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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ARCHAEAL HOLLIDAY JUNCTION RESOLVASE HJC
 
Authors :  T. Nishino, K. Komori, D. Tsuchiya, Y. Ishino, K. Morikawa
Date :  08 Nov 00  (Deposition) - 21 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Holliday Junction Resolvase, Hjc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nishino, K. Komori, D. Tsuchiya, Y. Ishino, K. Morikawa
Crystal Structure Of The Archaeal Holliday Junction Resolvase Hjc And Implications For Dna Recognition.
Structure V. 9 197 2001
PubMed-ID: 11286886  |  Reference-DOI: 10.1016/S0969-2126(01)00576-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOLLIDAY JUNCTION RESOLVASE
    Chains: A, B, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: HJC
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): A  E
Biological Unit 2 (1x):  BD 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET B:1 , TYR B:2 , ARG B:3 , LYS B:4 , HOH B:440 , HOH B:456BINDING SITE FOR RESIDUE SO4 B 401
2AC2SOFTWAREMET E:1 , TYR E:2 , ARG E:3 , LYS E:4 , HOH E:452BINDING SITE FOR RESIDUE SO4 E 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GEF)

(-) 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:120
 aligned with HJC_PYRFU | E7FHX4 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:120
                                    10        20        30        40        50        60        70        80        90       100       110       120
            HJC_PYRFU     1 MYRKGAQAERELIKLLEKHGFAVVRSAGSKKVDLVAGNGKKYLCIEVKVTKKDHLYVGKRDMGRLIEFSRRFGGIPVLAVKFLNVGWRFIEVSPKIEKFVFTPSSGVSLEVLLGIQKTLE 120
               SCOP domains d1gefa_ A: Archaeal Holliday junction resolvase Hjc                                                                      SCOP domains
               CATH domains 1gefA00 A:1-120  [code=3.40.1350.10, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..eeee.hhhh...eeee....eeeeeeeee....eeehhhhhhhhhhhhhhhh.eeeeeeee...eeeeee.......eeehhhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gef A   1 MYRKGAQAERELIKLLEKHGFAVVRSAGSKKVDLVAGNGKKYLCIEVKVTKKDHLYVGKRDMGRLIEFSRRFGGIPVLAVKFLNVGWRFIEVSPKIEKFVFTPSSGVSLEVLLGIQKTLE 120
                                    10        20        30        40        50        60        70        80        90       100       110       120


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with HJC_PYRFU | E7FHX4 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:116
                                    10        20        30        40        50        60        70        80        90       100       110      
            HJC_PYRFU     1 MYRKGAQAERELIKLLEKHGFAVVRSAGSKKVDLVAGNGKKYLCIEVKVTKKDHLYVGKRDMGRLIEFSRRFGGIPVLAVKFLNVGWRFIEVSPKIEKFVFTPSSGVSLEVLLGIQ 116
               SCOP domains d1gefb_ B: Archaeal Holliday junction resolvase Hjc                                                                  SCOP domains
               CATH domains 1gefB00 B:1-116  [code=3.40.1350.10, no name defined]                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..eeee........eeee....eeeeeeeee....eeehhhhhhhhhhhhhhhh.eeeeeeee...eeeeee.......eee......hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1gef B   1 MYRKGAQAERELIKLLEKHGFAVVRSAGSKKVDLVAGNGKKYLCIEVKVTKKDHLYVGKRDMGRLIEFSRRFGGIPVLAVKFLNVGWRFIEVSPKIEKFVFTPSSGVSLEVLLGIQ 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain D from PDB  Type:PROTEIN  Length:109
 aligned with HJC_PYRFU | E7FHX4 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:116
                                    10        20        30        40        50        60        70        80        90       100       110      
            HJC_PYRFU     1 MYRKGAQAERELIKLLEKHGFAVVRSAGSKKVDLVAGNGKKYLCIEVKVTKKDHLYVGKRDMGRLIEFSRRFGGIPVLAVKFLNVGWRFIEVSPKIEKFVFTPSSGVSLEVLLGIQ 116
               SCOP domains d1gefd_ D: Archaeal Holliday junction resolvase Hjc                                                                  SCOP domains
               CATH domains 1gefD00 D:1-116  [code=3.40.1350.10, no name defined]                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..eeee.hhhh...eeee....eeeeeeee.....ee.hhhhhhhhhhhhhhhh.eeeeeee.----.eeee....---.ee......hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1gef D   1 MYRKGAQAERELIKLLEKHGFAVVRSAGSKKVDLVAGNGKKYLCIEVKVTKKDHLYVGKRDMGRLIEFSRRFGGIPVLAVKF----WRFIEVSPK---FVFTPSSGVSLEVLLGIQ 116
                                    10        20        30        40        50        60        70        80 |    | 90    |  100       110      
                                                                                                            82   87      95  99                 


Chain E from PDB  Type:PROTEIN  Length:114
 aligned with HJC_PYRFU | E7FHX4 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:114
                                    10        20        30        40        50        60        70        80        90       100       110    
            HJC_PYRFU     1 MYRKGAQAERELIKLLEKHGFAVVRSAGSKKVDLVAGNGKKYLCIEVKVTKKDHLYVGKRDMGRLIEFSRRFGGIPVLAVKFLNVGWRFIEVSPKIEKFVFTPSSGVSLEVLLG 114
               SCOP domains d1gefe_ E: Archaeal Holliday junction resolvase Hjc                                                                SCOP domains
               CATH domains 1gefE00 E:1-114  [code=3.40.1350.10, no name defined]                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..eeee........eeee....eeeeeeeee....eeehhhhhhhhhhhhhhhh.eeeeeeee...eeeeee.......eee......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1gef E   1 MYRKGAQAERELIKLLEKHGFAVVRSAGSKKVDLVAGNGKKYLCIEVKVTKKDHLYVGKRDMGRLIEFSRRFGGIPVLAVKFLNVGWRFIEVSPKIEKFVFTPSSGVSLEVLLG 114
                                    10        20        30        40        50        60        70        80        90       100       110
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,D,E   (HJC_PYRFU | E7FHX4)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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.

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        HJC_PYRFU | E7FHX4: 1ipi

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