Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University , Nishitokyo-shi Tokyo , Japan
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Fundamental Characteristics of AAA+ Protein Family Structure and Function. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:9294307. [PMID: 27703410 PMCID: PMC5039278 DOI: 10.1155/2016/9294307] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 07/21/2016] [Indexed: 12/22/2022]
Abstract
Many complex cellular events depend on multiprotein complexes known as molecular machines to efficiently couple the energy derived from adenosine triphosphate hydrolysis to the generation of mechanical force. Members of the AAA+ ATPase superfamily (ATPases Associated with various cellular Activities) are critical components of many molecular machines. AAA+ proteins are defined by conserved modules that precisely position the active site elements of two adjacent subunits to catalyze ATP hydrolysis. In many cases, AAA+ proteins form a ring structure that translocates a polymeric substrate through the central channel using specialized loops that project into the central channel. We discuss the major features of AAA+ protein structure and function with an emphasis on pivotal aspects elucidated with archaeal proteins.
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