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(-) Description

Title :  THE 1.95 A CRYSTAL STRUCTURE OF VIBRIO CHOLERAE EXTRACELLULAR ENDONUCLEASE I
 
Authors :  B. Altermark, A. O. Smalaas, N. P. Willassen, R. Helland
Date :  28 Feb 06  (Deposition) - 31 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Vibrio Cholerae Nuclease; Enda; Endonuclease I; Buried Chloride, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Altermark, A. O. Smalas, N. P. Willassen, R. Helland
The Structure Of Vibrio Cholerae Extracellular Endonuclease I Reveals The Presence Of A Buried Chloride Ion.
Acta Crystallogr. , Sect. D V. 62 1387 2006
PubMed-ID: 17057343  |  Reference-DOI: 10.1107/S0907444906034196
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDONUCLEASE I
    Chains: A
    EC Number: 3.1.21.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector: PBAD/GIII
    Expression System Vector Type: PLASMID
    Gene: ENDA
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Strain: ATCC14035

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:41 , TYR A:43 , CYS A:44 , ILE A:123BINDING SITE FOR RESIDUE CL A 300
2AC2SOFTWAREGLU A:79 , ASN A:127 , HOH A:1000 , HOH A:1023 , HOH A:1026 , HOH A:1176BINDING SITE FOR RESIDUE MG A 301

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:44 -A:149
2A:46 -A:62
3A:93 -A:102
4A:207 -A:228

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G7F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G7F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2G7F)

(-) Exons   (0, 0)

(no "Exon" information available for 2G7F)

(-) 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:208
 aligned with Q2XSK9_VIBCL | Q2XSK9 from UniProtKB/TrEMBL  Length:231

    Alignment length:208
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
         Q2XSK9_VIBCL    24 SFSHAKNEAVKIYRDHPVSFYCGCEIRWQGKKGIPDLESCGYQVRKNENRASRIEWEHVVPAWQFGHQLQCWQQGGRKNCTRTSPEFNQMEADLHNLTPAIGEVNGNRSNFSFSQWNGIDGVTYGQCEMQVNFKERTAMPPERARGAIARTYLYMSEQYGLRLSKAQNQLMQAWNNQYPVSEWECVRDQKIEKVQGNSNRFVREQCPN 231
               SCOP domains d2g7fa_ A: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.........eeee..eeee.hhhhh.....hhhhhh.eeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhh..ee........eee..eeeeee....eee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g7f A  23 SFSHAKNEAVKIYRDHPVSFYCGCEIRWQGKKGIPDLESCGYQVRKNENRASRIEWEHVVPAWQFGHQLQCWQQGGRKNCTRTSPEFNQMEADLHNLTPAIGEVNGNRSNFSFSQWNGIDGVTYGQCEMQVNFKERTAMPPERARGAIARTYLYMSEQYGLRLSKAQNQLMQAWNNQYPVSEWECVRDQKIEKVQGNSNRFVREQCPN 230
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2G7F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G7F)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q2XSK9_VIBCL | Q2XSK9)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q2XSK9_VIBCL | Q2XSK9: 2vnd
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        Q2XSK9_VIBCL | Q2XSK9: 2g7e

(-) Related Entries Specified in the PDB File

2g7e CRYSTAL STRUCTURE OF VIBRIO ENDONUCLEASE I AT NEUTRAL PH THE RESIDUE NUMBERING FOLLOWS THAT OF VIBRIO VULNIFICUS ENDONUCLEASE (PDB 1OUO)