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

(-) Description

Title :  CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BPUJI RECOGNITION DOMAIN IN COMPLEX WITH COGNATE DNA
 
Authors :  R. Sukackaite, S. Grazulis, M. Bochtler, V. Siksnys
Date :  11 Jan 08  (Deposition) - 06 May 08  (Release) - 16 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,L,M
Keywords :  Restriction Endonuclease, Hydrolase, Endonuclease, Dna Recognition, Helix-Turn-Helix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Sukackaite, S. Grazulis, M. Bochtler, V. Siksnys
The Recognition Domain Of The Bpuji Restriction Endonuclease In Complex With Cognate Dna At 1. 3-A Resolution.
J. Mol. Biol. V. 378 1084 2008
PubMed-ID: 18433771  |  Reference-DOI: 10.1016/J.JMB.2008.03.041

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE R.BPUJI
    Chains: A
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAL-BPUJI
    Expression System Strain: ER2267
    Expression System Taxid: 562
    Fragment: RECOGNITION DOMAIN, RESIDUES 1-285
    Organism Scientific: BACILLUS PUMILUS
    Organism Taxid: 1408
    Strain: RFL1458
    Synonym: BPUJI
 
Molecule 2 - 5'-D(*GP*GP*TP*AP*CP*CP*CP*GP*TP*GP *GP*A)-3'
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*AP *CP*C)-3'
    Chains: M
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ALM

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2PG61Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:134 , GLN A:172 , GLY A:173 , ILE A:175 , TRP A:247 , ASN A:249 , LYS A:250 , NA A:1282BINDING SITE FOR RESIDUE PG6 A1281
2AC2SOFTWAREGLY A:173 , PG6 A:1281BINDING SITE FOR RESIDUE NA A1282

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Cys A:37 -Pro A:38
2Phe A:115 -Pro A:116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VLA)

(-) 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:280
 aligned with A3FMN7_BACPU | A3FMN7 from UniProtKB/TrEMBL  Length:462

    Alignment length:280
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280
         A3FMN7_BACPU     1 MNYNPEEQFRCTIIRGKAKNMLDNLLPAYANIIDDICPCDKASFVKDFNNRLIEILGEETTKKTLDNHRTEIAGKLFGMFYEDDEVIFPSGRTNKYIEDSDQPAFFKDICFKFQFPNGMDKLDKVIEKVGAKIQIRQFPYILQVLLTADNNNIQLSKDDIAYYVLNSLQVLQGKIKPIEVIEKIIEDRSNDITKKVRHPGKETSYSMQHIREQLNYLELANLIRIDGNLVKLNYREAENINYIAQFWGNKPEFNAYKYDFTSEDDKKSFFKDWQQYYSNV 280
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains BpuJI_N-2vlaA01 A:1-280                                                                                                                                                                                                                                                                  Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhh.....hhhhhhhhhhh.......eeee..eeee.hhhhhhhhh..hhhhhhhhhhh.........hhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhh...hhhhh....hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh..eee....eee....hhhhhhhhh.................hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vla A   1 MNYNPEEQFRCTIIRGKAKNMLDNLLPAYANIIDDICPCDKASFVKDFNNRLIEILGEETTKKTLDNHRTEIAGKLFGMFYEDDEVIFPSGRTNKYIEDSDQPAFFKDICFKFQFPNGMDKLDKVIEKVGAKIQIRQFPYILQVLLTADNNNIQLSKDDIAYYVLNSLQVLQGKIKPIEVIEKIIEDRSNDITKKVRHPGKETSYSMQHIREQLNYLELANLIRIDGNLVKLNYREAENINYIAQFWGNKPEFNAYKYDFTSEDDKKSFFKDWQQYYSNV 280
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280


Chain L from PDB  Type:DNA  Length:12
                                            
                 2vla L 101 GGTACCCGTGGA 112
                                   110  


Chain M from PDB  Type:DNA  Length:12
                                            
                 2vla M 201 TCCACGGGTACC 212
                                   210
   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 2VLA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: BpuJI_N] (1)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A3FMN7_BACPU | A3FMN7)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG6  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Cys A:37 - Pro A:38   [ RasMol ]  
    Phe A:115 - Pro A:116   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  2vla
    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
  A3FMN7_BACPU | A3FMN7
    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
  A3FMN7_BACPU | A3FMN7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A3FMN7_BACPU | A3FMN7: 5hlt 5hnf 5hnh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2VLA)