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(-) Description

Title :  SOLUTION STRUCTURE OF ESCHERICHIA COLI UVRB C-TERMINAL DOMAIN
 
Authors :  A. A. Alexandrovich, G. G. Kelly, T. A. Frenkiel, G. F. Moolenaar, N. N. Goosen, M. R. Sanderson, A. N. Lane
Date :  14 Jul 00  (Deposition) - 12 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Dna Excision Repair, Uvrb, Dna Repair, Uvrc Binding Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. A. Alexandrovich, M. M. Czisch, T. T. Frenkiel, G. G. Kelly, N. N. Goosen, G. G. Moolenaar, B. B. Chowdhry, M. M. Sanderson, A. A. Lane
Solution Structure, Hydrodynamics And Thermodynamics Of The Uvrb C-Terminal Domain.
J. Biomol. Struct. Dyn. V. 19 219 2001
PubMed-ID: 11697728

(-) Compounds

Molecule 1 - EXCINUCLEASE ABC SUBUNIT
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GeneUVRB(DOMAIN)
    Expression System PlasmidPNP118
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET-HIS
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN RESIDUES 618-673
    GeneUVRB
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    PlasmidPNP118
    StrainPP3398

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1E52)

(-) Sites  (0, 0)

(no "Site" information available for 1E52)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E52)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E52)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E52)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UVRPS50151 UVR domain profile.UVRB_ECO57633-668
 
  2A:23-58
B:23-58
UVRB_ECOLI633-668
 
  2A:23-58
B:23-58

(-) Exons   (0, 0)

(no "Exon" information available for 1E52)

(-) Sequences/Alignments

NMR Structure
   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:56
 aligned with UVRB_ECO57 | P0A8F9 from UniProtKB/Swiss-Prot  Length:673

    Alignment length:56
                                   627       637       647       657       667      
           UVRB_ECO57   618 VEPDNVPMDMSPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIAAS 673
               SCOP domains d1e52a_ A: C-terminal UvrC-binding domain of UvrB        SCOP domains
               CATH domains 1e52A00 A:8-63 DNA Excision Repair, UvrB; Chain A        CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------UVR  PDB: A:23-58 UniProt: 633-668  ----- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 1e52 A   8 LEPDNVPMDMSPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIAAS  63
                                    17        27        37        47        57      

Chain A from PDB  Type:PROTEIN  Length:56
 aligned with UVRB_ECOLI | P0A8F8 from UniProtKB/Swiss-Prot  Length:673

    Alignment length:56
                                   627       637       647       657       667      
           UVRB_ECOLI   618 VEPDNVPMDMSPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIAAS 673
               SCOP domains d1e52a_ A: C-terminal UvrC-binding domain of UvrB        SCOP domains
               CATH domains 1e52A00 A:8-63 DNA Excision Repair, UvrB; Chain A        CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------UVR  PDB: A:23-58 UniProt: 633-668  ----- PROSITE (2)
                 Transcript -------------------------------------------------------- Transcript
                 1e52 A   8 LEPDNVPMDMSPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIAAS  63
                                    17        27        37        47        57      

Chain B from PDB  Type:PROTEIN  Length:56
 aligned with UVRB_ECO57 | P0A8F9 from UniProtKB/Swiss-Prot  Length:673

    Alignment length:56
                                   627       637       647       657       667      
           UVRB_ECO57   618 VEPDNVPMDMSPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIAAS 673
               SCOP domains d1e52b_ B: C-terminal UvrC-binding domain of UvrB        SCOP domains
               CATH domains 1e52B00 B:8-63 DNA Excision Repair, UvrB; Chain A        CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------UVR  PDB: B:23-58 UniProt: 633-668  ----- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 1e52 B   8 LEPDNVPMDMSPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIAAS  63
                                    17        27        37        47        57      

Chain B from PDB  Type:PROTEIN  Length:56
 aligned with UVRB_ECOLI | P0A8F8 from UniProtKB/Swiss-Prot  Length:673

    Alignment length:56
                                   627       637       647       657       667      
           UVRB_ECOLI   618 VEPDNVPMDMSPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIAAS 673
               SCOP domains d1e52b_ B: C-terminal UvrC-binding domain of UvrB        SCOP domains
               CATH domains 1e52B00 B:8-63 DNA Excision Repair, UvrB; Chain A        CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------UVR  PDB: B:23-58 UniProt: 633-668  ----- PROSITE (2)
                 Transcript -------------------------------------------------------- Transcript
                 1e52 B   8 LEPDNVPMDMSPKALQQKIHELEGLMMQHAQNLEFEEAAQIRDQLHQLRELFIAAS  63
                                    17        27        37        47        57      

   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)

NMR Structure

(-) CATH Domains  (1, 2)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E52)

(-) Gene Ontology  (15, 28)

NMR Structure(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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 Related Entries

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

UniProtKB/Swiss-Prot
        UVRB_ECO57 | P0A8F91qoj
        UVRB_ECOLI | P0A8F81qoj

(-) Related Entries Specified in the PDB File

1qoj CRYSTAL STRUCTURE OF E.COLI UVRB C-TERMINAL DOMAIN, AND A MODEL FOR UVRB-UVRC INTERACTION.