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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PERIPLASMIC ENDONUCLEASE VVN COMPLEXED WITH A 16-BP DNA
 
Authors :  Y. T. Wang, W. J. Yang, C. L. Li, L. G. Doudeva, H. S. Yuan
Date :  14 Jun 06  (Deposition) - 02 Jan 07  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Dnase, Endonuclease, Dna Hydrolysis, Protein Nucleic Acid Interactions, Dna Cleavage Preference, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. T. Wang, W. J. Yang, C. L. Li, L. G. Doudeva, H. S. Yuan
Structural Basis For Sequence-Dependent Dna Cleavage By Nonspecific Endonucleases.
Nucleic Acids Res. V. 35 584 2007
PubMed-ID: 17175542  |  Reference-DOI: 10.1093/NAR/GKL621

(-) Compounds

Molecule 1 - ENDONUCLEASE I
    Chains: A, B, C, D
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Variant: DE3
    Expression System Vector: PTYB2
    Mutation: YES
    Organism Scientific: VIBRIO VULNIFICUS
    Organism Taxid: 672
    Synonym: VVN NUCLEASE
 
Molecule 2 - 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*T)-3'
    Chains: E, G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - 5'-D(*AP*AP*TP*TP*CP*GP*AP*TP*CP*GP *AP*AP*TP*TP*C)-3'
    Chains: F, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*TP*C)-3'
    Chains: I, J
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2IVK)

(-) Sites  (0, 0)

(no "Site" information available for 2IVK)

(-) SS Bonds  (16, 16)

Asymmetric/Biological 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
9C:44 -C:149
10C:46 -C:62
11C:93 -C:102
12C:207 -C:228
13D:44 -D:149
14D:46 -D:62
15D:93 -D:102
16D:207 -D:228

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IVK)

(-) 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:211
 aligned with Q7MHK3_VIBVY | Q7MHK3 from UniProtKB/TrEMBL  Length:231

    Alignment length:211
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228 
         Q7MHK3_VIBVY    19 APPSSFSAAKQQAVKIYQDHPISFYCGCDIEWQGKKGIPNLETCGYQVRKQQTRASRIEWEHVVPAWQFGHHRQCWQKGGRKNCSKNDQQFRLMEADLHNLTPAIGEVNGDRSNFNFSQWNGVDGVSYGRCEMQVNFKQRKVMPPDRARGSIARTYLYMSQEYGFQLSKQQQQLMQAWNKSYPVDEWECTRDDRIAKIQGNHNPFVQQSCQ 229
               SCOP domains d2ivka_ A: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh............eeee..eeeehhhhhh.....hhhhhhheeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhh..ee........ee......eee....eee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ivk A  19 APPSSFSAAKQQAVKIYQDHPISFYCGCDIEWQGKKGIPNLETCGYQVRKQQTRASRIEWEAVVPAWQFGHHRQCWQKGGRKNCSKNDQQFRLMEADLHNLTPAIGEVNGDRSNFNFSQWNGVDGVSYGRCEMQVNFKQRKVMPPDRARGSIARTYLYMSQEYGFQLSKQQQQLMQAWNKSYPVDEWECTRDDRIAKIQGNHNPFVQQSCQ 229
                                    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: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 d2ivkb_ B: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.........eeee..eeee.hhhhh.......hhhh.eeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhh...ee........eee..eeeee.....ee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ivk B  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 C 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 d2ivkc_ C: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.........eeee..eeee.hhhhh.....hhhhhh.eeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhh...ee........eee..eeeee.....ee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ivk C  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 D from PDB  Type:PROTEIN  Length:211
 aligned with Q7MHK3_VIBVY | Q7MHK3 from UniProtKB/TrEMBL  Length:231

    Alignment length:211
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228 
         Q7MHK3_VIBVY    19 APPSSFSAAKQQAVKIYQDHPISFYCGCDIEWQGKKGIPNLETCGYQVRKQQTRASRIEWEHVVPAWQFGHHRQCWQKGGRKNCSKNDQQFRLMEADLHNLTPAIGEVNGDRSNFNFSQWNGVDGVSYGRCEMQVNFKQRKVMPPDRARGSIARTYLYMSQEYGFQLSKQQQQLMQAWNKSYPVDEWECTRDDRIAKIQGNHNPFVQQSCQ 229
               SCOP domains d2ivkd_ D: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh............eeee..eeeehhhhhh.....hhhhhhheeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeehhhhhhhh..ee........ee......eee....eee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ivk D  19 APPSSFSAAKQQAVKIYQDHPISFYCGCDIEWQGKKGIPNLETCGYQVRKQQTRASRIEWEAVVPAWQFGHHRQCWQKGGRKNCSKNDQQFRLMEADLHNLTPAIGEVNGDRSNFNFSQWNGVDGVSYGRCEMQVNFKQRKVMPPDRARGSIARTYLYMSQEYGFQLSKQQQQLMQAWNKSYPVDEWECTRDDRIAKIQGNHNPFVQQSCQ 229
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228 


Chain E from PDB  Type:DNA  Length:15
                                               
                 2ivk E   1 GAATTCGATCGAATT  15
                                    10     


Chain F from PDB  Type:DNA  Length:15
                                               
                 2ivk F  18 AATTCGATCGAATTC  32
                                    27     


Chain G from PDB  Type:DNA  Length:15
                                               
                 2ivk G   1 GAATTCGATCGAATT  15
                                    10     


Chain H from PDB  Type:DNA  Length:15
                                               
                 2ivk H  18 AATTCGATCGAATTC  32
                                    27     


Chain I from PDB  Type:DNA  Length:16
                                                
                 2ivk I   1 GAATTCGATCGAATTC  16
                                    10      


Chain J from PDB  Type:DNA  Length:16
                                                
                 2ivk J  17 GAATTCGATCGAATTC  32
                                    26
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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 1oup

(-) Related Entries Specified in the PDB File

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