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Title :   ATOMIC STRUCTURE OF THE RUVC RESOLVASE: A HOLLIDAY JUNCTION-SPECIFIC ENDONUCLEASE FROM E. COLI

Authors :   M. Ariyoshi, D. G. Vassylyev, K. Morikawa

Date :   02 Dec 94 (Deposition) - 07 Feb 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Site-Specific Recombinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Ariyoshi, D. G. Vassylyev, H. Iwasaki, H. Nakamura, H. Shinagawa, K. Morikawa
Atomic Structure Of The Ruvc Resolvase: A Holliday Junction-Specific Endonuclease From E. Coli.
Cell(Cambridge, Mass. ) V. 78 1063 1994
PubMed-ID: 7923356 | Reference-DOI: 10.1016/0092-8674(94)90280-1
(for further references see the PDB file header)

Molecule 1 - HOLLIDAY JUNCTION RESOLVASE (RUVC)
	Chains	:	A, B, C, D
	EC Number	:	3.1.22.4
	Engineered	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1HJR)

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUVC	PS01321	Crossover junction endodeoxyribonuclease ruvC signature.	RUVC_ECOLI	113-147	4	A:112-146 B:112-146 C:112-146 D:112-146

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUVC	PS01321	Crossover junction endodeoxyribonuclease ruvC signature.	RUVC_ECOLI	113-147	2	A:112-146 - C:112-146 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUVC	PS01321	Crossover junction endodeoxyribonuclease ruvC signature.	RUVC_ECOLI	113-147	2	- B:112-146 - D:112-146

(no "Exon" information available for 1HJR)

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:158
 aligned with RUVC_ECOLI | P0A814 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           RUVC_ECOLI     2 AIILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPDYFAIEQVFMAKNADSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGIGSAEKSQVQHMVRTLLKLPANPQADAADALAIAITHCHVSQNAMQ 159
               SCOP domains d1hjra_ A: RuvC resolvase                                                                                                                                      SCOP domains
               CATH domains 1hjrA00 A:1-158  [code=3.30.420.10, no name defined]                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeeee.eeeeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------RUVC  PDB: A:112-146               ------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hjr A   1 AIILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPDYFAIEQVFMAKNADSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGIGSAEKSQVQHMVRTLLKLPANPQADAADALAIAITHCHVSQNAMQ 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:158
 aligned with RUVC_ECOLI | P0A814 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           RUVC_ECOLI     2 AIILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPDYFAIEQVFMAKNADSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGIGSAEKSQVQHMVRTLLKLPANPQADAADALAIAITHCHVSQNAMQ 159
               SCOP domains d1hjrb_ B: RuvC resolvase                                                                                                                                      SCOP domains
               CATH domains 1hjrB00 B:1-158  [code=3.30.420.10, no name defined]                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeeee.eeeeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------RUVC  PDB: B:112-146               ------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hjr B   1 AIILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPDYFAIEQVFMAKNADSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGIGSAEKSQVQHMVRTLLKLPANPQADAADALAIAITHCHVSQNAMQ 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:158
 aligned with RUVC_ECOLI | P0A814 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           RUVC_ECOLI     2 AIILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPDYFAIEQVFMAKNADSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGIGSAEKSQVQHMVRTLLKLPANPQADAADALAIAITHCHVSQNAMQ 159
               SCOP domains d1hjrc_ C: RuvC resolvase                                                                                                                                      SCOP domains
               CATH domains 1hjrC00 C:1-158  [code=3.30.420.10, no name defined]                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeeee.eeeeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------RUVC  PDB: C:112-146               ------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hjr C   1 AIILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPDYFAIEQVFMAKNADSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGIGSAEKSQVQHMVRTLLKLPANPQADAADALAIAITHCHVSQNAMQ 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain D from PDB  Type:PROTEIN  Length:158
 aligned with RUVC_ECOLI | P0A814 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           RUVC_ECOLI     2 AIILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPDYFAIEQVFMAKNADSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGIGSAEKSQVQHMVRTLLKLPANPQADAADALAIAITHCHVSQNAMQ 159
               SCOP domains d1hjrd_ D: RuvC resolvase                                                                                                                                      SCOP domains
               CATH domains 1hjrD00 D:1-158  [code=3.30.420.10, no name defined]                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeeeeeee.eeeeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------RUVC  PDB: D:112-146               ------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hjr D   1 AIILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPDYFAIEQVFMAKNADSALKLGQARGVAIVAAVNQELPVFEYAARQVKQTVVGIGSAEKSQVQHMVRTLLKLPANPQADAADALAIAITHCHVSQNAMQ 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: Ribonuclease H-like motif (1424)

Superfamily: Ribonuclease H-like (775)

Family: RuvC resolvase (1)

Protein domain: RuvC resolvase (1)

Escherichia coli [TaxId: 562] (1)

1a	d1hjra_	A:
1b	d1hjrb_	B:
1c	d1hjrc_	C:
1d	d1hjrd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Nucleotidyltransferase; domain 5 (788)

Homologous Superfamily: [code=3.30.420.10, no name defined] (372)

Escherichia coli. Organism_taxid: 562 (18)

1a	1hjrA00	A:1-158
1b	1hjrB00	B:1-158
1c	1hjrC00	C:1-158
1d	1hjrD00	D:1-158

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RUVC_ECOLI | P0A814)

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:0004520	endodeoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid 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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.
	GO:0000725	recombinational repair	A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA.
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.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	1hjr
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