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(-) Description

Title :  CRYSTAL STRUCTURE OF VIBRIO CHOLERAE DNCV 3'-DEOXY 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 :  1.55
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  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2GH32Ligand/Ion3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4NA1Ligand/IonSODIUM ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:131 , ASP A:133 , GH3 A:1014 , HOH A:1282binding site for residue MG A 1001
02AC2SOFTWAREASP A:131 , ASP A:133 , ASP A:193 , GH3 A:1013 , GH3 A:1014 , HOH A:1303binding site for residue MG A 1002
03AC3SOFTWAREALA A:292 , ASN A:394 , MET A:395 , GLY A:398 , HOH A:1221binding site for residue EDO A 1003
04AC4SOFTWAREGLY A:297 , GLY A:298 , SER A:300 , HOH A:1127 , HOH A:1188 , HOH A:1253binding site for residue EDO A 1004
05AC5SOFTWARELYS A:277 , ALA A:316 , GLU A:324binding site for residue EDO A 1005
06AC6SOFTWAREMET A:3 , TRP A:5 , GLU A:381 , SER A:382 , ALA A:383binding site for residue EDO A 1006
07AC7SOFTWAREPHE A:64 , TRP A:294 , ASP A:295 , VAL A:296 , HOH A:1116 , HOH A:1120 , HOH A:1141 , HOH A:1197binding site for residue EDO A 1007
08AC8SOFTWARELYS A:29 , SER A:114 , PHE A:115 , ASP A:118 , THR A:119 , LEU A:120 , ARG A:284 , HOH A:1183binding site for residue EDO A 1008
09AC9SOFTWAREARG A:108binding site for residue EDO A 1009
10AD1SOFTWARESER A:314 , HIS A:332 , GLU A:336 , HOH A:1340binding site for residue EDO A 1010
11AD2SOFTWAREPHE A:7 , TYR A:11 , GLY A:323 , LEU A:377 , GLU A:381 , ILE A:393binding site for residue EDO A 1011
12AD3SOFTWARELYS A:277 , HIS A:317 , ASP A:318 , ALA A:319 , HOH A:1106 , HOH A:1132 , HOH A:1137 , HOH A:1256binding site for residue EDO A 1012
13AD4SOFTWAREGLN A:112 , ASP A:133 , LYS A:177 , THR A:179 , CYS A:180 , ASP A:193 , TYR A:197 , SER A:259 , MG A:1002 , GH3 A:1014binding site for residue GH3 A 1013
14AD5SOFTWAREGLN A:112 , GLY A:113 , SER A:114 , TYR A:117 , ASP A:131 , ASP A:133 , LYS A:287 , SER A:301 , ASP A:348 , LEU A:352 , MG A:1001 , MG A:1002 , GH3 A:1013 , HOH A:1184 , HOH A:1199 , HOH A:1207 , HOH A:1250 , HOH A:1272 , HOH A:1279 , HOH A:1282 , HOH A:1283 , HOH A:1284 , HOH A:1286 , HOH A:1303binding site for residue GH3 A 1014
15AD6SOFTWARETRP A:289 , LYS A:369 , LEU A:373 , ILE A:376 , HOH A:1181binding site for residue NA A 1015

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XJ5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XJ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XJ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XJ5)

(-) Exons   (0, 0)

(no "Exon" information available for 4XJ5)

(-) 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:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhh.............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
                 4xj5 A   2 RMTWNFHQYYTNRNDGLMGKLVLTDEEKNNLKALRKIIRLRTRDVFEEAKGIAKAVKKSALTFEIIQEKVSTTQIKHLSDSEQREVAKLIYEMDDDARDEFLGLTPRFWTQGSFQYDTLNRPFQPGQEMDIDDGTYMPMPIKIGHSLLILLVDASLKSLVAENHGWKFEAKQTCGRIKIEAEKTHIDVPMYAIPKGSENVNLALREGDRKWINSDPKIVEDWFNDSCIRIGKHLRKVCRFMKAWRDAQWDVGGPSSISLMAATVNILDSVAHDASDLGETMKIIAKHLPSEFARGVESPDSTDEKPLFPPSYKHGPREMDIMSKLERLPEILSSAESADSKSEALKKINMAFGNRVTNSELIVLAKA 412
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141||     156       166       176       186       196    || 245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       
                                                                                                                                                                      142|                                                  201|                                                                                                                                                                           
                                                                                                                                                                       148                                                   241
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 4XJ5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XJ5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XJ5)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4xj3 4xj4 5go3

(-) Related Entries Specified in the PDB File

4xj1 4xj3 4xj4 4xj6