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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI 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 :  2.31
Chains :  Asym./Biol. Unit :  A
Keywords :  Cyclic Gmp-Amp Synthase, Bacterial Virulence, Nucleotidyltransferase (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 - VC0179-LIKE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-407
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: DI-NUCLEOTIDE CYCLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GH32Ligand/Ion3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:129 , ASP A:131 , MG A:502 , GH3 A:503 , HOH A:689binding site for residue MG A 501
2AC2SOFTWAREASP A:129 , ASP A:131 , ASP A:191 , MG A:501 , GH3 A:503 , GH3 A:504 , HOH A:691binding site for residue MG A 502
3AC3SOFTWAREGLN A:110 , GLY A:111 , SER A:112 , TYR A:115 , ASP A:129 , ASP A:131 , VAL A:260 , LYS A:283 , ARG A:286 , SER A:297 , ASP A:344 , MG A:501 , MG A:502 , GH3 A:504 , HOH A:639 , HOH A:650 , HOH A:651 , HOH A:665 , HOH A:668 , HOH A:689 , HOH A:691 , HOH A:695 , HOH A:697binding site for residue GH3 A 503
4AC4SOFTWAREGLN A:110 , ASP A:131 , LYS A:175 , THR A:177 , ASP A:191 , TYR A:195 , SER A:255 , MG A:502 , GH3 A:503binding site for residue GH3 A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XJ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XJ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XJ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XJ6)

(-) Exons   (0, 0)

(no "Exon" information available for 4XJ6)

(-) Sequences/Alignments

Asymmetric/Biological 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:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eeeeehhhh.............eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhh..eeeee....eeeee....eeeee.eeeee...hhhh.eee.......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xj6 A   2 PWDFNNYYSHNMDGLISKLKLSKTESDKLKALRQIVRERTRDVFQEARQVAIDVRRQALTLESVRLKLEKTNVRYLSPEERADLARLIFEMEDEARDDFIKFQPRFWTQGSFQYDTLNRPFHPGQEMDIDDGTYMPMTVFESEPSIGHTLLLLLVDTSLKSLEAENDGWVFEEKNTCGRIKIYREKTHIDVPMYAIPKEVESDKVNLALREGVRRWSVSDPKIVEDWFNESCKRIGGHLRSVCRFMKAWRDAQWEVGGPSSISLMTAVVNILDRESHNGSDLTGTMKLIARLLPEEFNRGVESPDDTDEKPLFPAESNHNVHHRAIVETMEGLYGILLAAEQSESREEALRKINEAFGKRVTNALLITSS 406
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406
                                                                                                                                                                                                                                200|                                                                                                                                                                          
                                                                                                                                                                                                                                 236
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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  (0, 0)

(no "SCOP Domain" information available for 4XJ6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XJ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XJ6)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4xj1 4xj3 4xj4 4xj5