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

Nucleic Acids Research

Volumn 29, Issue 8, 2001, Pages 1703-1714

  Grishin, N V ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; CELL NUCLEUS RECEPTOR; CYSTEINE; ENDONUCLEASE; ESTER DERIVATIVE; LIGAND; NUCLEIC ACID; PHOSPHATE; PHOSPHATIDYLINOSITOL; PROTEIN; PROTEIN KINASE; RIBOSOME PROTEIN; ZINC ION;

ALPHA HELIX; ARTICLE; BINDING SITE; CATALYSIS; CHEMICAL BOND; CLASSIFICATION; CONTROLLED STUDY; HYDROLYSIS; METAL BINDING; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

EID: 0035870760     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/29.8.1703     Document Type: Article

References (81)

1. Analysis of zinc binding sites in protein crystal structures
2. Zinc fingers are sticking together
3. SCOP: A structural classification of proteins database for the investigation of sequences and structures
4. Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
5. Crystal structure of carboxypeptidase T from Thermoactinomyces vulgaris
6. Calcium is needed for the thermostability of influenza B virus neuraminidase
7. Calcium-mediated thermostability in the subtilisin superfamily: The crystal structure of Bacillus Ak. 1 protease at 1.8 A resolution
8. Disulfide bonds and protein folding
9. DNA recognition by Cys2His2 zinc finger proteins
10. DNA-binding proteins and evolution of transcription regulation in the archaea
11. C-terminal domains of Escherichia coli topoisomerase 1 belong to the zinc-ribbon superfamily
12. Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription
13. High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases
14. The Protein Data Bank
15. Protein structure comparison by alignment of distance matrices
16. Surprising similarities in structure comparison
17. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
18. The structural basis of ribosome activity in peptide bond synthesis
19. The complete atomic structure of the large ribosomal subunit at 2.4 ̊ resolution
20. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics
21. Structure of the 30S ribosomal subunit
22. SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling
23. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities
24. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
25. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
26. Non-globular domains in protein sequences: Automated segmentation using complexity measures
27. Analysis of compositionally biased regions in sequence databases
28. Amino acid substitution matrices from protein blocks
29. SEALS: A system for easy analysis of lots of sequences
30. Crystal structure of the cys2 activator-binding domain of protein kinase C δ in complex with phorbol ester
31. Crystal structure of a phosphatidylinositol 3-phosphate-specific membrane-targeting motif, the FYVE domain of Vps27p
32. Left-handed topology of super-secondary structure formed by aligned α-helix and β-hairpin
33. Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns
34. Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family
35. Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family
36. Holliday junction resolvases and related nucleases: Identification of new families, phyletic distribution and evolutionary trajectories
37. Crystal structure of a Smad MH1 domain bound to DNA: Insights on DNA binding in TGF-β signaling
38. The U box is a modified RING finger-a common domain in ubiquitination
39. A similar active site for non-specific and specific endonucleases
40. Cleavage experiments with deoxythymidine 3′,5′-bis-(p-nitrophenyl phosphate) suggest that the homing endonuclease I-Ppol follows the same mechanism of phosphodiester bond hydrolysis as the non-specific Serratia nuclease
41. Structural parsimony in endonuclease active sites: Should the number of homing endonuclease families be redefined?
42. The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein
43. Structural and mechanistic basis of immunity toward endonuclease colicins
44. 2.1 Å structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA
45. Atomic structure of the Serratia marcescens endonuclease at 1.1 Å resolution and the enzyme reaction mechanism
46. DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI
47. X-ray structure of T4 endonuclease VII: A DNA junction resolvase with a novel fold and unusual domain-swapped dimer architecture
48. A novel endonuclease mechanism directly visualized for I-PpoI
49. Solution structure of the chicken cysteine-rich protein, CRP1, a double-LIM protein implicated in muscle differentiation
50. Solution structure of the carboxyl-terminal LIM domain from quail cysteine-rich protein CRP2
51. Structure of the cysteine-rich intestinal protein
52. Solution structure of a naturally-occurring zinc-peptide complex demonstrates that the N-terminal zinc-binding module of the Lasp-1 LIM domain is an independent folding unit
53. Structural basis of Rab effector specificity: Crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A
54. Crystal structure of the VHS and FYVE tandem domains of Hrs, a protein involved in membrane trafficking and signal transduction
55. Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster
56. Crystal structure of the ARF-GAP domain and ankyrin repeats of PYK2-associated protein β
57. Structural determinants of nuclear receptor assembly on DNA direct repeats
58. RING domains: Master builders of molecular scaffolds?
59. Structure of the C3HC4 domain by 1H-nuclear magnetic resonance spectroscopy. A new structural class of zinc-finger
60. The solution structure of the RING finger domain from the acute promyelocytic leukaemia proto-oncoprotein PML
61. Structure of a c-Cbl-UbcH7 complex: RING domain function in ubiquitin-protein ligases
62. Solution structure of the N-terminal domain of the human TFHH MAT1 subunit: New insights into the RING finger family
63. Structural and functional analysis of the ARF1-ARFGAP complex reveals a role for coatomer in GTP hydrolysis
64. Solution structure of cysteine-rich domain of protein kinase C α
65. The solution structure of the Raf-1 cysteine-rich domain: A novel ras and phospholipid binding site
66. NMR structure of a protein kinase C-γ phorbol-binding domain and study of protein-lipid micelle interactions
67. Phosphoinositides as regulators in membrane traffic
68. NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1
69. The solution structure of the N-terminal zinc finger of GATA-1 reveals a specific binding face for the transcriptional co-factor FOG
70. Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA
71. DNA-binding mechanism of the monomeric orphan nuclear receptor NGFI-B
72. Structural elements of an orphan nuclear receptor-DNA complex
73. Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1
74. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA
75. The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: How receptors discriminate between their response elements
76. Transcriptional control by the TGF-β/Smad signaling system
77. MH1 domain of Smad is a degraded homing endonuclease
78. RING fingers and B-boxes: Zinc-binding protein-protein interaction domains
79. Chemical mechanism of DNA cleavage by the homing endonuclease I-PpoI
80. RING fingers mediate ubiquitin-conjugating enzyme (E2)-dependent ubiquitination
81. A family of nuclear homing endonucleases