2B2N - JenaLib

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Title :   STRUCTURE OF TRANSCRIPTION-REPAIR COUPLING FACTOR

Authors :   N. Assenmacher, K. Wenig, A. Lammens, K. -P. Hopfner

Date :   19 Sep 05 (Deposition) - 24 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   X-Ray Crystallography; Strand-Specific Repair; Template Strand; Rna Polymerase; Rnap; Uvra/B/C Repair System, Transcription, Dna Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Assenmacher, K. Wenig, A. Lammens, K. -P. Hopfner
Structural Basis For Transcription-Coupled Repair: The N Terminus Of Mfd Resembles Uvrb With Degenerate Atpase Motif
J. Mol. Biol. V. 355 675 2006
PubMed-ID: 16309703 | Reference-DOI: 10.1016/J.JMB.2005.10.033

Molecule 1 - TRANSCRIPTION-REPAIR COUPLING FACTOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21B
	Expression System Strain	:	ROSETTA DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MFD
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	TRCF; MFD PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	NA	3	Ligand/Ion	SODIUM ION
2	P4C	2	Ligand/Ion	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	P4C	1	Ligand/Ion	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION
2	P4C	1	Ligand/Ion	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:60 , THR A:63 , SER B:60 , THR B:63 , HOH B:4853	BINDING SITE FOR RESIDUE NA B 1001
2	AC2	SOFTWARE	ARG A:201 , THR A:202 , HOH A:4150 , HOH A:4205 , ARG B:138 , ARG B:142 , HIS B:152 , THR B:164	BINDING SITE FOR RESIDUE SO4 B 4849
3	AC3	SOFTWARE	PHE A:62 , P4C A:4034 , HOH A:4176	BINDING SITE FOR RESIDUE NA A 345
4	AC4	SOFTWARE	PHE B:62 , P4C B:4035	BINDING SITE FOR RESIDUE NA B 4850
5	AC5	SOFTWARE	ALA A:32 , GLU A:33 , GLU A:36 , GLN A:61 , PHE A:62 , THR A:63 , ASP A:64 , NA A:345 , SER B:60 , HOH B:4993	BINDING SITE FOR RESIDUE P4C A 4034
6	AC6	SOFTWARE	SER A:60 , ALA B:32 , GLU B:33 , GLU B:36 , GLN B:61 , PHE B:62 , THR B:63 , ASP B:64 , NA B:4850	BINDING SITE FOR RESIDUE P4C B 4035

(no "SS Bond" information available for 2B2N)

(no "Cis Peptide Bond" information available for 2B2N)

(no "SAP(SNP)/Variant" information available for 2B2N)

(no "PROSITE Motif" information available for 2B2N)

(no "Exon" information available for 2B2N)

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
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Chain A from PDB  Type:PROTEIN  Length:308
 aligned with MFD_ECOLI | P30958 from UniProtKB/Swiss-Prot  Length:1148

    Alignment length:308
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325        
            MFD_ECOLI    26 ACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLIVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDPEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENRGVDPMRPLLPPQSLWLRVDELFSELKN 333
               SCOP domains d2b2na1 A:26-333 Transcription-repair coupling factor, TRCF                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh.....eee..............hhhhhhhhhhhhhhhhhh...eeeeehhhhh....hhhhhhhhheeee.....hhhhhhhhhhhh..ee........eeeee..eeee........eeeee....eeeeeeee....eeeeee.eeee........hhhhhhhhhhhhhh.........hhhhhhhh.....hhhhhhhhhh.....hhhhhh....eeee..hhhhhhhhhhhhhhhhhhhhh........hhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b2n A  26 ACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLIVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDPEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENRGVDPMRPLLPPQSLWLRVDELFSELKN 333
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with MFD_ECOLI | P30958 from UniProtKB/Swiss-Prot  Length:1148

    Alignment length:309
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325         
            MFD_ECOLI    26 ACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLIVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDPEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENRGVDPMRPLLPPQSLWLRVDELFSELKNW 334
               SCOP domains d2b2nb_ B: Transcription-repair coupling factor, TRCF                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh....eee..............hhhhhhhhhhhhhhhhhh...eeeeehhhhh....hhhhhhhhheeee.....hhhhhhhhhhhh..ee........eeeee..eeee........eeee.hhhh..eeeeee....eeeee..eeee........hhhhhhhhhhhhhh.........hhhhhhhh.....hhhhhhhhhh.....hhhhhh....eeee...hhhhhhhhhhhhhhhhhhhh........hhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b2n B  26 ACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLIVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDPEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENRGVDPMRPLLPPQSLWLRVDELFSELKNA 334
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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: Tandem AAA-ATPase domain (59)

Protein domain: Transcription-repair coupling factor, TRCF (2)

Escherichia coli [TaxId: 562] (2)

1a	d2b2na1	A:26-333
1b	d2b2nb_	B:

(no "CATH Domain" information available for 2B2N)

(no "Pfam Domain" information available for 2B2N)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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