1II8 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE P. FURIOSUS RAD50 ATPASE DOMAIN

Authors :   K. -P. Hopfner, A. Karcher, L. Craig, T. T. Woo, J. P. Carney, J. A. Tainer

Date :   20 Apr 01 (Deposition) - 30 May 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.02

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

Keywords :   Rad50, Mre11, Dna Double-Strand Break Repair, Atp, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. P. Hopfner, A. Karcher, L. Craig, T. T. Woo, J. P. Carney, J. A. Tainer
Structural Biochemistry And Interaction Architecture Of The Dna Double-Strand Break Repair Mre11 Nuclease And Rad50-Atpase.
Cell(Cambridge, Mass. ) V. 105 473 2001
PubMed-ID: 11371344 | Reference-DOI: 10.1016/S0092-8674(01)00335-X
(for further references see the PDB file header)

Molecule 1 - RAD50 ABC-ATPASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	N-TERMINAL FRAGMENT
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

Molecule 2 - RAD50 ABC-ATPASE
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	C-TERMINAL FRAGMENT
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	PO4	4	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:31 , ASN A:32 , GLY A:33 , SER A:34 , GLY A:35 , LYS A:36 , SER A:37 , HOH A:1004 , HOH A:1013	BINDING SITE FOR RESIDUE PO4 A 1001
2	AC2	SOFTWARE	TRP A:49 , PRO A:50 , LEU A:51 , ARG A:52 , ILE A:53 , ILE A:56 , PHE A:61	BINDING SITE FOR RESIDUE PO4 A 1003

(no "SS Bond" information available for 1II8)

Asymmetric Unit

No.	Residues
1	Trp A:49	-	Pro A:50

(no "SAP(SNP)/Variant" information available for 1II8)

(no "PROSITE Motif" information available for 1II8)

(no "Exon" information available for 1II8)

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:195
 aligned with RAD50_PYRFU | P58301 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     
          RAD50_PYRFU     1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVREVLNLDKFETAYKKLSELKKTINNRIKEYRDILARTE 195
               SCOP domains d1ii8.1 A:,B: Rad50                                                                                                                                                                                 SCOP domains
               CATH domains 1ii8A01 A:1-140 P-loop containing nucleotide triphosphate hydrolases                                                                        ------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......eeee...eeeeee.....hhhhhhhhhhhhhhh........hhhhhh.....eeeeeeeee..eeeeeeeeee.....eeeeeeeeee..eee.....hhhhhhhhhhhhhhhhhhh...ee....hhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ii8 A   1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVREVLNLDKFETAYKKLSELKKTINNRIKEYRDILARTE 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:174
 aligned with RAD50_PYRFU | P58301 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:174
                                   718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878    
          RAD50_PYRFU   709 RERVKKEIKDLEKAKDFTEELIEKVKKYKALAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
               SCOP domains d1ii8.1 A:,B: Rad50                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh..eeeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ii8 B 709 RERVKKEIKDLEKAKDFTEELIEKVKKYKALAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
                                   718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878

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

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: ABC transporter ATPase domain-like (94)

Protein domain: Rad50 (4)

Pyrococcus furiosus [TaxId: 2261] (4)

d1ii8.1

A:,B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Pyrococcus furiosus. Organism_taxid: 2261. (5)

1ii8A01

A:1-140

(no "Pfam Domain" information available for 1II8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RAD50_PYRFU | P58301)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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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	RAD50_PYRFU \| P58301	:	1f2t 1f2u 1l8d 1us8 3qkr 3qks 3qkt 3qku 4nch 4nci 4ncj 4nck

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