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Biological Unit 2 (Jmol Viewer)

Title :   CORE UVRA/TRCF COMPLEX

Authors :   A. M. Deaconescu, N. Grigorieff

Date :   23 Jan 12 (Deposition) - 02 May 12 (Release) - 02 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Alpha/Beta Domains, Dna Repair, Atp Binding, Dna Binding, Nucleotide Excision Repair, Hydrolase-Dna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Deaconescu, A. Sevostyanova, I. Artsimovitch, N. Grigorieff
Nucleotide Excision Repair (Ner) Machinery Recruitment By The Transcription-Repair Coupling Factor Involves Unmasking Of A Conserved Intramolecular Interface.
Proc. Natl. Acad. Sci. Usa V. 109 3353 2012
PubMed-ID: 22331906 | Reference-DOI: 10.1073/PNAS.1115105109

Molecule 1 - TRANSCRIPTION-REPAIR-COUPLING FACTOR
	Chains	:	A, C
	EC Number	:	3.6.4.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A DERIVATIVE
	Expression System Strain	:	ROSETTA2(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	TRCF-D2 DOMAIN, UNP RESIDUES 127-213
	Gene	:	B1114, ESCHERICHIA COLI, JW1100, MFD
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	TRCF, ATP-DEPENDENT HELICASE MFD

Molecule 2 - UVRABC SYSTEM PROTEIN A
	Chains	:	B, D
	EC Number	:	3.6.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A DERIVATIVE
	Expression System Strain	:	ROSETTA2(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 131-250
	Gene	:	B4058, DINE, ESCHERICHIA COLI, JW4019, UVRA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	UVRA PROTEIN, EXCINUCLEASE ABC SUBUNIT A

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4DFC)

(no "Site" information available for 4DFC)

(no "SS Bond" information available for 4DFC)

(no "Cis Peptide Bond" information available for 4DFC)

(no "SAP(SNP)/Variant" information available for 4DFC)

(no "PROSITE Motif" information available for 4DFC)

(no "Exon" information available for 4DFC)

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:85
 aligned with MFD_ECOLI | P30958 from UniProtKB/Swiss-Prot  Length:1148

    Alignment length:85
                                   138       148       158       168       178       188       198       208     
            MFD_ECOLI   129 VMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLP 213
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....hhhhhhhhhhhh..ee........eeeee..eeeee.......eeeeee..eeeeeeee......eeeee.ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 4dfc A 129 VMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLP 213
                                   138       148       158       168       178       188       198       208

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with UVRA_ECOLI | P0A698 from UniProtKB/Swiss-Prot  Length:940

    Alignment length:123
                                   137       147       157       167       177       187       197       207       217       227       237       247   
           UVRA_ECOLI   128 AAQTVSQMVDNVLSQPEGKRLMLLAPIIKERKGEHTKTLENLASQGYIRARIDGEVCDLSDPPKLELQKKHTIEVVVDRFKVRDDLTQRLAESFETALELSGGTAVVADMDDPKAEELLFSAN 250
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh........eeeeeeeeeeee..hhhhhhhhhhhh..eeee..eeee...........eeeeeeeeeee...--..hhhhhhhhhhhhhh..eeeeee........eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dfc B 128 MASTVSQMVDNVLSQPEGKRLMLLAPIIKERKGEHTKTLENLASQGYIRARIDGEVCDLSDPPKLELQKKHTIEVVVDRFKVR--LTQRLAESFETALELSGGTAVVADMDDPKAEELLFSAN 250
                                   137       147       157       167       177       187       197       207  |  | 217       227       237       247   
                                                                                                            210  |                                     
                                                                                                               213

Chain C from PDB  Type:PROTEIN  Length:79
 aligned with MFD_ECOLI | P30958 from UniProtKB/Swiss-Prot  Length:1148

    Alignment length:79
                                   138       148       158       168       178       188       198         
            MFD_ECOLI   129 VMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVE 207
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhh..ee........eeeee..eeee........eeeeee..eeeeeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 4dfc C 129 VMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVE 207
                                   138       148       158       168       178       188       198

Chain D from PDB  Type:PROTEIN  Length:122
 aligned with UVRA_ECOLI | P0A698 from UniProtKB/Swiss-Prot  Length:940

    Alignment length:124
                                   136       146       156       166       176       186       196       206       216       226       236       246    
           UVRA_ECOLI   127 LAAQTVSQMVDNVLSQPEGKRLMLLAPIIKERKGEHTKTLENLASQGYIRARIDGEVCDLSDPPKLELQKKHTIEVVVDRFKVRDDLTQRLAESFETALELSGGTAVVADMDDPKAEELLFSAN 250
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.......eeeeeeeeeeeee..hhhhhhhhhhh...eeee..eeee...........eeeeeeeeeeee...--.hhhhhhhhhhhhhhh.eeeeee........eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dfc D 127 HMASTVSQMVDNVLSQPEGKRLMLLAPIIKERKGEHTKTLENLASQGYIRARIDGEVCDLSDPPKLELQKKHTIEVVVDRFKVRD--TQRLAESFETALELSGGTAVVADMDDPKAEELLFSAN 250
                                   136       146       156       166       176       186       196       206    |  216       226       236       246    
                                                                                                              211  |                                    
                                                                                                                 214

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 '\|'

(no "SCOP Domain" information available for 4DFC)

(no "CATH Domain" information available for 4DFC)

(no "Pfam Domain" information available for 4DFC)

Asymmetric Unit(hide GO term definitions)

Chain A,C (MFD_ECOLI | P30958)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008026	ATP-dependent helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0015616	DNA translocase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule.
	GO:0043175	RNA polymerase core enzyme binding	Interacting selectively and non-covalently with an RNA polymerase core enzyme, containing a specific subunit composition defined as the core enzyme.
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	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:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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: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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0000716	transcription-coupled nucleotide-excision repair, DNA damage recognition	The identification of lesions on the actively transcribed strand of the DNA duplex as well as a small subset of lesions not recognized by the general nucleotide-excision repair pathway.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain B,D (UVRA_ECOLI | P0A698)

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:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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: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: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: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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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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	4dfc
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	3.6.1.3
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	MFD_ECOLI \| P30958	:	2b2n 2eyq 3hjh

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