메뉴 건너뛰기




Volumn 23, Issue 4, 2015, Pages 615-627

Catalytic pocket inaccessibility of activation-induced cytidine deaminase is a safeguard against excessive mutagenic activity

Author keywords

[No Author keywords available]

Indexed keywords

CYTIDINE; CYTIDINE DEAMINASE; DNA; PROTEIN BINDING;

EID: 84930190209     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2015.01.016     Document Type: Article
Times cited : (33)

References (56)
  • 2
    • 79551613290 scopus 로고    scopus 로고
    • Toward the estimation of the absolute quality of individual protein structure models
    • P. Benkert, M. Biasini, and T. Schwede Toward the estimation of the absolute quality of individual protein structure models Bioinformatics 27 2011 343 350
    • (2011) Bioinformatics , vol.27 , pp. 343-350
    • Benkert, P.1    Biasini, M.2    Schwede, T.3
  • 4
    • 36649006227 scopus 로고    scopus 로고
    • Activation-induced deaminase, AID, is catalytically active as a monomer on single-stranded DNA
    • S.S. Brar, E.J. Sacho, I. Tessmer, D.L. Croteau, D.A. Erie, and M. Diaz Activation-induced deaminase, AID, is catalytically active as a monomer on single-stranded DNA DNA Repair (Amst) 7 2008 77 87
    • (2008) DNA Repair (Amst) , vol.7 , pp. 77-87
    • Brar, S.S.1    Sacho, E.J.2    Tessmer, I.3    Croteau, D.L.4    Erie, D.A.5    Diaz, M.6
  • 9
    • 50349093233 scopus 로고    scopus 로고
    • The AID/APOBEC family of nucleic acid mutators
    • S.G. Conticello The AID/APOBEC family of nucleic acid mutators Genome Biol. 9 2008 229
    • (2008) Genome Biol. , vol.9 , pp. 229
    • Conticello, S.G.1
  • 11
    • 34249807921 scopus 로고    scopus 로고
    • DNA deamination in immunity: AID in the context of its APOBEC relatives
    • S.G. Conticello, M.A. Langlois, Z. Yang, and M.S. Neuberger DNA deamination in immunity: AID in the context of its APOBEC relatives Adv. Immunol. 94 2007 37 73
    • (2007) Adv. Immunol. , vol.94 , pp. 37-73
    • Conticello, S.G.1    Langlois, M.A.2    Yang, Z.3    Neuberger, M.S.4
  • 13
    • 84860914465 scopus 로고    scopus 로고
    • Differences in the enzymatic efficiency of human and bony fish AID are mediated by a single residue in the C terminus modulating single-stranded DNA binding
    • A.M. Dancyger, J.J. King, M.J. Quinlan, H. Fifield, S. Tucker, H.L. Saunders, M. Berru, B.G. Magor, A. Martin, and M. Larijani Differences in the enzymatic efficiency of human and bony fish AID are mediated by a single residue in the C terminus modulating single-stranded DNA binding FASEB J. 26 2012 1517 1525
    • (2012) FASEB J. , vol.26 , pp. 1517-1525
    • Dancyger, A.M.1    King, J.J.2    Quinlan, M.J.3    Fifield, H.4    Tucker, S.5    Saunders, H.L.6    Berru, M.7    Magor, B.G.8    Martin, A.9    Larijani, M.10
  • 14
    • 0037561998 scopus 로고    scopus 로고
    • AID mediates hypermutation by deaminating single stranded DNA
    • S.K. Dickerson, E. Market, E. Besmer, and F.N. Papavasiliou AID mediates hypermutation by deaminating single stranded DNA J. Exp. Med. 197 2003 1291 1296
    • (2003) J. Exp. Med. , vol.197 , pp. 1291-1296
    • Dickerson, S.K.1    Market, E.2    Besmer, E.3    Papavasiliou, F.N.4
  • 16
    • 79958242366 scopus 로고    scopus 로고
    • Fast docking using the CHARMM force field with EADock DSS
    • A. Grosdidier, V. Zoete, and O. Michielin Fast docking using the CHARMM force field with EADock DSS J. Comput. Chem. 32 2011 2149 2159
    • (2011) J. Comput. Chem. , vol.32 , pp. 2149-2159
    • Grosdidier, A.1    Zoete, V.2    Michielin, O.3
  • 17
    • 79960029361 scopus 로고    scopus 로고
    • SwissDock, a protein-small molecule docking web service based on EADock DSS
    • A. Grosdidier, V. Zoete, and O. Michielin SwissDock, a protein-small molecule docking web service based on EADock DSS Nucleic Acids Res. 39 2011 W270 W277
    • (2011) Nucleic Acids Res. , vol.39 , pp. W270-W277
    • Grosdidier, A.1    Zoete, V.2    Michielin, O.3
  • 19
    • 33646945580 scopus 로고    scopus 로고
    • Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution
    • T.I. Igumenova, K.K. Frederick, and A.J. Wand Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution Chem. Rev. 106 2006 1672 1699
    • (2006) Chem. Rev. , vol.106 , pp. 1672-1699
    • Igumenova, T.I.1    Frederick, K.K.2    Wand, A.J.3
  • 22
    • 69249137076 scopus 로고    scopus 로고
    • A portable hot spot recognition loop transfers sequence preferences from APOBEC family members to activation-induced cytidine deaminase
    • R.M. Kohli, S.R. Abrams, K.S. Gajula, R.W. Maul, P.J. Gearhart, and J.T. Stivers A portable hot spot recognition loop transfers sequence preferences from APOBEC family members to activation-induced cytidine deaminase J. Biol. Chem. 284 2009 22898 22904
    • (2009) J. Biol. Chem. , vol.284 , pp. 22898-22904
    • Kohli, R.M.1    Abrams, S.R.2    Gajula, K.S.3    Maul, R.W.4    Gearhart, P.J.5    Stivers, J.T.6
  • 24
    • 36849011485 scopus 로고    scopus 로고
    • Single-stranded DNA structure and positional context of the target cytidine determine the enzymatic efficiency of AID
    • M. Larijani, and A. Martin Single-stranded DNA structure and positional context of the target cytidine determine the enzymatic efficiency of AID Mol. Cell. Biol. 27 2007 8038 8048
    • (2007) Mol. Cell. Biol. , vol.27 , pp. 8038-8048
    • Larijani, M.1    Martin, A.2
  • 25
    • 84865177920 scopus 로고    scopus 로고
    • The biochemistry of activation-induced deaminase and its physiological functions
    • M. Larijani, and A. Martin The biochemistry of activation-induced deaminase and its physiological functions Semin. Immunol. 24 2012 255 263
    • (2012) Semin. Immunol. , vol.24 , pp. 255-263
    • Larijani, M.1    Martin, A.2
  • 26
    • 17144424674 scopus 로고    scopus 로고
    • The mutation spectrum of purified AID is similar to the mutability index in Ramos cells and in ung(-/-)msh2(-/-) mice
    • M. Larijani, D. Frieder, W. Basit, and A. Martin The mutation spectrum of purified AID is similar to the mutability index in Ramos cells and in ung(-/-)msh2(-/-) mice Immunogenetics 56 2005 840 845
    • (2005) Immunogenetics , vol.56 , pp. 840-845
    • Larijani, M.1    Frieder, D.2    Basit, W.3    Martin, A.4
  • 27
    • 33845730352 scopus 로고    scopus 로고
    • AID associates with single-stranded DNA with high affinity and a long complex half-life in a sequence-independent manner
    • M. Larijani, A.P. Petrov, O. Kolenchenko, M. Berru, S.N. Krylov, and A. Martin AID associates with single-stranded DNA with high affinity and a long complex half-life in a sequence-independent manner Mol. Cell. Biol. 27 2007 20 30
    • (2007) Mol. Cell. Biol. , vol.27 , pp. 20-30
    • Larijani, M.1    Petrov, A.P.2    Kolenchenko, O.3    Berru, M.4    Krylov, S.N.5    Martin, A.6
  • 28
    • 0030339738 scopus 로고    scopus 로고
    • AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
    • R.A. Laskowski, J.A. Rullmannn, M.W. MacArthur, R. Kaptein, and J.M. Thornton AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR J. Biomol. NMR 8 1996 477 486
    • (1996) J. Biomol. NMR , vol.8 , pp. 477-486
    • Laskowski, R.A.1    Rullmannn, J.A.2    Macarthur, M.W.3    Kaptein, R.4    Thornton, J.M.5
  • 29
    • 32244445417 scopus 로고    scopus 로고
    • Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA
    • H.C. Losey, A.J. Ruthenburg, and G.L. Verdine Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA Nat. Struct. Mol. Biol. 13 2006 153 159
    • (2006) Nat. Struct. Mol. Biol. , vol.13 , pp. 153-159
    • Losey, H.C.1    Ruthenburg, A.J.2    Verdine, G.L.3
  • 30
    • 84865791616 scopus 로고    scopus 로고
    • Biochemical analysis of hypermutation by the deoxycytidine deaminase APOBEC3A
    • R.P. Love, H. Xu, and L. Chelico Biochemical analysis of hypermutation by the deoxycytidine deaminase APOBEC3A J. Biol. Chem. 287 2012 30812 30822
    • (2012) J. Biol. Chem. , vol.287 , pp. 30812-30822
    • Love, R.P.1    Xu, H.2    Chelico, L.3
  • 31
    • 84885595546 scopus 로고    scopus 로고
    • A mathematical model for scanning and catalysis on single-stranded DNA, illustrated with activation-induced deoxycytidine deaminase
    • C.H. Mak, P. Pham, S.A. Afif, and M.F. Goodman A mathematical model for scanning and catalysis on single-stranded DNA, illustrated with activation-induced deoxycytidine deaminase J. Biol. Chem. 288 2013 29786 29795
    • (2013) J. Biol. Chem. , vol.288 , pp. 29786-29795
    • Mak, C.H.1    Pham, P.2    Afif, S.A.3    Goodman, M.F.4
  • 34
    • 84861430206 scopus 로고    scopus 로고
    • An ancient history of gene duplications, fusions and losses in the evolution of APOBEC3 mutators in mammals
    • C. Munk, A. Willemsen, and I.G. Bravo An ancient history of gene duplications, fusions and losses in the evolution of APOBEC3 mutators in mammals BMC Evol. Biol. 12 2012 71
    • (2012) BMC Evol. Biol. , vol.12 , pp. 71
    • Munk, C.1    Willemsen, A.2    Bravo, I.G.3
  • 35
    • 0033603340 scopus 로고    scopus 로고
    • Specific expression of activation-induced cytidine deaminase (AID), a novel member of the RNA-editing deaminase family in germinal center B cells
    • M. Muramatsu, V.S. Sankaranand, S. Anant, M. Sugai, K. Kinoshita, N.O. Davidson, and T. Honjo Specific expression of activation-induced cytidine deaminase (AID), a novel member of the RNA-editing deaminase family in germinal center B cells J. Biol. Chem. 274 1999 18470 18476
    • (1999) J. Biol. Chem. , vol.274 , pp. 18470-18476
    • Muramatsu, M.1    Sankaranand, V.S.2    Anant, S.3    Sugai, M.4    Kinoshita, K.5    Davidson, N.O.6    Honjo, T.7
  • 36
    • 0034268780 scopus 로고    scopus 로고
    • Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme
    • M. Muramatsu, K. Kinoshita, S. Fagarasan, S. Yamada, Y. Shinkai, and T. Honjo Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme Cell 102 2000 553 563
    • (2000) Cell , vol.102 , pp. 553-563
    • Muramatsu, M.1    Kinoshita, K.2    Fagarasan, S.3    Yamada, S.4    Shinkai, Y.5    Honjo, T.6
  • 42
    • 0037926476 scopus 로고    scopus 로고
    • Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation
    • P. Pham, R. Bransteitter, J. Petruska, and M.F. Goodman Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation Nature 424 2003 103 107
    • (2003) Nature , vol.424 , pp. 103-107
    • Pham, P.1    Bransteitter, R.2    Petruska, J.3    Goodman, M.F.4
  • 43
    • 79960145089 scopus 로고    scopus 로고
    • Analysis of a single-stranded DNA-scanning process in which activation-induced deoxycytidine deaminase (AID) deaminates C to U haphazardly and inefficiently to ensure mutational diversity
    • P. Pham, P. Calabrese, S.J. Park, and M.F. Goodman Analysis of a single-stranded DNA-scanning process in which activation-induced deoxycytidine deaminase (AID) deaminates C to U haphazardly and inefficiently to ensure mutational diversity J. Biol. Chem. 286 2011 24931 24942
    • (2011) J. Biol. Chem. , vol.286 , pp. 24931-24942
    • Pham, P.1    Calabrese, P.2    Park, S.J.3    Goodman, M.F.4
  • 44
    • 33846555779 scopus 로고    scopus 로고
    • The APOBEC-2 crystal structure and functional implications for the deaminase AID
    • C. Prochnow, R. Bransteitter, M.G. Klein, M.F. Goodman, and X.S. Chen The APOBEC-2 crystal structure and functional implications for the deaminase AID Nature 445 2007 447 451
    • (2007) Nature , vol.445 , pp. 447-451
    • Prochnow, C.1    Bransteitter, R.2    Klein, M.G.3    Goodman, M.F.4    Chen, X.S.5
  • 45
    • 77749335648 scopus 로고    scopus 로고
    • APOBEC deaminases-mutases with defensive roles for immunity
    • C. Prochnow, R. Bransteitter, and X.S. Chen APOBEC deaminases-mutases with defensive roles for immunity Sci. China C Life Sci. 52 2009 893 902
    • (2009) Sci. China C Life Sci. , vol.52 , pp. 893-902
    • Prochnow, C.1    Bransteitter, R.2    Chen, X.S.3
  • 48
    • 84864460609 scopus 로고    scopus 로고
    • COFACTOR: An accurate comparative algorithm for structure-based protein function annotation
    • A. Roy, J. Yang, and Y. Zhang COFACTOR: an accurate comparative algorithm for structure-based protein function annotation Nucleic Acids Res. 40 2012 W471 W477
    • (2012) Nucleic Acids Res. , vol.40 , pp. W471-W477
    • Roy, A.1    Yang, J.2    Zhang, Y.3
  • 49
    • 70349334428 scopus 로고    scopus 로고
    • X-ray vs. NMR structures as templates for computational protein design
    • M. Schneider, X. Fu, and A.E. Keating X-ray vs. NMR structures as templates for computational protein design Proteins 77 2009 97 110
    • (2009) Proteins , vol.77 , pp. 97-110
    • Schneider, M.1    Fu, X.2    Keating, A.E.3
  • 51
    • 0037901850 scopus 로고    scopus 로고
    • Human activation-induced cytidine deaminase causes transcription-dependent, strand-biased C to U deaminations
    • A. Sohail, J. Klapacz, M. Samaranayake, A. Ullah, and A.S. Bhagwat Human activation-induced cytidine deaminase causes transcription-dependent, strand-biased C to U deaminations Nucleic Acids Res. 31 2003 2990 2994
    • (2003) Nucleic Acids Res. , vol.31 , pp. 2990-2994
    • Sohail, A.1    Klapacz, J.2    Samaranayake, M.3    Ullah, A.4    Bhagwat, A.S.5
  • 52
    • 67650330317 scopus 로고    scopus 로고
    • AID upmutants isolated using a high-throughput screen highlight the immunity/cancer balance limiting DNA deaminase activity
    • M. Wang, Z. Yang, C. Rada, and M.S. Neuberger AID upmutants isolated using a high-throughput screen highlight the immunity/cancer balance limiting DNA deaminase activity Nat. Struct. Mol. Biol. 16 2009 769 776
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 769-776
    • Wang, M.1    Yang, Z.2    Rada, C.3    Neuberger, M.S.4
  • 53
    • 84867270112 scopus 로고    scopus 로고
    • Efficient deamination of 5-methylcytosines in DNA by human APOBEC3A, but not by AID or APOBEC3G
    • P. Wijesinghe, and A.S. Bhagwat Efficient deamination of 5-methylcytosines in DNA by human APOBEC3A, but not by AID or APOBEC3G Nucleic Acids Res. 40 2012 9206 9217
    • (2012) Nucleic Acids Res. , vol.40 , pp. 9206-9217
    • Wijesinghe, P.1    Bhagwat, A.S.2
  • 54
    • 2542542827 scopus 로고    scopus 로고
    • The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1
    • K. Xie, M.P. Sowden, G.S. Dance, A.T. Torelli, H.C. Smith, and J.E. Wedekind The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1 Proc. Natl. Acad Sci. USA 101 2004 8114 8119
    • (2004) Proc. Natl. Acad Sci. USA , vol.101 , pp. 8114-8119
    • Xie, K.1    Sowden, M.P.2    Dance, G.S.3    Torelli, A.T.4    Smith, H.C.5    Wedekind, J.E.6
  • 55
    • 39449115394 scopus 로고    scopus 로고
    • I-TASSER server for protein 3D structure prediction
    • Y. Zhang I-TASSER server for protein 3D structure prediction BMC Bioinformatics 9 2008 40
    • (2008) BMC Bioinformatics , vol.9 , pp. 40
    • Zhang, Y.1
  • 56
    • 79958841703 scopus 로고    scopus 로고
    • SwissParam: A fast force field generation tool for small organic molecules
    • V. Zoete, M.A. Cuendet, A. Grosdidier, and O. Michielin SwissParam: a fast force field generation tool for small organic molecules J. Comput. Chem. 32 2011 2359 2368
    • (2011) J. Comput. Chem. , vol.32 , pp. 2359-2368
    • Zoete, V.1    Cuendet, M.A.2    Grosdidier, A.3    Michielin, O.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.