Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  HOLLIDAY JUNCTION RESOLVING ENZYME
 
Authors :  C. L. Middleton, J. L. Parker, D. J. Richard, M. F. White, C. S. Bond
Date :  28 Jan 03  (Deposition) - 15 Oct 04  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Enzyme, Homologous Recombination, Holliday Junction Resolving Enzyme, Nuclease, Archaea, Thermophile (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Middleton, J. L. Parker, D. J. Richard, M. F. White, C. S. Bond
Substrate Recognition And Catalysis By The Holliday Junctio Resolving Enzyme Hje.
Nucleic Acids Res. V. 32 5442 2004
PubMed-ID: 15479781  |  Reference-DOI: 10.1093/NAR/GKH869

(-) Compounds

Molecule 1 - HOLLIDAY-JUNCTION RESOLVASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21
    Expression System Plasmid: PET19B
    Expression System Strain: DE3
    Expression System Taxid: 562
    Expression System Variant: RIL
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: HOLLIDAY JUNCTION ENDONUCLEASE

 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  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2SO43Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:11 , ARG A:26 , HOH A:2117BINDING SITE FOR RESIDUE SO4 A1001
2AC2SOFTWAREGLY A:45 , ASN A:46 , ILE A:128 , HOH A:2055BINDING SITE FOR RESIDUE SO4 A1002
3AC3SOFTWARELYS A:81 , LYS A:89 , LYS A:91 , ARG A:127 , EDO A:1135 , HOH A:2120BINDING SITE FOR RESIDUE SO4 A1003
4AC4SOFTWAREGLU A:20 , LYS A:44 , GLY B:6 , ASN B:8 , ALA B:9 , SER B:55 , HOH B:2061 , HOH B:2119 , HOH B:2120 , HOH B:2121BINDING SITE FOR RESIDUE SO4 B1001
5AC5SOFTWAREARG B:11 , ARG B:26 , HOH B:2122BINDING SITE FOR RESIDUE SO4 B1002
6AC6SOFTWAREGLY B:45 , ASN B:46 , THR B:47 , LYS B:81 , ILE B:128 , LYS B:131 , HOH B:2125BINDING SITE FOR RESIDUE SO4 B1003
7AC7SOFTWAREGLN A:92 , ILE A:115 , ASP A:119 , HOH A:2121 , HOH A:2122BINDING SITE FOR RESIDUE EDO A1133
8AC8SOFTWAREASP A:73 , SER A:76 , MET A:77 , HOH A:2123 , HOH A:2124 , ASN B:23BINDING SITE FOR RESIDUE EDO A1134
9AC9SOFTWARETRP A:57 , GLY A:82 , PRO A:84 , LYS A:91 , ARG A:127 , SO4 A:1003 , HOH A:2125BINDING SITE FOR RESIDUE EDO A1135

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OB8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OB8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OB8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OB8)

(-) Exons   (0, 0)

(no "Exon" information available for 1OB8)

(-) 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:119
 aligned with HJE_SULSO | Q97YX6 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:124
                                    15        25        35        45        55        65        75        85        95       105       115       125    
            HJE_SULSO     6 GKNAERELVSILRGEGFNAVRIPTSNSSPNPLPDIFATKGNTLLSIECKSTWENKVKVKEHQVRKLLDFLSMFTMKGVPLIAIKFKQVHEWRVLVPEKAEDIIVTIDNSIPIEDLFKILEKRIE 129
               SCOP domains d1ob8a_ A: Holliday-junc     tion resolvase SSO1176                                                                          SCOP domains
               CATH domains 1ob8A00 A:6-129  [code=3     .40.1350.10, no name defined]                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..eeee...-----.....eeeee..eeeeeeeeee...eeeehhhhhhhhhhhhhh...eeeeeeeeee.hhheeeee.......eeee....eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ob8 A   6 GKNAERELVSILRGEGFNAVRIPT-----NPLPDIFATKGNTLLSIECKSTWENKVKVKEHQVRKLLDFLSMFTMKGVPLIAIKFKQVHEWRVLVPEKAEDIIVTIDNSIPIEDLFKILEKRIE 129
                                    15        25   |    35        45        55        65        75        85        95       105       115       125    
                                                  29    35                                                                                              


Chain B from PDB  Type:PROTEIN  Length:127
 aligned with HJE_SULSO | Q97YX6 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:132
                                    13        23        33        43        53        63        73        83        93       103       113       123       133  
            HJE_SULSO     4 DIGKNAERELVSILRGEGFNAVRIPTSNSSPNPLPDIFATKGNTLLSIECKSTWENKVKVKEHQVRKLLDFLSMFTMKGVPLIAIKFKQVHEWRVLVPEKAEDIIVTIDNSIPIEDLFKILEKRIEEKILTP 135
               SCOP domains d1ob8b_ B: Holliday-juncti     on resolvase SSO1176                                                                                  SCOP domains
               CATH domains 1ob8B00 B:4-135  [code=3.4     0.1350.10, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..eeee...-----.....eeeee..eeeeeeeeee...eeeehhhhhhhhhhhhh....eeeeeeeeee....eeeee.......eeee....eehhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ob8 B   4 DIGKNAERELVSILRGEGFNAVRIPT-----NPLPDIFATKGNTLLSIECKSTWENKVKVKEHQVRKLLDFLSMFTMKGVPLIAIKFKQVHEWRVLVPEKAEDIIVTIDNSIPIEDLFKILEKRIEEKILTP 135
                                    13        23     |   - |      43        53        63        73        83        93       103       113       123       133  
                                                    29    35
   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  (0, 0)

(no "Pfam Domain" information available for 1OB8)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HJE_SULSO | Q97YX6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008821    crossover junction endodeoxyribonuclease activity    Catalysis of the endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction).
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ob8)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  1ob8
    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
  HJE_SULSO | Q97YX6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  HJE_SULSO | Q97YX6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        HJE_SULSO | Q97YX6: 1ob9

(-) Related Entries Specified in the PDB File

1ob9 HOLLIDAY JUNCTION RESOLVING ENZYME BOUND IN THE ACTIVE SITE.