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(-) Description

Title :  CRYSTAL STRUCTURES OF HOLLIDAY JUNCTION RESOLVASES FROM ARCHAEOGLOBUS FULGIDUS BOUND TO DNA SUBSTRATE
 
Authors :  C. Carolis, C. Koehler, C. Sauter, J. Basquin, D. Suck, I. Toeroe
Date :  18 May 09  (Deposition) - 26 May 09  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Hydrolase Dna Complex, Type Ii Restriction Endonuclease, Holliday Junction Resolvase, Hydrolase, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Carolis, C. Koehler, C. Sauter, J. Basquin, D. Suck, I. Toeroe
Crystal Structures Of Holliday Junction Resolvases From Archaeoglobus Fulgidus Bound To Dna Substrate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ARCHAEAL HJC
    Atcc: 49558
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM12
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Fragment: RESIDUES 2-136
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Other Details: N-TERMINUS CONTAINS EXTRA RESIDUES AS A RESULT OF CLONING PROCEDURE
    Other Details - Source: GERMAN COLLECTION OF MICROORGANISMS (DSM)
    Strain: 4304
 
Molecule 2 - HALF-JUNCTION
    Chains: C
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHESIZED
    Other Details - Source: SYNTHESIZED BY METABION GMBH, MARTINSRIED, GERMANY
    Synthetic: YES
 
Molecule 3 - HALF-JUNCTION
    Chains: D
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHESIZED
    Other Details - Source: SYNTHESIZED BY METABION GMBH, MARTINSRIED, GERMANY
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NCO1Ligand/IonCOBALT HEXAMMINE(III)
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NCO2Ligand/IonCOBALT HEXAMMINE(III)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:29 , PRO B:33 , PHE B:34 , CYS B:36 , ASP B:38 , GLU B:51 , GLN B:69 , DG C:13 , DC C:14BINDING SITE FOR RESIDUE NCO B1129

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WJ0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:58 -Pro A:59
2Leu B:58 -Pro B:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WJ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WJ0)

(-) Exons   (0, 0)

(no "Exon" information available for 2WJ0)

(-) 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:125
 aligned with HJC_ARCFU | O28314 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:125
                                    12        22        32        42        52        62        72        82        92       102       112       122     
            HJC_ARCFU     3 SKGTRFERDLLVELWKAGFAAIRVAGSGVSPFPCPDIVAGNGRTYLAIEVKMRKELPLYLSADEVEQLVTFARGFGAEAYVALKLPRKKWRFFPVQMLERTEKNFKIDESVYPLGLEIAEVAGKF 127
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wj0A00 A:3-127  [code=3.40.1350.10, no name defined]                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..eeee.............eeee....eeeeeeee.....eeeehhhhhhhhhhhhhhh.eeeeeee......eeee.hhhee...eeee...hhhhh.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wj0 A   3 SKGTRFERDLLVELWKAGFAAIRVAGSGVSPFPCPDIVAGNGRTYLAIEVKMRKELPLYLSADEVEQLVTFARGFGAEAYVALKLPRKKWRFFPVQMLERTEKNFKIDESVYPLGLEIAEVAGKF 127
                                    12        22        32        42        52        62        72        82        92       102       112       122     


Chain B from PDB  Type:PROTEIN  Length:125
 aligned with HJC_ARCFU | O28314 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:125
                                    13        23        33        43        53        63        73        83        93       103       113       123     
            HJC_ARCFU     4 KGTRFERDLLVELWKAGFAAIRVAGSGVSPFPCPDIVAGNGRTYLAIEVKMRKELPLYLSADEVEQLVTFARGFGAEAYVALKLPRKKWRFFPVQMLERTEKNFKIDESVYPLGLEIAEVAGKFF 128
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wj0B00 B:4-128  [code=3.40.1350.10, no name defined]                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh..eeee.............eeee....eeeeeeee.....eeeehhhhhhhhhhhhhhh.eeeeeee.......eee....ee...eeee...hhhhh.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wj0 B   4 KGTRFERDLLVELWKAGFAAIRVAGSGVSPFPCPDIVAGNGRTYLAIEVKMRKELPLYLSADEVEQLVTFARGFGAEAYVALKLPRKKWRFFPVQMLERTEKNFKIDESVYPLGLEIAEVAGKFF 128
                                    13        23        33        43        53        63        73        83        93       103       113       123     


Chain C from PDB  Type:DNA  Length:24
                                                        
                 2wj0 C   1 GGGGATCCCTAAGCTCCATCGATG  24
                                    10        20    


Chain D from PDB  Type:DNA  Length:24
                                                        
                 2wj0 D   1 CATCGATGGAGCTTAGGGATCCCC  24
                                    10        20
   Legend:   → Mismatch (orange background)
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  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 2WJ0)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WJ0)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HJC_ARCFU | O28314)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        HJC_ARCFU | O28314: 2wcw 2wcz 2wiw 2wiz

(-) Related Entries Specified in the PDB File

2wcw 1.6A RESOLUTION STRUCTURE OF ARCHAEOGLOBUS FULGIDUS HJC, A HOLLIDAY JUNCTION RESOLVASE FROM AN ARCHAEAL HYPERTHERMOPHILE
2wcz 1.6A RESOLUTION STRUCTURE OF ARCHAEOGLOBUS FULGIDUS HJC, A HOLLIDAY JUNCTION RESOLVASE FROM AN ARCHAEAL HYPERTHERMOPHILE
2wiw CRYSTAL STRUCTURES OF HOLLIDAY JUNCTION RESOLVASES FROM ARCHAEOGLOBUS FULGIDUS BOUND TO DNA SUBSTRATE
2wiz CRYSTAL STRUCTURES OF HOLLIDAY JUNCTION RESOLVASES FROM ARCHAEOGLOBUS FULGIDUS BOUND TO DNA SUBSTRATE