Treble clef finger - a functionally diverse zinc-binding structural motif

被引:112
作者
Grishin, NV
机构
[1] Univ Texas, SW Med Ctr, Howard Hughes Med Inst, Dallas, TX 75390 USA
[2] Univ Texas, SW Med Ctr, Dept Biochem, Dallas, TX 75390 USA
关键词
D O I
10.1093/nar/29.8.1703
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
Detection of similarity is particularly difficult for small proteins and thus connections between many of them remain unnoticed. Structure and sequence analysis of several metal-binding proteins reveals unexpected similarities in structural domains classified as different protein folds in SCOP and suggests unification of seven folds that belong to two protein classes. The common motif, termed treble clef finger in this study, forms the protein structural core and is 25-45 residues long, The treble clef motif is assembled around the central zinc ion and consists of a zinc knuckle, loop, P-hairpin and an a-helix, The knuckle and the first turn of the helix each incorporate two zinc ligands. Treble clef domains constitute the core of many structures such as ribosomal proteins L24E and S14, RING fingers, protein kinase cysteine-rich domains, nuclear receptor-like fingers, LIM domains, phosphatidylinositol-3-phosphate-binding domains and His-Me finger endonucleases, The treble clef finger is a uniquely versatile motif adaptable for various functions. This small domain with a 25 residue structural core can accommodate eight different metal-binding sites and can have many types of functions from binding of nucleic acids, proteins and small molecules, to catalysis of phosphodiester bond hydrolysis, Treble clef motifs are frequently incorporated in larger structures or occur in doublets. Present analysis suggests that the treble clef motif defines a distinct structural fold found in proteins with diverse functional properties and forms one of the major zinc finger groups.
引用
收藏
页码:1703 / 1714
页数:12
相关论文
共 81 条
[1]   Analysis of zinc binding sites in protein crystal structures [J].
Alberts, IL ;
Nadassy, K ;
Wodak, SJ .
PROTEIN SCIENCE, 1998, 7 (08) :1700-1716
[2]   Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].
Altschul, SF ;
Madden, TL ;
Schaffer, AA ;
Zhang, JH ;
Zhang, Z ;
Miller, W ;
Lipman, DJ .
NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402
[3]   Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories [J].
Aravind, L ;
Makarova, KS ;
Koonin, EV .
NUCLEIC ACIDS RESEARCH, 2000, 28 (18) :3417-3432
[4]   The U box is a modified RING finger - a common domain in ubiquitination [J].
Aravind, L ;
Koonin, EV .
CURRENT BIOLOGY, 2000, 10 (04) :R132-R134
[5]   DNA-binding proteins and evolution of transcription regulation in the archaea [J].
Aravind, L ;
Koonin, EV .
NUCLEIC ACIDS RESEARCH, 1999, 27 (23) :4658-4670
[6]   The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution [J].
Ban, N ;
Nissen, P ;
Hansen, J ;
Moore, PB ;
Steitz, TA .
SCIENCE, 2000, 289 (5481) :905-920
[7]   STRUCTURE OF THE C3HC4 DOMAIN BY H-1-NUCLEAR MAGNETIC-RESONANCE SPECTROSCOPY - A NEW STRUCTURAL CLASS OF ZINC-FINGER [J].
BARLOW, PN ;
LUISI, B ;
MILNER, A ;
ELLIOTT, M ;
EVERETT, R .
JOURNAL OF MOLECULAR BIOLOGY, 1994, 237 (02) :201-211
[8]   Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins [J].
Bateman, A ;
Birney, E ;
Durbin, R ;
Eddy, SR ;
Finn, RD ;
Sonnhammer, ELL .
NUCLEIC ACIDS RESEARCH, 1999, 27 (01) :260-262
[9]   Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster [J].
Bellon, SF ;
Rodgers, KK ;
Schatz, DG ;
Coleman, JE ;
Steitz, TA .
NATURE STRUCTURAL BIOLOGY, 1997, 4 (07) :586-591
[10]   The Protein Data Bank [J].
Berman, HM ;
Westbrook, J ;
Feng, Z ;
Gilliland, G ;
Bhat, TN ;
Weissig, H ;
Shindyalov, IN ;
Bourne, PE .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242