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(-) Description

Title :  RESTRICTION ENDONUCLEASE MVAI IN THE ABSENCE OF DNA
 
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) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Monomeric Endonuclease, Restriction Enzyme, Mvai, Hydrolase (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 - 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

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CD15Ligand/IonCADMIUM ION
3CL2Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CD-1Ligand/IonCADMIUM ION
3CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CD-1Ligand/IonCADMIUM ION
3CL-1Ligand/IonCHLORIDE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS B:100 , GLN B:101 , ACT B:601 , CD B:910 , HOH B:955BINDING SITE FOR RESIDUE ACT B 600
02AC2SOFTWAREGLN B:101 , SER B:111 , ASN B:112 , SER B:113 , TYR B:114 , ACT B:600 , CD B:910BINDING SITE FOR RESIDUE ACT B 601
03AC3SOFTWAREVAL A:246 , CD A:911BINDING SITE FOR RESIDUE CL A 800
04AC4SOFTWAREHIS A:21 , CD A:913BINDING SITE FOR RESIDUE CL A 801
05AC5SOFTWAREHIS A:59 , GLU A:234 , ASP B:203 , GLU B:238BINDING SITE FOR RESIDUE CD A 900
06AC6SOFTWAREASP A:203 , GLU A:238 , HIS B:59 , GLU B:234BINDING SITE FOR RESIDUE CD B 901
07AC7SOFTWAREHIS B:100 , ASP B:207 , HOH B:935 , HOH B:938 , HOH B:1030BINDING SITE FOR RESIDUE CD B 902
08AC8SOFTWAREHIS A:100 , ASP A:207 , HOH A:919 , HOH A:935 , HOH A:966BINDING SITE FOR RESIDUE CD A 903
09AC9SOFTWAREASP A:121 , HOH A:988 , GLU B:169BINDING SITE FOR RESIDUE CD A 904
10BC1SOFTWAREGLU A:169 , HOH A:1059 , HOH A:1064 , ASP B:121 , HOH B:951 , HOH B:1007BINDING SITE FOR RESIDUE CD A 906
11BC2SOFTWAREGLU A:40 , GLU A:43 , ASP A:50 , HIS A:52 , HOH A:998BINDING SITE FOR RESIDUE CD A 907
12BC3SOFTWAREGLU B:40 , GLU B:43 , HIS B:52BINDING SITE FOR RESIDUE CD B 908
13BC4SOFTWAREASP A:50 , HOH A:998 , ASP B:53 , HOH B:1032BINDING SITE FOR RESIDUE CD A 909
14BC5SOFTWAREACT B:600 , ACT B:601 , HOH B:985BINDING SITE FOR RESIDUE CD B 910
15BC6SOFTWAREASP A:17 , VAL A:246 , CL A:800BINDING SITE FOR RESIDUE CD A 911
16BC7SOFTWAREHIS A:223 , HIS A:225BINDING SITE FOR RESIDUE CD A 912
17BC8SOFTWAREHIS A:21 , CL A:801 , HOH A:1055BINDING SITE FOR RESIDUE CD A 913
18BC9SOFTWAREGLN B:13 , ASP B:17 , VAL B:246BINDING SITE FOR RESIDUE CD B 914
19CC1SOFTWAREASP A:47BINDING SITE FOR RESIDUE CD A 915

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OA9)

(-) 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 2OA9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OA9)

(-) Exons   (0, 0)

(no "Exon" information available for 2OA9)

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

    Alignment length:249
                               1                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         
         Q8RNV5_KOCVA     - ---MSEYLNLLKEAIQNVVDGGWHETKRKGNTGIGKTFEDLLEKEEDNLDAPDFHDIEIKTHETAAKSLLTLFTKSPTNPRGANTMLRNRYGKKDEYGNNILHQTVSGNRKTNSNSYNYDFKIDIDWESQVVRLEVFDKQDIMIDNSVYWSFDSLQNQLDKKLKYIAVISAESKIENEKKYYKYNSANLFTDLTVQSLCRGIENGDIKVDIRIGAYHSGKKKGKTHDHGTAFRINMEKLLEYGEVKVIV 246
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh...eee..---hhhhhhhhhhhhhhhhhhh.......eeeehhhhhh.eeeeee.......hhhhhhhhhhhee.....eeeeeee............eeeeeeee....eeeeeeee....eeeeeeeeehhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeeeeeee.hhhhhhhhhhh..eeeeeeeee.........eee...eeeeehhhhhhhheeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oa9 A  -2 MKSMSEYLNLLKEAIQNVVDGGWHETKR---TGIGKTFEDLLEKEEDNLDAPDFHDIEIKTHETAAKSLLTLFTKSPTNPRGANTMLRNRYGKKDEYGNNILHQTVSGNRKTNSNSYNYDFKIDIDWESQVVRLEVFDKQDIMIDNSVYWSFDSLQNQLDKKLKYIAVISAESKIENEKKYYKYNSANLFTDLTVQSLCRGIENGDIKVDIRIGAYHSGKKKGKTHDHGTAFRINMEKLLEYGEVKVIV 246
                                     7        17       | - |      37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         
                                                      25  29                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with Q8RNV5_KOCVA | Q8RNV5 from UniProtKB/TrEMBL  Length:246

    Alignment length:243
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
         Q8RNV5_KOCVA     4 YLNLLKEAIQNVVDGGWHETKRKGNTGIGKTFEDLLEKEEDNLDAPDFHDIEIKTHETAAKSLLTLFTKSPTNPRGANTMLRNRYGKKDEYGNNILHQTVSGNRKTNSNSYNYDFKIDIDWESQVVRLEVFDKQDIMIDNSVYWSFDSLQNQLDKKLKYIAVISAESKIENEKKYYKYNSANLFTDLTVQSLCRGIENGDIKVDIRIGAYHSGKKKGKTHDHGTAFRINMEKLLEYGEVKVIV 246
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh...ee..-----hhhhhhhhhhhhhhhhh...hhhhheeeehhhhh..eeeeee.......hhhhhhhhhh.ee.....eeeeeee.............eeeeeee....eeeeeee.....eeeeeeeeehhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeeeeeee.hhhhhhhhhhh..eeeeeee..-------------..eeeeehhhhhhhheeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oa9 B   4 YLNLLKEAIQNVVDGGWHETK-----GIGKTFEDLLEKEEDNLDAPDFHDIEIKTHETAAKSLLTLFTKSPTNPRGANTMLRNRYGKKDEYGNNILHQTVSGNRKTNSNSYNYDFKIDIDWESQVVRLEVFDKQDIMIDNSVYWSFDSLQNQLDKKLKYIAVISAESKIENEKKYYKYNSANLFTDLTVQSLCRGIENGDIKVDIRIGA-------------GTAFRINMEKLLEYGEVKVIV 246
                                    13        23|     | 33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        |-         -  |    233       243   
                                               24    30                                                                                                                                                                                   212           226
   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 2OA9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OA9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OA9)

(-) 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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  2oa9
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 Related Entries

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        Q8RNV5_KOCVA | Q8RNV5: 2oaa

(-) Related Entries Specified in the PDB File

2oaa RESTRICTION ENDONUCLEASE MVAI-COGNATE DNA SUBSTRATE COMPLEX