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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PERIPLASMIC ENDONUCLEASE VVN COMPLEXED WITH OCTAMER DOUBLE STRANDED DNA
 
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. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  B,C,D  (1x)
Biol. Unit 2:  A,E,F,G  (1x)
Keywords :  Non-Specific Endonuclease, Beta-Beta-Alpha Metal Motif, Hydrolase/Dna Complex (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 - 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'
    Chains: C, D, F
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*GP*CP*GP*AP*TP*C)-3'
    Chains: E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(P*GP*C)-3'
    Chains: G
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - NUCLEASE
    Chains: A, B
    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: RESIDUES 19-231
    Mutation: YES
    Organism Scientific: VIBRIO VULNIFICUS
    Organism Taxid: 672
    Synonym: VVN NUCLEASE

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFG
Biological Unit 1 (1x):  BCD   
Biological Unit 2 (1x): A   EFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:79 , ASN A:127 , HOH A:420 , HOH A:719 , DG G:7 , HOH G:720BINDING SITE FOR RESIDUE CA A 300
2AC2SOFTWAREGLU B:79 , ASN B:127 , HOH B:443 , HOH B:718 , DG C:7 , HOH C:461BINDING SITE FOR RESIDUE CA B 300

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:44 -A:149
2A:46 -A:62
3A:93 -A:102
4A:207 -A:228
5B:44 -B:149
6B:46 -B:62
7B:93 -B:102
8B:207 -B:228

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OUP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OUP)

(-) Sequences/Alignments

Asymmetric 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:213
 aligned with Q7MHK3_VIBVY | Q7MHK3 from UniProtKB/TrEMBL  Length:231

    Alignment length:213
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228   
         Q7MHK3_VIBVY    19 APPSSFSAAKQQAVKIYQDHPISFYCGCDIEWQGKKGIPNLETCGYQVRKQQTRASRIEWEHVVPAWQFGHHRQCWQKGGRKNCSKNDQQFRLMEADLHNLTPAIGEVNGDRSNFNFSQWNGVDGVSYGRCEMQVNFKQRKVMPPDRARGSIARTYLYMSQEYGFQLSKQQQQLMQAWNKSYPVDEWECTRDDRIAKIQGNHNPFVQQSCQTQ 231
               SCOP domains d1oupa_ A: Periplasmic endonuclease Vvn                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh............eeee..eeee...........hhhhhh.eeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhh..ee........eee..eeeeee....eee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oup A  19 APPSSFSAAKQQAVKIYQDHPISFYCGCDIEWQGKKGIPNLETCGYQVRKQQTRASRIEWEAVVPAWQFGHHRQCWQKGGRKNCSKNDQQFRLMEADLHNLTPAIGEVNGDRSNFNFSQWNGVDGVSYGRCEMQVNFKQRKVMPPDRARGSIARTYLYMSQEYGFQLSKQQQQLMQAWNKSYPVDEWECTRDDRIAKIQGNHNPFVQQSCQTQ 231
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228   


Chain B 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 d1oupb_ B: Periplasmic endonuclease Vvn                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Endonuclease_1-1oupB01 B:19-228                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) Endonuclease_1-1oupB02 B:19-228                                                                                                                                                                                    Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhh............ee......ee...........hhhhhh.eeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhh..ee........eee..eeeeee....eee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1oup B  19 APPSSFSAAKQQAVKIYQDHPISFYCGCDIEWQGKKGIPNLETCGYQVRKQQTRASRIEWEAVVPAWQFGHHRQCWQKGGRKNCSKNDQQFRLMEADLHNLTPAIGEVNGDRSNFNFSQWNGVDGVSYGRCEMQVNFKQRKVMPPDRARGSIARTYLYMSQEYGFQLSKQQQQLMQAWNKSYPVDEWECTRDDRIAKIQGNHNPFVQQSC 228
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228


Chain C from PDB  Type:DNA  Length:8
                                        
                 1oup C   1 GCGATCGC   8


Chain D from PDB  Type:DNA  Length:8
                                        
                 1oup D   9 GCGATCGC  16


Chain E from PDB  Type:DNA  Length:6
                                      
                 1oup E   1 GCGATC   6


Chain F from PDB  Type:DNA  Length:8
                                        
                 1oup F   9 GCGATCGC  16


Chain G from PDB  Type:DNA  Length:2
                                  
                 1oup G   7 GC   8
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1OUP)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

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

UniProtKB/TrEMBL
        Q7MHK3_VIBVY | Q7MHK3: 1ouo 2ivk

(-) Related Entries Specified in the PDB File

1ouo 1OUO CONTAINS THE SAME PROTEIN COMPLEXED WITH MG