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(-) Description

Title :  CRYSTAL STRUCTURE OF VIBRIO CHOLERAE DNCV GTP BOUND 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 :  1.65
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  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:131 , ASP A:133 , MG A:1002 , GTP A:1012 , HOH A:1320binding site for residue MG A 1001
02AC2SOFTWAREASP A:131 , MG A:1001 , GTP A:1012 , GTP A:1013 , HOH A:1322 , HOH A:1323 , HOH A:1327binding site for residue MG A 1002
03AC3SOFTWARELYS A:277 , HIS A:278 , LYS A:281 , ASP A:318 , ALA A:319 , SER A:320 , HOH A:1110binding site for residue EDO A 1003
04AC4SOFTWAREALA A:292 , GLN A:293 , ASN A:394 , MET A:395 , GLY A:398 , HOH A:1230binding site for residue EDO A 1004
05AC5SOFTWAREARG A:290 , GLY A:297 , GLY A:298 , HOH A:1271binding site for residue EDO A 1005
06AC6SOFTWARETRP A:267 , ALA A:306 , ASN A:310 , GLU A:342 , PRO A:344binding site for residue EDO A 1006
07AC7SOFTWAREHIS A:317 , GLU A:324binding site for residue EDO A 1007
08AC8SOFTWAREGLU A:129 , ASP A:291 , GTP A:1012 , HOH A:1210binding site for residue EDO A 1008
09AC9SOFTWAREMET A:3 , TRP A:5 , GLU A:381 , SER A:382 , ALA A:383 , LEU A:409binding site for residue EDO A 1009
10AD1SOFTWAREPHE A:64 , TRP A:294 , ASP A:295 , VAL A:296 , HOH A:1122 , HOH A:1203binding site for residue EDO A 1010
11AD2SOFTWARELEU A:24 , LYS A:29 , PHE A:115 , ASP A:118 , LEU A:120 , ARG A:284 , HOH A:1189 , HOH A:1332binding site for residue EDO A 1011
12AD3SOFTWAREGLN A:112 , GLY A:113 , SER A:114 , TYR A:117 , ASP A:131 , ASP A:133 , PRO A:261 , LYS A:287 , SER A:301 , ASP A:348 , LEU A:352 , MG A:1001 , MG A:1002 , EDO A:1008 , GTP A:1013 , HOH A:1190 , HOH A:1206 , HOH A:1215 , HOH A:1268 , HOH A:1292 , HOH A:1301 , HOH A:1314 , HOH A:1321 , HOH A:1322 , HOH A:1326 , HOH A:1327 , HOH A:1363binding site for residue GTP A 1012
13AD4SOFTWAREGLN A:112 , ASP A:131 , ASP A:133 , LYS A:177 , THR A:179 , CYS A:180 , ARG A:182 , ASP A:193 , TYR A:197 , SER A:259 , MG A:1002 , GTP A:1012 , HOH A:1324 , HOH A:1352binding site for residue GTP A 1013

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XJ3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XJ3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XJ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XJ3)

(-) Exons   (0, 0)

(no "Exon" information available for 4XJ3)

(-) 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    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
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:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.................eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeee....eeeee....eeeee.eeeee..hhhh.eee.......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhheeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xj3 A   2 RMTWNFHQYYTNRNDGLMGKLVLTDEEKNNLKALRKIIRLRTRDVFEEAKGIAKAVKKSALTFEIIQEKVSTTQIKHLSDSEQREVAKLIYEMDDDARDEFLGLTPRFWTQGSFQYDTLNRPFQPGQEMDIDDGTYMPMPIFKIGHSLLILLVDASLKSLVAENHGWKFEAKQTCGRIKIEAEKTHIDVPMYAIPKDGSENVNLALREGDRKWINSDPKIVEDWFNDSCIRIGKHLRKVCRFMKAWRDAQWDVGGPSSISLMAATVNILDSVAHDASDLGETMKIIAKHLPSEFARGVESPDSTDEKPLFPPSYKHGPREMDIMSKLERLPEILSSAESADSKSEALKKINMAFGNRVTNSELIVLAKA 412
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 ||    155       165       175       185       195      |243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403         
                                                                                                                                                                       143|                                                   202|                                                                                                                                                                           
                                                                                                                                                                        148                                                    241
   Legend:   → Mismatch (orange background)
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  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 4XJ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XJ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XJ3)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  4xj3
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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 4xj1 4xj4 4xj5 5go3

(-) Related Entries Specified in the PDB File

4xj1 4xj4 4xj5 4xj6