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(-) Description

Title :  A RIGID N-TERMINAL CLAMP RESTRAINS THE MOTOR DOMAINS OF THE BACTERIAL TRANSCRIPTION-REPAIR COUPLING FACTOR
 
Authors :  M. Murphy, P. Gong, K. Ralto, L. Manelyte, N. Savery, K. Theis
Date :  21 May 09  (Deposition) - 20 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Mfd, Mutation Frequency Decline, Transcription-Coupled Dna Repair, Transcription-Repair Coupling Factor, Atp-Binding, Dna Damage, Dna Repair, Dna-Binding, Helicase, Hydrolase, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. N. Murphy, P. Gong, K. Ralto, L. Manelyte, N. J. Savery, K. Theis
An N-Terminal Clamp Restrains The Motor Domains Of The Bacterial Transcription-Repair Coupling Factor Mfd.
Nucleic Acids Res. V. 37 6042 2009
PubMed-ID: 19700770  |  Reference-DOI: 10.1093/NAR/GKP680

(-) Compounds

Molecule 1 - TRANSCRIPTION-REPAIR-COUPLING FACTOR
    Chains: A
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-470
    Gene: B1114, JW1100, MFD
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: TRCF, ATP-DEPENDENT HELICASE MFD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:343 , HOH A:499 , HOH A:517BINDING SITE FOR RESIDUE CO A 484

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HJH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HJH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HJH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HJH)

(-) Exons   (0, 0)

(no "Exon" information available for 3HJH)

(-) Sequences/Alignments

Asymmetric/Biological 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:446
 aligned with MFD_ECOLI | P30958 from UniProtKB/Swiss-Prot  Length:1148

    Alignment length:446
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444      
            MFD_ECOLI     5 YRYTLPVKAGEQRLLGELTGAACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLIVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDPEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENRGVDPMRPLLPPQSLWLRVDELFSELKNWPRVQLKTEHLPTKAANANLGFQKLPDLAVQAQQKAPLDALRKFLETFDGPVVFSVESEGRREALGELLARIKIAPQRIMRLDEASDRGRYLMIGAAEHGFVDTVRNLALICESDLL 450
               SCOP domains d3hjha1 A:5-348 automated matches                                                                                                                                                                                                                                                                                                                       d3hjha2 A:349-450 automated matches                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee....hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh....eee..............hhhhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhh.eeee.....hhhhhhhhhhhh..ee........eeeee..eeee........eeeeee..eeeeeeeee....eeeeee.eeee........hhhhhhhhhhhhhhhh.......hhhhhhhh.....hhhhhhhhhh.....hhhhhh....eeee..hhhhhhhhhhhhhhhhhhhhh........hhhhh..hhhhhhhhhh...eeee..........eee..ee..............hhhhhhhhhhh...eeeee........hhhhhhhhh...ee..hhhhh....eeeee......eee....eeeeehhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hjh A   5 YRYTLPVKAGEQRLLGELTGAACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLIVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDPEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENRGVDPMRPLLPPQSLWLRVDELFSELKNWPRVQLKTEHLPTKAANANLGFQKLPDLAVQAQQKAPLDALRKFLETFDGPVVFSVESEGRREALGELLARIKIAPQRIMRLDEASDRGRYLMIGAAEHGFVDTVRNLALICESDLL 450
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HJH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HJH)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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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  3hjh
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MFD_ECOLI | P30958: 2b2n 2eyq 4dfc

(-) Related Entries Specified in the PDB File

2b2n CRYSTAL STRUCTURE OF MFD RESIDUES 1 TO 333
2eyq CRYSTAL STRUCTURE OF FULL LENGTH MFD PROTEIN