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(-) Description

Title :  THE N69Q MUTANT OF VIBRIO CHOLERAE ENDONUCLEASE I
 
Authors :  L. Niiranen, B. Altermark, B. O. Brandsdal, H. -K. S. Leiros, R. Helland A. O. Smalas, N. P. Willassen
Date :  04 Feb 08  (Deposition) - 12 Feb 08  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Endonuclease, Endonuclease I, Salt Adaptation, Vibrio, Nuclease, Kinetics, Secreted, Hydrolase, Thermodynamic Stability (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Niiranen, B. Altermark, B. O. Brandsdal, H. -K. S. Leiros, R. Helland, A. O. Smalas, N. P. Willassen
Effects Of Salt On The Kinetics And Thermodynamic Stability Of Endonuclease I From Vibrio Salmonicida And Vibrio Cholerae.
Febs J. V. 275 1593 2008
PubMed-ID: 18312415  |  Reference-DOI: 10.1111/J.1742-4658.2008.06317.X

(-) Compounds

Molecule 1 - ENDONUCLEASE I
    Atcc: 14035
    Chains: A
    EC Number: 3.1.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Variant: PBADGIII
    Mutation: YES
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Other Details: 1 MUTATION : N69Q

 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 A1231
2AC2SOFTWAREGLU A:79 , ASN A:127 , HOH A:2075 , HOH A:2076 , HOH A:2118 , HOH A:2119BINDING SITE FOR RESIDUE MG A1232

(-) 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 2VND)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VND)

(-) 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:207
 aligned with DRNE_VIBCH | P08038 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:207
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       
           DRNE_VIBCH    25 FSHAKNEAVKIYRDHPVSFYCGCEIRWQGKKGIPDLESCGYQVRKNENRASRIEWEHVVPAWQFGHQLQCWQQGGRKNCTRTSPEFNQMEADLHNLTPAIGEVNGDRSNFSFSQWNGVDGVTYGQCEMQVNFKERTAMPPERARGAIARTYLYMSEQYGLRLSKAQSQLMQAWNNQYPVSEWECVRDQRIEKVQGNSNRFVREQCPN 231
               SCOP domains d2vnda_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Endonuclease_1-2vndA01 A:24-228                                                                                                                                                                              -- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..........eeeee..eeeeehhhhh.....hhhhhh.eeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhh..ee........eee..eeeeee....eee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vnd A  24 FSHAKNEAVKIYRDHPVSFYCGCEIRWQGKKGIPDLESCGYQVRKQENRASRIEWEHVVPAWQFGHQLQCWQQGGRKNCTRTSPEFNQMEADLHNLTPAIGEVNGNRSNFSFSQWNGIDGVTYGQCEMQVNFKERTAMPPERARGAIARTYLYMSEQYGLRLSKAQNQLMQAWNNQYPVSEWECVRDQKIEKVQGNSNRFVREQCPN 230
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       


Chain A from PDB  Type:PROTEIN  Length:207
 aligned with Q2XSK9_VIBCL | Q2XSK9 from UniProtKB/TrEMBL  Length:231

    Alignment length:207
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       
         Q2XSK9_VIBCL    25 FSHAKNEAVKIYRDHPVSFYCGCEIRWQGKKGIPDLESCGYQVRKNENRASRIEWEHVVPAWQFGHQLQCWQQGGRKNCTRTSPEFNQMEADLHNLTPAIGEVNGNRSNFSFSQWNGIDGVTYGQCEMQVNFKERTAMPPERARGAIARTYLYMSEQYGLRLSKAQNQLMQAWNNQYPVSEWECVRDQKIEKVQGNSNRFVREQCPN 231
               SCOP domains d2vnda_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Endonuclease_1-2vndA01 A:24-228                                                                                                                                                                              -- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..........eeeee..eeeeehhhhh.....hhhhhh.eeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhh..ee........eee..eeeeee....eee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vnd A  24 FSHAKNEAVKIYRDHPVSFYCGCEIRWQGKKGIPDLESCGYQVRKQENRASRIEWEHVVPAWQFGHQLQCWQQGGRKNCTRTSPEFNQMEADLHNLTPAIGEVNGNRSNFSFSQWNGIDGVTYGQCEMQVNFKERTAMPPERARGAIARTYLYMSEQYGLRLSKAQNQLMQAWNNQYPVSEWECVRDQKIEKVQGNSNRFVREQCPN 230
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 2VND)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: His-Me_finger (38)

(-) Gene Ontology  (7, 11)

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.

Chain A   (DRNE_VIBCH | P08038)
molecular function
    GO:0004536    deoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
    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:0006308    DNA catabolic process    The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/TrEMBL
        Q2XSK9_VIBCL | Q2XSK9: 2g7e 2g7f

(-) Related Entries Specified in the PDB File

2g7e THE 1.6 A CRYSTAL STRUCTURE OF VIBRIO CHOLERAEEXTRACELLULAR ENDONUCLEASE I
2g7f THE 1.6 A CRYSTAL STRUCTURE OF VIBRIO CHOLERAEEXTRACELLULAR ENDONUCLEASE I