2H8C - JenaLib

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Title :   STRUCTURE OF RUSA D70N IN COMPLEX WITH DNA

Authors :   R. A. Macmaster

Date :   07 Jun 06 (Deposition) - 24 Apr 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Protein-Dna Complex, Recombination, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Macmaster, S. Sedelnikova, P. J. Baker, E. L. Bolt, R. G. Lloyd, J. B. Rafferty
Rusa Holliday Junction Resolvase: Dna Complex Structure--Insights Into Selectivity And Specificity.
Nucleic Acids Res. V. 34 5577 2006
PubMed-ID: 17028102 | Reference-DOI: 10.1093/NAR/GKL447

*Molecule 1 - 5'-D(CPCPGPGPTPAPCPCPGPGPT)-3'**
	Chains	:	Y, Z, W, X
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUSA
	Chains	:	A, B, C, D
	EC Number	:	3.1.22.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	RUSA, RUS
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	HOLLIDAY JUNCTION NUCLEASE RUSA, HOLLIDAY JUNCTION RESOLVASE

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	W	X	Y	Z
Biological Unit 1 (1x)	:	A	B			W	X
Biological Unit 2 (1x)	:			C	D			Y	Z

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2H8C)

(no "Site" information available for 2H8C)

(no "SS Bond" information available for 2H8C)

(no "Cis Peptide Bond" information available for 2H8C)

(no "SAP(SNP)/Variant" information available for 2H8C)

(no "PROSITE Motif" information available for 2H8C)

(no "Exon" information available for 2H8C)

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:117
 aligned with RUSA_ECOLI | P0AG74 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           RUSA_ECOLI     2 NTYSITLPWPPSNNRYYRHNRGRTHVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRDLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
               SCOP domains d2h8ca_ A: automated matches                                                                                          SCOP domains
               CATH domains 2h8cA00 A:2-118 Holliday junction resolvase RusA. Chain A                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhheee....eeehhhhhhhhhhhhhhhhhh.........eeeeeeee.......hhhhhhhhhhhhhhhhh.......eeeeeeeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8c A   2 NTYSITLPWPPSNNRYYRHNRGRTHVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRNLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
                                    11        21        31        41        51        61        71        81        91       101       111

Chain B from PDB  Type:PROTEIN  Length:116
 aligned with RUSA_ECOLI | P0AG74 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:116
                                    11        21        31        41        51        61        71        81        91       101       111      
           RUSA_ECOLI     2 NTYSITLPWPPSNNRYYRHNRGRTHVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRDLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEM 117
               SCOP domains d2h8cb_ B: automated matches                                                                                         SCOP domains
               CATH domains 2h8cB00 B:2-117 Holliday junction resolvase RusA. Chain A                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhee......eehhhhhhhhhhhhhhhhhhh........eeeeeeee........hhhhhhhhhhhhhhh....hhh.eeeeeeeee......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8c B   2 NTYSITLPWPPSNNRYYRHNRGRTHVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRNLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEM 117
                                    11        21        31        41        51        61        71        81        91       101       111

Chain C from PDB  Type:PROTEIN  Length:111
 aligned with RUSA_ECOLI | P0AG74 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           RUSA_ECOLI     2 NTYSITLPWPPSNNRYYRHNRGRTHVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRDLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
               SCOP domains d2h8cc_ C: automate      d matches                                                                                    SCOP domains
               CATH domains 2h8cC00 C:2-118 Hol      liday junction resolvase RusA. Chain A                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhh..------.hhhhhhhhhhhhhhhh...........eeeeeeee.......hhhhhhhhhhhhhhhh....hhh.eeeeeeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8c C   2 NTYSITLPWPPSNNRYYRH------VSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRNLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
                                    11        |-     |  31        41        51        61        71        81        91       101       111       
                                             20     27

Chain D from PDB  Type:PROTEIN  Length:112
 aligned with RUSA_ECOLI | P0AG74 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           RUSA_ECOLI     2 NTYSITLPWPPSNNRYYRHNRGRTHVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRDLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
               SCOP domains d2h8cd_ D: automat     ed matches                                                                                     SCOP domains
               CATH domains 2h8cD00 D:2-118 Ho     lliday junction resolvase RusA. Chain A                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhh.-----...hhhhhhhhhhhhhhhhhh.........eeeeeeee.......hhhhhhhhhhhhhhhh....hhh.eeeeeeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8c D   2 NTYSITLPWPPSNNRYYR-----THVSAEGQAYRDNVARIIKNAMLDIGLAMPVKIRIECHMPDRRRRNLDNLQKAAFDALTKAGFWLDDAQVVDYRVVKMPVTKGGRLELTITEMG 118
                                    11       | -   |    31        41        51        61        71        81        91       101       111       
                                            19    25

Chain W from PDB  Type:DNA  Length:11
                                           
                 2h8c W   2 CCGGTACCGGT  12
                                    11

Chain X from PDB  Type:DNA  Length:11
                                           
                 2h8c X   2 CCGGTACCGGT  12
                                    11

Chain Y from PDB  Type:DNA  Length:11
                                           
                 2h8c Y   2 CCGGTACCGGT  12
                                    11

Chain Z from PDB  Type:DNA  Length:10
                                          
                 2h8c Z   2 CCGGTACCGG  11
                                    11

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) (23004)

Fold: Bacillus chorismate mutase-like (324)

Superfamily: Holliday junction resolvase RusA (3)

Family: Holliday junction resolvase RusA (3)

Protein domain: automated matches (2)

Escherichia coli [TaxId: 562] (2)

1a	d2h8ca_	A:
1b	d2h8cb_	B:
1c	d2h8cc_	C:
1d	d2h8cd_	D:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: Holliday junction resolvase RusA. Chain A (3)

[unclassified] (1)

1a	2h8cB00	B:2-117
1b	2h8cA00	A:2-118
1c	2h8cD00	D:2-118
1d	2h8cC00	C:2-118

(no "Pfam Domain" information available for 2H8C)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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.

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	Ligands, Modified Residues, Ions
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Biological Units
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Access by PDB/NDB ID
	2h8c
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	RUSA_ECOLI \| P0AG74
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	3.1.22.-
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	RUSA_ECOLI \| P0AG74	:	1q8r 2h8e

2h8e	STRUCTURE OF RUSA D70N

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

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SCOP Domains (1, 4)

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