2V1C - JenaLib

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Title :   CRYSTAL STRUCTURE AND MUTATIONAL STUDY OF RECOR PROVIDE INSIGHT INTO ITS ROLE IN DNA REPAIR

Authors :   J. Timmins, I. Leiros, S. Mcsweeney

Date :   23 May 07 (Deposition) - 03 Jul 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.80

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

Keywords :   Recombination, Homologous Recombination, Recfor Pathway, Dna Recombination, Dna Binding, Zinc-Finger, Metal-Binding, Recor Complex, Hypothetical Protein, Deinococcus Radiodurans, Recr, Zinc, Reco, Dna Damage, Dna Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Timmins, I. Leiros, S. Mcsweeney
Crystal Structure And Mutational Study Of Recor Provide Insight Into Its Mode Of Dna Binding.
Embo J. V. 26 3260 2007
PubMed-ID: 17581636 | Reference-DOI: 10.1038/SJ.EMBOJ.7601760

Molecule 1 - RECOMBINATION PROTEIN RECR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PDEST17
	Organism Scientific	:	DEINOCOCCUS RADIODURANS
	Organism Taxid	:	243230
	Strain	:	R1
	Synonym	:	RECR

Molecule 2 - HYPOTHETICAL PROTEIN
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PDEST17
	Organism Scientific	:	DEINOCOCCUS RADIODURANS
	Organism Taxid	:	243230
	Strain	:	R1
	Synonym	:	RECO

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:57 , CYS A:60 , CYS A:69 , CYS A:72	BINDING SITE FOR RESIDUE ZN A 230
2	AC2	SOFTWARE	CYS B:57 , CYS B:60 , CYS B:69 , CYS B:72	BINDING SITE FOR RESIDUE ZN B 230
3	AC3	SOFTWARE	CYS C:153 , CYS C:156 , CYS C:173 , CYS C:176	BINDING SITE FOR RESIDUE ZN C 266

(no "SS Bond" information available for 2V1C)

(no "Cis Peptide Bond" information available for 2V1C)

(no "SAP(SNP)/Variant" information available for 2V1C)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECR	PS01300	RecR protein signature.	RECR_DEIRA	57-78	2	A:57-78 B:57-78
2	TOPRIM	PS50880	Toprim domain profile.	RECR_DEIRA	80-173	2	A:80-173 B:80-173

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECR	PS01300	RecR protein signature.	RECR_DEIRA	57-78	4	A:57-78 B:57-78
2	TOPRIM	PS50880	Toprim domain profile.	RECR_DEIRA	80-173	4	A:80-173 B:80-173

(no "Exon" information available for 2V1C)

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:199
 aligned with RECR_DEIRA | Q9ZNA2 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191         
           RECR_DEIRA     2 KYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVSKPQ 200
               SCOP domains d2v1ca1 A:2-199 Recombination protein RecR                                                                                                                                                            - SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhee......ee....hhhhhh......eeeee.hhhhhhhh........eeee.................hhhhhhhh....eeee....hhhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhhhh.eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------RECR  PDB: A:57-78    -TOPRIM  PDB: A:80-173 UniProt: 80-173                                                         --------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v1c A   2 KYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVSKPQ 200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain B from PDB  Type:PROTEIN  Length:199
 aligned with RECR_DEIRA | Q9ZNA2 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191         
           RECR_DEIRA     2 KYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVSKPQ 200
               SCOP domains d2v1cb1 B:2-199 Recombination protein RecR                                                                                                                                                            - SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------RecR-2v1cB03 B:38-78                     --Toprim-2v1cB01 B:81-171                                                                    ----------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------RecR-2v1cB04 B:38-78                     --Toprim-2v1cB02 B:81-171                                                                    ----------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhee......ee....hhhhhh......eeeee.hhhhhhhh........eeee......hhhh.......hhhhhhhh....eeee....hhhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhhhh.ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------RECR  PDB: B:57-78    -TOPRIM  PDB: B:80-173 UniProt: 80-173                                                         --------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v1c B   2 KYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVSKPQ 200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain C from PDB  Type:PROTEIN  Length:229
 aligned with Q9RW50_DEIRA | Q9RW50 from UniProtKB/TrEMBL  Length:244

    Alignment length:234
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    
         Q9RW50_DEIRA     3 SRTANRSGIVIRRRVTPAGDIIVTLLTPQGKLKAIARGGVKGPLSSSLNLFHHVGVQVYQGPHNDLASVKQAVLEGALPTLAEPERYAFAHLMAEFADALFQEGEFSEQAFDLFAASLRGVAHQPDPEWVALVMSYKLLGLAGVIPQTARCARCGAPDPEHPDPLGGQLLCSKCAALPPYPPAVLDFLRHAVRRTVRASFEQPVPSADRPALWRALEKFVTVQVGGVHSWRQLV 236
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains RecO_N-2v1cC01 C:3-79                                                        ---RecO_C-2v1cC02 C:83-233                                                                                                                                --- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee.....eeeeee.....eeeee..-----.........eeeeeee.......eeeeee.....hhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..................ee......ee..........hhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2v1c C   3 SRTANRSGIVIRRRVTPAGDIIVTLLTPQGKLKAIARG-----LSSSLNLFHHVGVQVYQGPHNDLASVKQAVLEGALPTLAEPERYAFAHLMAEFADALFQEGEFSEQAFDLFAASLRGVAHQPDPEWVALVMSYKLLGLAGVIPQTARCARCGAPDPEHPDPLGGQLLCSKCAALPPYPPAVLDFLRHAVRRTVRASFEQPVPSADRPALWRALEKFVTVQVGGVHSWRQLV 236
                                    12        22        32       | -   |    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    
                                                                40    46

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: Recombination protein RecR (4)

Superfamily: Recombination protein RecR (4)

Family: Recombination protein RecR (4)

Protein domain: Recombination protein RecR (4)

Deinococcus radiodurans [TaxId: 1299] (2)

1a	d2v1ca1	A:2-199
1b	d2v1cb1	B:2-199

(no "CATH Domain" information available for 2V1C)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: OB (224)

Family: RecO_N (4)

Deinococcus radiodurans (3)

RecO_N-2v1cC01

C:3-79

Clan: Toprim-like (19)

Family: Toprim (19)

Deinococcus radiodurans (1)

2a	Toprim-2v1cB01	B:81-171
2b	Toprim-2v1cB02	B:81-171

Clan: no clan defined [family: RecO_C] (4)

Family: RecO_C (4)

Deinococcus radiodurans (3)

RecO_C-2v1cC02

C:83-233

Clan: no clan defined [family: RecR] (1)

Family: RecR (1)

Deinococcus radiodurans (1)

4a	RecR-2v1cB03	B:38-78
4b	RecR-2v1cB04	B:38-78

Asymmetric Unit(hide GO term definitions)

Chain A,B (RECR_DEIRA | Q9ZNA2)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0006302	double-strand break repair	The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.

Chain C (Q9RW50_DEIRA | Q9RW50)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0006302	double-strand break repair	The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.

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UniProtKB/Swiss-Prot
	RECR_DEIRA \| Q9ZNA2	:	1vdd 4jcv
UniProtKB/TrEMBL
	Q9RW50_DEIRA \| Q9RW50	:	1u5k 1w3s 4jcv

1u5k	RECOMBINATIONAL REPAIR PROTEIN RECO
1vdd	CRYSTAL STRUCTURE OF RECOMBINATIONAL REPAIR PROTEIN RECR
1w3s	THE CRYSTAL STRUCTURE OF RECO FROM DEINOCOCCUS RADIODURANS.

Description

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Ligands, Modified Residues, Ions (1, 3)

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Related Entries Specified in the PDB File