Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  BSE634I RESTRICTION ENDONUCLEASE
 
Authors :  S. Grazulis, M. Deibert, R. Rimseliene, R. Skirgaila, G. Sasnauskas, A. Lagunavicius, V. Repin, C. Urbanke, R. Huber, V. Siksnys
Date :  19 Dec 01  (Deposition) - 27 Feb 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Restriction Endonuclease, Apo-Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Grazulis, M. Deibert, R. Rimseliene, R. Skirgaila, G. Sasnauskas, A. Lagunavicius, V. Repin, C. Urbanke, R. Huber, V. Siksnys
Crystal Structure Of The Bse634I Restriction Endonuclease: Comparison Of Two Enzymes Recognizing The Same Dna Sequence
Nucleic Acids Res. V. 30 876 2002
PubMed-ID: 11842098  |  Reference-DOI: 10.1093/NAR/30.4.876

(-) Compounds

Molecule 1 - BSE634I RESTRICTION ENDONUCLEASE
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC18
    Expression System Strain: ER2267
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL5Ligand/IonCHLORIDE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:27 , HIS A:169 , ASP A:173BINDING SITE FOR RESIDUE ACT A 1001
2AC2SOFTWAREASP B:273 , ILE B:274BINDING SITE FOR RESIDUE ACT B 1002
3AC3SOFTWAREARG B:113 , ARG B:121 , HIS B:125BINDING SITE FOR RESIDUE CL B 3001
4AC4SOFTWARELYS B:25 , PHE B:27BINDING SITE FOR RESIDUE CL B 3002
5AC5SOFTWARELYS A:25 , PRO A:26 , PHE A:27 , ASN A:28BINDING SITE FOR RESIDUE CL A 3003
6AC6SOFTWARELYS B:123 , ARG B:226 , HOH B:3110BINDING SITE FOR RESIDUE CL B 3004
7AC7SOFTWARELYS A:123 , ARG A:226BINDING SITE FOR RESIDUE CL A 3005

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KNV)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KNV)

(-) 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:290
 aligned with Q8RT53_GEOSE | Q8RT53 from UniProtKB/TrEMBL  Length:293

    Alignment length:290
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
         Q8RT53_GEOSE     4 NLTNSNCVEEYKENGKTKIRIKPFNALIELYHHQTPTGSIKENLDKLENYVKDVVKAKGLAIPTSGAFSNTRGTWFEVMIAIQSWNYRVKRELNDYLIIKMPNVKTLHFRKIFDNETREKLHQLEKTLLTHKQQVRLITSNPDLLIIRQKDLIKSEYNLPINKLTHENIDVALTLFKDIEGKCKWDSLVAGVGLKTSLRPDRRLQLVHEGNILKSLFAHLKMRYWNPKAEFKYYGASSEPVSKADDDALQTAATHTIVNVNSTPERAVDDIFSLTSFEDIDKMLDQIIKK 293
               SCOP domains d1knva_ A: Restriction endonuclease Bse634I                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1knvA00 A:4-293  [code=3.40.91.10, no name defined]                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eeee......eeeehhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhhhh.............eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....hhhhhhhh...hhhhh............eeee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1knv A   4 NLTNSNCVEEYKENGKTKIRIKPFNALIELYHHQTPTGSIKENLDKLENYVKDVVKAKGLAIPTSGAFSNTRGTWFEVMIAIQSWNYRVKRELNDYLIIKMPNVKTFDFRKIFDNETREKLHQLEKSLLTHKQQVRLITSNPDLLIIRQKDLIKSEYNLPINKLTHENIDVALTLFKDIEGKCKWDSLVAGVGLKTSLRPDRRLQLVHEGNILKSLFAHLKMRYWNPKAEFKYYGASSEPVSKADDDALQTAATHTIVNVNSTPERAVDDIFSLTSFEDIDKMLDQIIKK 293
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with Q8RT53_GEOSE | Q8RT53 from UniProtKB/TrEMBL  Length:293

    Alignment length:291
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292 
         Q8RT53_GEOSE     3 TNLTNSNCVEEYKENGKTKIRIKPFNALIELYHHQTPTGSIKENLDKLENYVKDVVKAKGLAIPTSGAFSNTRGTWFEVMIAIQSWNYRVKRELNDYLIIKMPNVKTLHFRKIFDNETREKLHQLEKTLLTHKQQVRLITSNPDLLIIRQKDLIKSEYNLPINKLTHENIDVALTLFKDIEGKCKWDSLVAGVGLKTSLRPDRRLQLVHEGNILKSLFAHLKMRYWNPKAEFKYYGASSEPVSKADDDALQTAATHTIVNVNSTPERAVDDIFSLTSFEDIDKMLDQIIKK 293
               SCOP domains d1knvb_ B: Restriction endonuclease Bse634I                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1knvB00 B:3-293  [code=3.40.91.10, no name defined]                                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) -----Bse634I-1knvB01 B:8-293                                                                                                                                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) -----Bse634I-1knvB02 B:8-293                                                                                                                                                                                                                                                                        Pfam domains (2)
         Sec.struct. author ........eeeeee..eeeeeehhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhhhhhh..............eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhh.....hhh.eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....hhhhhhhh...hhhhhh...........eeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1knv B   3 TNLTNSNCVEEYKENGKTKIRIKPFNALIELYHHQTPTGSIKENLDKLENYVKDVVKAKGLAIPTSGAFSNTRGTWFEVMIAIQSWNYRVKRELNDYLIIKMPNVKTFDFRKIFDNETREKLHQLEKSLLTHKQQVRLITSNPDLLIIRQKDLIKSEYNLPINKLTHENIDVALTLFKDIEGKCKWDSLVAGVGLKTSLRPDRRLQLVHEGNILKSLFAHLKMRYWNPKAEFKYYGASSEPVSKADDDALQTAATHTIVNVNSTPERAVDDIFSLTSFEDIDKMLDQIIKK 293
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
   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) (23833)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Bse634I] (5)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8RT53_GEOSE | Q8RT53)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0009036    Type II site-specific deoxyribonuclease activity    Catalysis of the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates and 3' hydroxyls. Cleavage is dependent on the presence in the DNA of a specific recognition site; cleavage occurs at or very near this recognition site.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
biological process
    GO:0009307    DNA restriction-modification system    A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1knv)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1knv
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8RT53_GEOSE | Q8RT53
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.1.21.4
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q8RT53_GEOSE | Q8RT53
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8RT53_GEOSE | Q8RT53: 3v1z 3v20 3v21

(-) Related Entries Specified in the PDB File

1cfr 1CFR CONTAINS RESTRICTION ENDONUCLEASE CFR10I OF CITROBACTER FREUNDII