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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PERIPLASMIC ENDONUCLEASE VVN
 
Authors :  H. S. Yuan, C. L. Li
Date :  25 Mar 03  (Deposition) - 05 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Non-Specific Endonuclease, Beta-Beta-Alpha-Metal Motif, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. -L. Li, L. -I. Hor, Z. -F. Chang, L. -C. Tsai, W. -Z. Yang, H. S. Yuan
Dna Binding And Cleavage By The Periplasmic Nuclease Vvn: A Novel Structure With A Known Active Site.
Embo J. V. 22 4014 2003
PubMed-ID: 12881435  |  Reference-DOI: 10.1093/EMBOJ/CDG377
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEASE
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB2
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUE 19-228
    Organism Scientific: VIBRIO VULNIFICUS
    Organism Taxid: 672
    Synonym: VVN NUCLEASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:79 , ASN A:127 , HOH A:323 , HOH A:336 , HOH A:492 , HOH A:493BINDING SITE FOR RESIDUE MG A 494

(-) 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 1OUO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OUO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OUO)

(-) Exons   (0, 0)

(no "Exon" information available for 1OUO)

(-) 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:210
 aligned with Q7MHK3_VIBVY | Q7MHK3 from UniProtKB/TrEMBL  Length:231

    Alignment length:210
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228
         Q7MHK3_VIBVY    19 APPSSFSAAKQQAVKIYQDHPISFYCGCDIEWQGKKGIPNLETCGYQVRKQQTRASRIEWEHVVPAWQFGHHRQCWQKGGRKNCSKNDQQFRLMEADLHNLTPAIGEVNGDRSNFNFSQWNGVDGVSYGRCEMQVNFKQRKVMPPDRARGSIARTYLYMSQEYGFQLSKQQQQLMQAWNKSYPVDEWECTRDDRIAKIQGNHNPFVQQSC 228
               SCOP domains d1ouoa_ A: Periplasmic endonuclease Vvn                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh............eeee..eeee...........hhhhhh.eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhh..ee........eee..eeeeee....eee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ouo A  19 APPSSFSAAKQQAVKIYQDHPISFYCGCDIEWQGKKGIPNLETCGYQVRKQQTRASRIEWEHVVPAWQFGHHRQCWQKGGRKNCSKNDQQFRLmEADLHNLTPAIGEVNGDRSNFNFSQWNGVDGVSYGRCEmQVNFKQRKVmPPDRARGSIARTYLYmSQEYGFQLSKQQQQLmQAWNKSYPVDEWECTRDDRIAKIQGNHNPFVQQSC 228
                                    28        38        48        58        68        78        88        98       108   |   118       128       138       148  |    158  |    168       178       188    |  198       208       218       228
                                                                                                                       112-MSE                                151-MSE   161-MSE         177-MSE         193-MSE
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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 1OUO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1OUO)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q7MHK3_VIBVY | Q7MHK3)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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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  1ouo
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 Related Entries

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

UniProtKB/TrEMBL
        Q7MHK3_VIBVY | Q7MHK3: 1oup 2ivk

(-) Related Entries Specified in the PDB File

1oup 1OUP CONTAINS THE SAME PROTEIN COMPLEXED WITH DNA