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(-) Description

Title :  STRUCTURE OF E.COLI RUSA HOLLIDAY JUNCTION RESOLVASE
 
Authors :  J. B. Rafferty, E. L. Bolt, T. A. Muranova, S. E. Sedelnikova, P. Leonard A. Pasquo, P. J. Baker, D. W. Rice, G. J. Sharples, R. G. Lloyd
Date :  22 Aug 03  (Deposition) - 06 Jan 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Extended Mixed Beta Sheet, Chorismate Mutase-Like Fold, Recombination, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Rafferty, E. L. Bolt, T. A. Muranova, S. E. Sedelnikova, P. Leonard, A. Pasquo, P. J. Baker, D. W. Rice, G. J. Sharples, R. G. Lloy
The Structure Of Escherichia Coli Rusa Endonuclease Reveals A New Holliday Junction Dna Binding Fold
Structure V. 11 1557 2003
PubMed-ID: 14656440  |  Reference-DOI: 10.1016/J.STR.2003.11.004

(-) Compounds

Molecule 1 - CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUSA
    Chains: A, B
    EC Number: 3.1.22.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEB259
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PT7-7
    Gene: RUSA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RUSA RESOLVASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1Q8R)

(-) Sites  (0, 0)

(no "Site" information available for 1Q8R)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q8R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q8R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q8R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q8R)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q8R)

(-) 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:118
 aligned with RUSA_ECOL6 | P0AG75 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:118
                                    10        20        30        40        50        60        70        80        90       100       110        
           RUSA_ECOL6     1 MNTYSITLPWPPSNNRYYRHNRGRTHVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRDLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
               SCOP domains d1q8ra_ A: Holliday junction resolvase RusA                                                                            SCOP domains
               CATH domains 1q8rA00 A:1-118 Holliday junction resolvase RusA. Chain A                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhheee....eeehhhhhhhhhhhhhhhhhh.........eeeeeeee.......hhhhhhhhhhhhhhhh....hhh.eeeeeeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1q8r A   1 MNTYSITLPWPPSNNRYYRHNRGRTHVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRDLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
                                    10        20        30        40        50        60        70        80        90       100       110        


Chain A from PDB  Type:PROTEIN  Length:118
 aligned with RUSA_ECOLI | P0AG74 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:118
                                    10        20        30        40        50        60        70        80        90       100       110        
           RUSA_ECOLI     1 MNTYSITLPWPPSNNRYYRHNRGRTHVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRDLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
               SCOP domains d1q8ra_ A: Holliday junction resolvase RusA                                                                            SCOP domains
               CATH domains 1q8rA00 A:1-118 Holliday junction resolvase RusA. Chain A                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhheee....eeehhhhhhhhhhhhhhhhhh.........eeeeeeee.......hhhhhhhhhhhhhhhh....hhh.eeeeeeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1q8r A   1 MNTYSITLPWPPSNNRYYRHNRGRTHVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRDLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
                                    10        20        30        40        50        60        70        80        90       100       110        


Chain B from PDB  Type:PROTEIN  Length:109
 aligned with RUSA_ECOL6 | P0AG75 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:118
                                    10        20        30        40        50        60        70        80        90       100       110        
           RUSA_ECOL6     1 MNTYSITLPWPPSNNRYYRHNRGRTHVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRDLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
               SCOP domains d1q8rb_ B: Hollid         ay junction resolvase RusA                                                                   SCOP domains
               CATH domains 1q8rB00 B:1-118 H         olliday junction resolvase RusA. Chain A                                                     CATH domains
           Pfam domains (1) -------RusA-1q8rB         01 B:8-117                                                                                 - Pfam domains (1)
           Pfam domains (2) -------RusA-1q8rB         02 B:8-117                                                                                 - Pfam domains (2)
         Sec.struct. author ..eeeeeee...hhhhh---------.hhhhhhhhhhhhhhhhhh.........eeeeeeee.......hhhhhhhhhhhhhhhh....hhh.eeeeeeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1q8r B   1 MNTYSITLPWPPSNNRY---------VSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRDLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
                                    10      |  -      | 30        40        50        60        70        80        90       100       110        
                                           17        27                                                                                           


Chain B from PDB  Type:PROTEIN  Length:109
 aligned with RUSA_ECOLI | P0AG74 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:118
                                    10        20        30        40        50        60        70        80        90       100       110        
           RUSA_ECOLI     1 MNTYSITLPWPPSNNRYYRHNRGRTHVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRDLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
               SCOP domains d1q8rb_ B: Hollid         ay junction resolvase RusA                                                                   SCOP domains
               CATH domains 1q8rB00 B:1-118 H         olliday junction resolvase RusA. Chain A                                                     CATH domains
           Pfam domains (1) -------RusA-1q8rB         01 B:8-117                                                                                 - Pfam domains (1)
           Pfam domains (2) -------RusA-1q8rB         02 B:8-117                                                                                 - Pfam domains (2)
         Sec.struct. author ..eeeeeee...hhhhh---------.hhhhhhhhhhhhhhhhhh.........eeeeeeee.......hhhhhhhhhhhhhhhh....hhh.eeeeeeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1q8r B   1 MNTYSITLPWPPSNNRY---------VSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRDLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
                                    10      |  -      | 30        40        50        60        70        80        90       100       110        
                                           17        27
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (12, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RUSA_ECOLI | P0AG74)
molecular function
    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:0010844    recombination hotspot binding    Interacting selectively and non-covalently with a region in a genome which promotes recombination.
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.
cellular component
    GO:0048476    Holliday junction resolvase complex    A protein complex that mediates the conversion of a Holliday junction into two separate duplex DNA molecules; the complex includes a single- or multisubunit helicase that catalyzes the extension of heteroduplex DNA by branch migration and a nuclease that resolves the junction by nucleolytic cleavage.

Chain A,B   (RUSA_ECOL6 | P0AG75)
molecular function
    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.
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
        RUSA_ECOLI | P0AG74: 2h8c 2h8e

(-) Related Entries Specified in the PDB File

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