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(-) Description

Title :  SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF UVRC FROM E-COLI
 
Authors :  S. Singh, G. E. Folkers, A. M. J. J. Bonvin, R. Boelens, R. Wechselberger, A. Niztayev, R. Kaptein
Date :  23 Nov 01  (Deposition) - 20 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (22x)
Keywords :  Helix-Hairpin-Helix, Hhh Domain, Dna-Binding Domain, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Singh, G. E. Folkers, A. M. J. J. Bonvin, R. Boelens, R. Wechselberger, A. Niztayev, R. Kaptein
Solution Structure And Dna-Binding Properties Of The C-Terminal Domain Of Uvrc From E. Coli
Embo J. V. 21 6257 2002
PubMed-ID: 12426397  |  Reference-DOI: 10.1093/EMBOJ/CDF627
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EXCINUCLEASE ABC SUBUNIT C
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET13B
    Expression System Strain: BL21 (DE3)-P-LYS-S
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HHH DOMAIN(C-TERMINAL DOMAIN)
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: DE3
    Synonym: UVRC

 Structural Features

(-) Chains, Units

  
NMR Structure (22x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1KFT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KFT)

(-) Exons   (0, 0)

(no "Exon" information available for 1KFT)

(-) 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 UVRC_ECO57 | P0A8G2 from UniProtKB/Swiss-Prot  Length:610

    Alignment length:56
                                   564       574       584       594       604      
           UVRC_ECO57   555 TSSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLKH 610
               SCOP domains d1kfta_ A: Excinuclease UvrC C-terminal domain           SCOP domains
               CATH domains 1kftA00 A:23-78                                          CATH domains
               Pfam domains -----------------------HHH-1kftA01 A:46-75           --- Pfam domains
         Sec.struct. author .hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 1kft A  23 TSSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLKH  78
                                    32        42        52        62        72      


Chain A from PDB  Type:PROTEIN  Length:56
 aligned with UVRC_ECOL6 | P0A8G1 from UniProtKB/Swiss-Prot  Length:610

    Alignment length:56
                                   564       574       584       594       604      
           UVRC_ECOL6   555 TSSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLKH 610
               SCOP domains d1kfta_ A: Excinuclease UvrC C-terminal domain           SCOP domains
               CATH domains 1kftA00 A:23-78                                          CATH domains
               Pfam domains -----------------------HHH-1kftA01 A:46-75           --- Pfam domains
         Sec.struct. author .hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 1kft A  23 TSSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLKH  78
                                    32        42        52        62        72      


Chain A from PDB  Type:PROTEIN  Length:56
 aligned with UVRC_ECOLI | P0A8G0 from UniProtKB/Swiss-Prot  Length:610

    Alignment length:56
                                   564       574       584       594       604      
           UVRC_ECOLI   555 TSSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLKH 610
               SCOP domains d1kfta_ A: Excinuclease UvrC C-terminal domain           SCOP domains
               CATH domains 1kftA00 A:23-78                                          CATH domains
               Pfam domains -----------------------HHH-1kftA01 A:46-75           --- Pfam domains
         Sec.struct. author .hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 1kft A  23 TSSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWSLKH  78
                                    32        42        52        62        72
   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, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HHH (112)

(-) Gene Ontology  (10, 30)

NMR Structure(hide GO term definitions)
Chain A   (UVRC_ECOLI | P0A8G0)
molecular function
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
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.

Chain A   (UVRC_ECOL6 | P0A8G1)
molecular function
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
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.

Chain A   (UVRC_ECO57 | P0A8G2)
molecular function
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
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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