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(-) Description

Title :  CRYSTAL STRUCTURE OF HTH_3 FAMILY TRANSCRIPTIONAL REGULATOR FROM VIBRIO CHOLERAE
 
Authors :  D. Kumaran, S. Swaminathan, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  16 Dec 04  (Deposition) - 04 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hth_3 Family, Transcriptional Regulaator, Strucutral Genomics, Protein Structure Initiative, Psi, New York Sgx Research Center For Structural Genomics, Nysgxrc, Dimer, Two-Domain Structure, Structural Genomics, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kumaran, S. Swaminathan, New York Structural Genomics Research Consortium (Nysgrc)
Crystal Structure Of Hth_3 Family Transcriptional Regulator From Vibrio Cholerae
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, HTH_3 FAMILY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1MED1Ligand/IonD-METHIONINE
2MSE5Mod. Amino AcidSELENOMETHIONINE
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1MED2Ligand/IonD-METHIONINE
2MSE10Mod. Amino AcidSELENOMETHIONINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:122 , GLU A:128 , HIS A:162 , TYR A:164 , MED A:201BINDING SITE FOR RESIDUE ZN A 202
2AC2SOFTWARETRP A:57 , PHE A:107 , ILE A:109 , SER A:119 , HIS A:122 , GLU A:128 , HIS A:162 , TYR A:164 , ASN A:175 , ZN A:202 , HOH A:239 , HOH A:322BINDING SITE FOR RESIDUE MED A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y9Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y9Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:178
 aligned with Q9KQN0_VIBCH | Q9KQN0 from UniProtKB/TrEMBL  Length:181

    Alignment length:178
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
         Q9KQN0_VIBCH     2 TDVMFKSQIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASFSAFFANDPQLLSSERSFPDDLNMKIHTLFPYAADTGLEIFEITLLDHHQQMSSPHALGVIEYIHVLEGIMKVFFDEQWHELQQGEHIRFFSDQPHGYAAVTEKAVFQNIVAYPR 179
               SCOP domains d1y9qa1 A:4-82 Probable transcriptional regulator VC1968, N-terminal domain    d1y9qa2 A:83-181 Probable transcriptional regulator VC1968, C-terminal domain                       SCOP domains
               CATH domains 1y9qA01 A:4-88 lambda repressor-like DNA-binding domains                             1y9qA02 A:89-181 Jelly Rolls                                                                  CATH domains
               Pfam domains ------------HTH_3-1y9qA02 A:16-70                                  ---------------------------------------Cupin_2-1y9qA01 A:110-177                                           ---- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhh..hhhhhhh........eeeeeeeeee....eeeeeeee....eeee.......eeeeeeee..eeeee..eeeee....eeeee....eeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y9q A   4 TDVmFKSQIANQLKNLRKSRGLSLDATAQLTGVSKAmLGQIERGESSPTIATLWKIASGLEASFSAFFANDPQLLSSERSFPDDLNmKIHTLFPYAADTGLEIFEITLLDHHQQmSSPHALGVIEYIHVLEGImKVFFDEQWHELQQGEHIRFFSDQPHGYAAVTEKAVFQNIVAYPR 181
                               |    13        23        33      | 43        53        63        73        83      | 93       103       113    |  123       133   |   143       153       163       173        
                               |                               40-MSE                                            90-MSE                     118-MSE            137-MSE                                        
                               7-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Cupin (179)
(-)
Clan: HTH (544)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9KQN0_VIBCH | Q9KQN0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

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