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(-) Description

Title :  CRYSTAL STRUCTURE OF VIBRIO CHOLERAE DNCV APO FORM
 
Authors :  K. Kato, R. Ishii, R. Ishitani, O. Nureki
Date :  08 Jan 15  (Deposition) - 29 Apr 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A
Keywords :  Cyclic Gmp-Amp Synthase, Bacterial Virulence, Nucleotidyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kato, R. Ishii, S. Hirano, R. Ishitani, O. Nureki
Structural Basis For The Catalytic Mechanism Of Dncv, Bacterial Homolog Of Cyclic Gmp-Amp Synthase
Structure V. 23 843 2015
PubMed-ID: 25865248  |  Reference-DOI: 10.1016/J.STR.2015.01.023

(-) Compounds

Molecule 1 - CYCLIC AMP-GMP SYNTHASE
    Chains: A
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-215, 242-412
    Gene: DNCV, VC_0179
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR STR. N16961
    Organism Taxid: 243277
    Strain: N16961
    Synonym: C-AMP-GMP SYNTHASE,DINUCLEOTIDE CYCLASE DNCV

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric/Biological Unit (2, 17)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MSE13Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMSE A:3 , THR A:4 , TRP A:5 , GLU A:381 , SER A:382 , ALA A:383 , LEU A:409binding site for residue EDO A 1001
2AC2SOFTWAREASN A:121 , PRO A:123 , GLU A:129 , ASP A:291 , HOH A:1222binding site for residue EDO A 1002
3AC3SOFTWAREPRO A:354 , GLU A:363 , ILE A:366 , HOH A:1112 , HOH A:1306binding site for residue EDO A 1003
4AC4SOFTWAREPRO A:334 , GLU A:371 , HOH A:1266binding site for residue EDO A 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XJ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XJ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XJ1)

(-) Exons   (0, 0)

(no "Exon" information available for 4XJ1)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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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:373
                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh...........eeeeeeeeee..........hhhhhhhhhhhhhhhhhhhh...eeee....eeeeehhh.eeeee.eeee........eee.......eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhheeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xj1 A   2 RmTWNFHQYYTNRNDGLmGKLVLTDEEKNNLKALRKIIRLRTRDVFEEAKGIAKAVKKSALTFEIIQEKVSTTQIKHLSDSEQREVAKLIYEmDDDARDEFLGLTPRFWTQGSFQYDTLNRPFQPGQEmDIDDGTYmPmPIFESEPKIGHSLLILLVDASLKSLVAENHGWKFEAKQTCGRIKIEAEKTHIDVPmYAIPKDGSENVNLALREGDRKWINSDPKIVEDWFNDSCIRIGKHLRKVCRFmKAWRDAQWDVGGPSSISLmAATVNILDSVAHDASDLGETmKIIAKHLPSEFARGVESPDSTDEKPLFPPSYKHGPREmDImSKLERLPEILSSAESADSKSEALKKINmAFGNRVTNSELIVLAKA 412
                             |      11       |21        31        41        51        61        71        81        91  |    101       111       121       131      |141       151       161       171       181       191    |  201||     249       259       269       279      |289       299     | 309       319      |329       339       349       359    |  369       379       389     | 399       409   
                             |              19-MSE                                                                     94-MSE                             130-MSE 138-MSE                                                   196-MSE02|                                          286-MSE            305-MSE              326-MSE                               364-MSE                        395-MSE             
                             3-MSE                                                                                                                                  140-MSE                                                        241                                                                                                                           367-MSE
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4XJ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XJ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XJ1)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4xj1
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  DNCV_VIBCH | Q9KVG7
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DNCV_VIBCH | Q9KVG7: 4txy 4txz 4ty0 4u03 4u0l 4u0m 4u0n 4xj3 4xj4 4xj5 5go3

(-) Related Entries Specified in the PDB File

4xj3 4xj4 4xj5 4xj6