2Z43 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF A TWINNED CRYSTAL OF RADA

Authors :   L. T. Chen, T. P. Ko, A. H. J. Wang, T. F. Wang

Date :   12 Jun 07 (Deposition) - 13 Nov 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Archaea, Filament, Dna Binding, Recombination, Molecular Switch, Reca, Rad51, Dmc1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. T. Chen, T. P. Ko, Y. W. Chang, K. A. Lin, A. H. J. Wang, T. F. Wang
Structural And Functional Analyses Of Five Conserved Positively Charged Residues In The L1 And N-Terminal Dna Binding Motifs Of Archaeal Rada Protein
Plos One V. 2 E858 2007
PubMed-ID: 17848989 | Reference-DOI: 10.1371/JOURNAL.PONE.0000858

Molecule 1 - DNA REPAIR AND RECOMBINATION PROTEIN RADA
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET32
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	RADA
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	273057
	Strain	:	P2
	Synonym	:	DNA STRAND EXCHANGE PROTEIN

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2Z43)

(no "Site" information available for 2Z43)

(no "SS Bond" information available for 2Z43)

(no "Cis Peptide Bond" information available for 2Z43)

(no "SAP(SNP)/Variant" information available for 2Z43)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECA_2	PS50162	RecA family profile 1.	RADA_SULSO	85-257	3	A:85-257 B:85-257 C:85-257
2	RECA_3	PS50163	RecA family profile 2.	RADA_SULSO	262-324	3	A:282-323 B:281-324 C:281-323

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECA_2	PS50162	RecA family profile 1.	RADA_SULSO	85-257	1	A:85-257 - -
2	RECA_3	PS50163	RecA family profile 2.	RADA_SULSO	262-324	1	A:282-323 - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECA_2	PS50162	RecA family profile 1.	RADA_SULSO	85-257	1	- B:85-257 -
2	RECA_3	PS50163	RecA family profile 2.	RADA_SULSO	262-324	1	- B:281-324 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RECA_2	PS50162	RecA family profile 1.	RADA_SULSO	85-257	1	- - C:85-257
2	RECA_3	PS50163	RecA family profile 2.	RADA_SULSO	262-324	1	- - C:281-323

(no "Exon" information available for 2Z43)

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:228
 aligned with RADA_SULSO | Q55075 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:252
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321  
           RADA_SULSO    72 RFKTALEVKKERMNVKKISTGSQALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKALGLDIDNVMNNIYYIRAINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFRAEYPGRENLAVRQQKLNKHLHQLTRLAEVYDIAVIITNQVMARPDMFYGDPTVAVGGHTLYHVPGIRIQLKKSRGNRRIARVVDAPHLPEGEVVFALTEEGIRDAE 323
               SCOP domains d2z43a_ A: DNA repair protein Rad51, catalytic domain                                                                                                                                                                                                        SCOP domains
               CATH domains 2z43A00 A:72-323 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhh...ee...hhhhhhhh...ee...eeeeee....hhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhh..hhhhhhhheeeee..hhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.------------------------.eeeeeee....eeeeeeee......eeeeeeee..eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------RECA_2  PDB: A:85-257 UniProt: 85-257                                                                                                                                        ----RECA_3  PDB: A:282-323 UniProt: 262-324                        PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z43 A  72 RFKTALEVKKERMNVKKISTGSQALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKALGLDIDNVMNNIYYIRAINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFRAEYPGRENLAVRQQKLNKHLHQLTRLAEVYDIAVIITNQV------------------------GIRIQLKKSRGNRRIARVVDAPHLPEGEVVFALTEEGIRDAE 323
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     |   -         -         -|      291       301       311       321  
                                                                                                                                                                                                                   257                      282

Chain B from PDB  Type:PROTEIN  Length:290
 aligned with RADA_SULSO | Q55075 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:313
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
           RADA_SULSO    12 KTINDLPGISQTVINKLIEAGYSSLETLAVASPQDLSVAAGIPLSTAQKIIKEARDALDIRFKTALEVKKERMNVKKISTGSQALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKALGLDIDNVMNNIYYIRAINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFRAEYPGRENLAVRQQKLNKHLHQLTRLAEVYDIAVIITNQVMARPDMFYGDPTVAVGGHTLYHVPGIRIQLKKSRGNRRIARVVDAPHLPEGEVVFALTEEGIRDAEE 324
               SCOP domains d2z43b1 B:12-72 DNA repair protein Rad51, N-terminal domain  d2z43b2 B:73-324 DNA repair protein Rad51, catalytic domain                                                                                                                                                                                                  SCOP domains
               CATH domains ---------2z43B01 B:21-84 5' to 3' exonuclease, C-terminal subdomain      2z43B02 B:85-324 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...hhhhhhhhhh....hhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhh...ee...hhhhhhhh...ee..eeeeeee....hhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhh..hhhhhhhheeeee..hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.-----------------------..eeeeeee....eeeeeeee.......eeeeeee..eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------RECA_2  PDB: B:85-257 UniProt: 85-257                                                                                                                                        ----RECA_3  PDB: B:281-324 UniProt: 262-324                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z43 B  12 KTINDLPGISQTVINKLIEAGYSSLETLAVASPQDLSVAAGIPLSTAQKIIKEARDALDIRFKTALEVKKERMNVKKISTGSQALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKALGLDIDNVMNNIYYIRAINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFRAEYPGRENLAVRQQKLNKHLHQLTRLAEVYDIAVIITNQV-----------------------PGIRIQLKKSRGNRRIARVVDAPHLPEGEVVFALTEEGIRDAEE 324
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     |   -         -       281       291       301       311       321   
                                                                                                                                                                                                                                                                               257                     281

Chain C from PDB  Type:PROTEIN  Length:289
 aligned with RADA_SULSO | Q55075 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:312
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321  
           RADA_SULSO    12 KTINDLPGISQTVINKLIEAGYSSLETLAVASPQDLSVAAGIPLSTAQKIIKEARDALDIRFKTALEVKKERMNVKKISTGSQALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKALGLDIDNVMNNIYYIRAINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFRAEYPGRENLAVRQQKLNKHLHQLTRLAEVYDIAVIITNQVMARPDMFYGDPTVAVGGHTLYHVPGIRIQLKKSRGNRRIARVVDAPHLPEGEVVFALTEEGIRDAE 323
               SCOP domains d2z43c1 C:12-72 DNA repair protein Rad51, N-terminal domain  d2z43c2 C:73-323 DNA repair protein Rad51, catalytic domain                                                                                                                                                                                                 SCOP domains
               CATH domains ---------2z43C01 C:21-84 5' to 3' exonuclease, C-terminal subdomain      2z43C02 C:85-323 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                           CATH domains
           Pfam domains (1) -----------------------------------------------------Rad51-2z43C01 C:65-323                                                                                                                                                                                                                                              Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------Rad51-2z43C02 C:65-323                                                                                                                                                                                                                                              Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------Rad51-2z43C03 C:65-323                                                                                                                                                                                                                                              Pfam domains (3)
         Sec.struct. author .hhhhh...hhhhhhhhhh....hhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhhhh...ee...hhhhhhhh...ee..eeeeeee....hhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhh..hhhhhhhheeeee..hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.-----------------------..eeeeeee....eeeeeeee.......eeeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------RECA_2  PDB: C:85-257 UniProt: 85-257                                                                                                                                        ----RECA_3  PDB: C:281-323 UniProt: 262-324                        PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z43 C  12 KTINDLPGISQTVINKLIEAGYSSLETLAVASPQDLSVAAGIPLSTAQKIIKEARDALDIRFKTALEVKKERMNVKKISTGSQALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKALGLDIDNVMNNIYYIRAINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFRAEYPGRENLAVRQQKLNKHLHQLTRLAEVYDIAVIITNQV-----------------------PGIRIQLKKSRGNRRIARVVDAPHLPEGEVVFALTEEGIRDAE 323
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     |   -         -       281       291       301       311       321  
                                                                                                                                                                                                                                                                               257                     281

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Rad51 (10)

Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (4)

1a	Rad51-2z43C01	C:65-323
1b	Rad51-2z43C02	C:65-323
1c	Rad51-2z43C03	C:65-323

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RADA_SULSO | Q55075)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008094	DNA-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0004520	endodeoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
	GO:0000400	four-way junction DNA binding	Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0000150	recombinase activity	Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA.
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
biological process
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0000730	DNA recombinase assembly	The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA.
	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:0006312	mitotic recombination	The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles.
	GO:0010212	response to ionizing radiation	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
	GO:0042148	strand invasion	The process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules.

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	2z43
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	RADA_SULSO \| Q55075
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	RADA_SULSO \| Q55075	:	2bke 2dfl 2zub 2zuc 2zud

2dfl	TETRAGONAL LEFT-HANDED FILAMENT

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