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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB
 
Authors :  K. Theis, P. J. Chen, M. Skorvaga, B. Van Houten, C. Kisker
Date :  30 Oct 99  (Deposition) - 03 May 00  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Apo Protein, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Theis, P. J. Chen, M. Skorvaga, B. Van Houten, C. Kisker
Crystal Structure Of Uvrb, A Dna Helicase Adapted For Nucleotide Excision Repair.
Embo J. V. 18 6899 1999
PubMed-ID: 10601012  |  Reference-DOI: 10.1093/EMBOJ/18.24.6899
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EXCINUCLEASE UVRABC COMPONENT UVRB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS CALDOTENAX
    Organism Taxid: 1395

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:403 , HOH A:716 , HOH A:727 , HOH A:748 , HOH A:785BINDING SITE FOR RESIDUE ZN A 701
2AC2SOFTWAREGLU A:295 , LYS A:580 , HIS A:581BINDING SITE FOR RESIDUE ZN A 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D9X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1D9X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D9X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1D9X)

(-) Exons   (0, 0)

(no "Exon" information available for 1D9X)

(-) 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:590
 aligned with UVRB_BACCA | P56981 from UniProtKB/Swiss-Prot  Length:658

    Alignment length:593
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592   
           UVRB_BACCA     3 EGRFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPHNAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLRVGMEIERNALLRRLVDIQYDRNDIDFRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGKVLGEREHVAIFPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPYTLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEHSPGVVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNRKHGIVPRTVKKEIRDV 595
               SCOP domains d1d9xa1 A:2-414 Nucleotide excision repair enzyme UvrB                                                                                                                                                                                                                                                                                                                                                                      d1d9xa2 A:415-595 Nucleotide excision repair enzyme UvrB                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1d9xA04 A:414-595 P-loop containing nucleotide triphosphate hydrolases                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh...eeeee.hhhhh.....ee....ee........hhhhhhhhhhhhhh.....eeeee.hhhhh....hhhhhh..eeee........hhhhhhhh........-..................................--.eee...........eeee........hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhh.........hhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh...hhhhhhhhh..eeee....hhhhhhhh...eee..........eeeee...hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh................hhhhhhhhh.....eeee............eeeeee......hhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d9x A   2 EGRFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPHNAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLRVGMEIERNALLRRLVDIQYDRNDI-FRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIE--AEVDALTGKVLGEREHVAIFPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPYTLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEHSPGVVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNRKHGIVPRTVKKEIRDV 595
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181    | |191       201       211       221  |    232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592   
                                                                                                                                                                                                                  186 |                              221  |                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                                    188                                 225
   Legend:   → Mismatch (orange background)
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  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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D9X)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UVRB_BACCA | P56981)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UVRB_BACCA | P56981: 1d9z 1t5l 2fdc

(-) Related Entries Specified in the PDB File

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