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Title :   CRYSTAL STRUCTURE OF E.COLI UVRB C-TERMINAL DOMAIN, AND A MODEL FOR UVRB-UVRC INTERACTION.

Authors :   M. Sohi, A. Alexandrovich, G. Moolenaar, R. Visse, N. Goosen, X. Vernede, J. Fontecilla-Camps, J. Champness, M. R. Sanderson

Date :   10 Nov 99 (Deposition) - 10 Nov 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Dna Excision Repair, Nucleotide Excision Repair, X-Ray Crystallography, Uvrb Protein, Uvrb-C Interaction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sohi, A. Alexandrovich, G. Moolenaar, R. Visse, N. Goosen, X. Vernede, J. Fontecilla-Camps, J. Champness, M. R. Sanderson
Crystal Structure Of E. Coli Uvrb C-Terminal Domain, And A Model For Uvrb-Uvrc Interaction
Febs Lett. V. 465 161 2000
PubMed-ID: 10631326 | Reference-DOI: 10.1016/S0014-5793(99)01690-7

Molecule 1 - UVRB
	Chains	:	A, B
	Fragment	:	C-TERMINAL DOMAIN
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	PP3398

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	MSE	5	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 10)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1QOJ)

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UVR	PS50151	UVR domain profile.	UVRB_ECO57	633-668	2	A:633-668 B:633-668
1	UVR	PS50151	UVR domain profile.	UVRB_ECOLI	633-668	2	A:633-668 B:633-668

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UVR	PS50151	UVR domain profile.	UVRB_ECO57	633-668	4	A:633-668 B:633-668
1	UVR	PS50151	UVR domain profile.	UVRB_ECOLI	633-668	4	A:633-668 B:633-668

(no "Exon" information available for 1QOJ)

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:46
 aligned with UVRB_ECO57 | P0A8F9 from UniProtKB/Swiss-Prot  Length:673

    Alignment length:46
                                   637       647       657       667      
           UVRB_ECO57   628 SPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIAAS 673
               SCOP domains d1qoja_ A:                                     SCOP domains
               CATH domains 1qojA00 A:628-673                              CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE -----UVR  PDB: A:633-668 UniProt: 633-668----- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 1qoj A 628 SPKALQQKIHELEGLmmQHAQNLEFEEAAQIRDQLHQLRELFIAAS 673
                                   637     ||647       657       667      
                                         643-MSE                          
                                          644-MSE

Chain A from PDB  Type:PROTEIN  Length:46
 aligned with UVRB_ECOLI | P0A8F8 from UniProtKB/Swiss-Prot  Length:673

    Alignment length:46
                                   637       647       657       667      
           UVRB_ECOLI   628 SPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIAAS 673
               SCOP domains d1qoja_ A:                                     SCOP domains
               CATH domains 1qojA00 A:628-673                              CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----UVR  PDB: A:633-668 UniProt: 633-668----- PROSITE (2)
                 Transcript ---------------------------------------------- Transcript
                 1qoj A 628 SPKALQQKIHELEGLmmQHAQNLEFEEAAQIRDQLHQLRELFIAAS 673
                                   637     ||647       657       667      
                                         643-MSE                          
                                          644-MSE

Chain B from PDB  Type:PROTEIN  Length:47
 aligned with UVRB_ECO57 | P0A8F9 from UniProtKB/Swiss-Prot  Length:673

    Alignment length:47
                                   636       646       656       666       
           UVRB_ECO57   627 MSPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIAAS 673
               SCOP domains d1qojb_ B:                                      SCOP domains
               CATH domains -1qojB00 B:628-673                              CATH domains
           Pfam domains (1) ------UVR-1qojB01 B:633-668               ----- Pfam domains (1)
           Pfam domains (2) ------UVR-1qojB02 B:633-668               ----- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ------UVR  PDB: B:633-668 UniProt: 633-668----- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 1qoj B 627 mSPKALQQKIHELEGLmmQHAQNLEFEEAAQIRDQLHQLRELFIAAS 673
                            |      636      |646       656       666       
                          627-MSE         643-MSE                          
                                           644-MSE

Chain B from PDB  Type:PROTEIN  Length:47
 aligned with UVRB_ECOLI | P0A8F8 from UniProtKB/Swiss-Prot  Length:673

    Alignment length:47
                                   636       646       656       666       
           UVRB_ECOLI   627 MSPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIAAS 673
               SCOP domains d1qojb_ B:                                      SCOP domains
               CATH domains -1qojB00 B:628-673                              CATH domains
           Pfam domains (1) ------UVR-1qojB01 B:633-668               ----- Pfam domains (1)
           Pfam domains (2) ------UVR-1qojB02 B:633-668               ----- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------UVR  PDB: B:633-668 UniProt: 633-668----- PROSITE (2)
                 Transcript ----------------------------------------------- Transcript
                 1qoj B 627 mSPKALQQKIHELEGLmmQHAQNLEFEEAAQIRDQLHQLRELFIAAS 673
                            |      636      |646       656       666       
                          627-MSE         643-MSE                          
                                           644-MSE

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Long alpha-hairpin (315)

Superfamily: C-terminal UvrC-binding domain of UvrB (2)

Family: C-terminal UvrC-binding domain of UvrB (2)

Protein domain: C-terminal UvrC-binding domain of UvrB (2)

Escherichia coli [TaxId: 562] (2)

1a	d1qoja_	A:
1b	d1qojb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: DNA Excision Repair, Uvrb; Chain A (2)

Homologous Superfamily: DNA Excision Repair, UvrB; Chain A (2)

Escherichia coli. Organism_taxid: 562. Strain: pp3398 (1)

1a	1qojA00	A:628-673
1b	1qojB00	B:628-673

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: UVR] (3)

Family: UVR (3)

Escherichia coli (strain K12) (1)

1a	UVR-1qojB01	B:633-668
1b	UVR-1qojB02	B:633-668

Asymmetric Unit(hide GO term definitions)

Chain A,B (UVRB_ECO57 | P0A8F9)

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:0009381	excinuclease ABC activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid at sites flanking regions of damaged DNA to which the Uvr ABC excinuclease complexes bind.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	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.
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:0009432	SOS response	An error-prone process for repairing damaged microbial DNA.
	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:0006289	nucleotide-excision repair	A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B (UVRB_ECOLI | P0A8F8)

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:0009381	excinuclease ABC activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid at sites flanking regions of damaged DNA to which the Uvr ABC excinuclease complexes bind.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	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).
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:0009432	SOS response	An error-prone process for repairing damaged microbial DNA.
	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:0006289	nucleotide-excision repair	A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0009380	excinuclease repair complex	Any of the protein complexes formed by the UvrABC excinuclease system, which carries out nucleotide excision repair. Three different complexes are formed by the 3 proteins as they proceed through the excision repair process. First a complex consisting of two A subunits and two B subunits bind DNA and unwind it around the damaged site. Then, the A subunits disassociate leaving behind a stable complex between B subunits and DNA. Now, subunit C binds to this B+DNA complex and causes subunit B to nick the DNA on one side of the complex while subunit C nicks the DNA on the other side of the complex. DNA polymerase I and DNA ligase can then repair the resulting gap.

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UniProtKB/Swiss-Prot
	UVRB_ECO57 \| P0A8F9	:	1e52
	UVRB_ECOLI \| P0A8F8	:	1e52

1e52	SOLUTION STRUCTURE OF ESCHERICHIA COLI UVRB C-TERMINAL DOMAIN

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