Predicted role for the archease protein family based on structural and sequence analysis of TM1083 and MTH1598, two proteins structurally characterized through structural genomics efforts

被引:11
作者
Canaves, JM [1 ]
机构
[1] Joint Ctr Struct Genom, San Diego Supercomp Ctr, Bioinformat Core, La Jolla, CA 92093 USA
关键词
archease; structural genomics; functional prediction; genomic context;
D O I
10.1002/prot.20141
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Recently, the structures of two proteins belonging to the archease family, TM1083 from Thermotoga maritima and MTH1598 from Methanobacterium thermoautotrophicum, have been solved independently by two Protein Structure Initiative structural genomics pilot centers using X-ray crystallography and NMR, respectively. The archease protein family is a good example of one of the paradoxes of structural genomics: Approximately one third of protein structures produced by structural genomics centers have no known function and are still annotated as "hypothetical proteins" in the Protein Data Bank. In the case of archeases, despite the existence of two protein structures and abundant sequence information, there is still no function assigned to this protein family. Here, our group predicts, based on structural similarity, sequence conservation, and gene context analyses, that members of this protein family might function as chaperones or modulators of proteins involved in DNA/RNA processing. The conservation of genomic context for this protein family is constant from Archaea and Bacteria to humans, and suggests that unannotated open reading frames contiguous to them could be novel RNA/DNA binding proteins. (C) 2004 Wiley-Liss, Inc.
引用
收藏
页码:19 / 27
页数:9
相关论文
共 32 条
  • [1] Alexandrov NN, 1996, PROTEINS, V25, P354, DOI 10.1002/(SICI)1097-0134(199607)25:3<354::AID-PROT7>3.3.CO
  • [2] 2-W
  • [3] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    Altschul, SF
    Madden, TL
    Schaffer, AA
    Zhang, JH
    Zhang, Z
    Miller, W
    Lipman, DJ
    [J]. NUCLEIC ACIDS RESEARCH, 1997, 25 (17) : 3389 - 3402
  • [4] [Anonymous], 1997, EMBnet News
  • [5] Guilt by association: Contextual information in genome analysis
    Aravind, L
    [J]. GENOME RESEARCH, 2000, 10 (08) : 1074 - 1077
  • [6] Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkr1065, 10.1093/nar/gkh121]
  • [7] The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
    Boeckmann, B
    Bairoch, A
    Apweiler, R
    Blatter, MC
    Estreicher, A
    Gasteiger, E
    Martin, MJ
    Michoud, K
    O'Donovan, C
    Phan, I
    Pilbout, S
    Schneider, M
    [J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (01) : 365 - 370
  • [8] Conservation of gene order: a fingerprint of proteins that physically interact
    Dandekar, T
    Snel, B
    Huynen, M
    Bork, P
    [J]. TRENDS IN BIOCHEMICAL SCIENCES, 1998, 23 (09) : 324 - 328
  • [9] DURBIN R, 1998, PROBALISTIC SEQUENCE
  • [10] Gattiker Alexandre, 2002, Appl Bioinformatics, V1, P107