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(-) Description

Title :  RESTRICTION ENDONUCLEASE MVAI-COGNATE DNA SUBSTRATE COMPLEX
 
Authors :  M. Kaus-Drobek, H. Czapinska, M. Sokolowska, G. Tamulaitis, R. H. Szczepanowski, K. Urbanke, V. Siksnys, M. Bochtler
Date :  15 Dec 06  (Deposition) - 20 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Monomeric Endonuclease, Dna Substrate Complex, Restriction Enzyme, Mvai, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kaus-Drobek, H. Czapinska, M. Sokolowska, G. Tamulaitis, R. H. Szczepanowski, C. Urbanke, V. Siksnys, M. Bochtler
Restriction Endonuclease Mvai Is A Monomer That Recognizes Its Target Sequence Asymmetrically.
Nucleic Acids Res. V. 35 2035 2007
PubMed-ID: 17344322  |  Reference-DOI: 10.1093/NAR/GKM064
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*GP*TP*AP*CP*CP*TP*GP*GP*AP*T)-3'
    Chains: C, E
    Engineered: YES
    Other Details: T STRAND
    Synthetic: YES
 
Molecule 2 - 5'-D(*CP*AP*TP*CP*CP*AP*GP*GP*TP*AP*C)-3'
    Chains: D, F
    Engineered: YES
    Other Details: A STRAND
    Synthetic: YES
 
Molecule 3 - R.MVAI
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD24_R.MVAI
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector: PBAD24(APR)
    Expression System Vector Type: PLASMID
    Gene: MVAIR
    Organism Scientific: KOCURIA VARIANS
    Organism Taxid: 1272

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1CA7Ligand/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  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:50 , HOH A:608 , HOH A:699 , HOH A:748 , HOH A:773 , DC C:-1 , DT C:0BINDING SITE FOR RESIDUE CA C 605
2AC2SOFTWAREASP B:50 , HOH B:674 , HOH B:737 , HOH B:754 , DC E:-1 , DT E:0BINDING SITE FOR RESIDUE CA E 606
3AC3SOFTWAREASP A:50 , GLU A:55 , ILE A:56 , HOH A:615 , DT C:0 , HOH C:76BINDING SITE FOR RESIDUE CA A 601
4AC4SOFTWAREASP A:121 , ILE A:122 , HOH A:655 , HOH A:667 , HOH A:759 , HOH A:774 , HOH A:805BINDING SITE FOR RESIDUE CA A 607
5AC5SOFTWAREASP B:50 , GLU B:55 , ILE B:56 , HOH B:621 , DT E:0 , HOH E:148BINDING SITE FOR RESIDUE CA B 602
6AC6SOFTWARELYS B:64 , HOH B:647 , HOH B:661 , HOH B:714 , HOH B:726 , HOH F:280BINDING SITE FOR RESIDUE CA B 603
7AC7SOFTWAREASP B:121 , ILE B:122 , HOH B:687 , HOH B:690 , HOH B:751 , HOH B:779BINDING SITE FOR RESIDUE CA B 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OAA)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:76 -Pro A:77
2Asn B:76 -Pro B:77

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OAA)

(-) 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:247
 aligned with Q8RNV5_KOCVA | Q8RNV5 from UniProtKB/TrEMBL  Length:246

    Alignment length:247
                             1                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       
         Q8RNV5_KOCVA     - -MSEYLNLLKEAIQNVVDGGWHETKRKGNTGIGKTFEDLLEKEEDNLDAPDFHDIEIKTHETAAKSLLTLFTKSPTNPRGANTMLRNRYGKKDEYGNNILHQTVSGNRKTNSNSYNYDFKIDIDWESQVVRLEVFDKQDIMIDNSVYWSFDSLQNQLDKKLKYIAVISAESKIENEKKYYKYNSANLFTDLTVQSLCRGIENGDIKVDIRIGAYHSGKKKGKTHDHGTAFRINMEKLLEYGEVKVIV 246
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..eee......hhhhhhhhhhh..............eeeeeee.hhh..eeeee.......hhhhhhhhhhhee.....eeeeeee............eeeeeeee....eeeeeeee....eee...eeehhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeeeeee..hhhhhhhhhhh..eeeeeeeee.........eee...eeee.hhhhhhh.eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oaa A   0 SMSEYLNLLKEAIQNVVDGGWHETKRKGNTGIGKTFEDLLEKEEDNLDAPDFHDIEIKTHETAAKSLLTLFTKSPTNPRGANTMLRNRYGKKDEYGNNILHQTVSGNRKTNSNSYNYDFKIDIDWESQVVRLEVFDKQDIMIDNSVYWSFDSLQNQLDKKLKYIAVISAESKIENEKKYYKYNSANLFTDLTVQSLCRGIENGDIKVDIRIGAYHSGKKKGKTHDHGTAFRINMEKLLEYGEVKVIV 246
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       


Chain B from PDB  Type:PROTEIN  Length:248
 aligned with Q8RNV5_KOCVA | Q8RNV5 from UniProtKB/TrEMBL  Length:246

    Alignment length:248
                              1                                                                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238        
         Q8RNV5_KOCVA     - --MSEYLNLLKEAIQNVVDGGWHETKRKGNTGIGKTFEDLLEKEEDNLDAPDFHDIEIKTHETAAKSLLTLFTKSPTNPRGANTMLRNRYGKKDEYGNNILHQTVSGNRKTNSNSYNYDFKIDIDWESQVVRLEVFDKQDIMIDNSVYWSFDSLQNQLDKKLKYIAVISAESKIENEKKYYKYNSANLFTDLTVQSLCRGIENGDIKVDIRIGAYHSGKKKGKTHDHGTAFRINMEKLLEYGEVKVIV 246
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh...ee......hhhhhhhhhhh...............eeeeee.hhh..eeeee.......hhhhhhhhhhhee.....eeeeeee............eeeeeeee....eeeeeeee....eee...eeehhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeeeeee..hhhhhhhhhhhh.eeeeeeeee.........eee...eeee.hhhhhhh.eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oaa B  -1 KSMSEYLNLLKEAIQNVVDGGWHETKRKGNTGIGKTFEDLLEKEEDNLDAPDFHDIEIKTHETAAKSLLTLFTKSPTNPRGANTMLRNRYGKKDEYGNNILHQTVSGNRKTNSNSYNYDFKIDIDWESQVVRLEVFDKQDIMIDNSVYWSFDSLQNQLDKKLKYIAVISAESKIENEKKYYKYNSANLFTDLTVQSLCRGIENGDIKVDIRIGAYHSGKKKGKTHDHGTAFRINMEKLLEYGEVKVIV 246
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238        


Chain C from PDB  Type:DNA  Length:10
                                          
                 2oaa C  -5 GTACCTGGAT   4
                                     4


Chain D from PDB  Type:DNA  Length:11
                                           
                 2oaa D  -5 CATCCAGGTAC   5
                                     4 


Chain E from PDB  Type:DNA  Length:11
                                           
                 2oaa E  -6 GGTACCTGGAT   4
                                     3 


Chain F from PDB  Type:DNA  Length:11
                                           
                 2oaa F  -5 CATCCAGGTAC   5
                                     4
   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  (0, 0)

(no "SCOP Domain" information available for 2OAA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8RNV5_KOCVA | Q8RNV5)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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        Q8RNV5_KOCVA | Q8RNV5: 2oa9

(-) Related Entries Specified in the PDB File

2oa9 RESTRICTION ENDONUCLEASE MVAI IN THE ABSENCE OF DNA