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(-) Description

Title :  CRYSTAL STRUCTURE OF A UVRB DIMER-DNA COMPLEX
 
Authors :  M. P. J. Webster, R. Jukes, T. Barrett
Date :  15 Dec 11  (Deposition) - 04 Jul 12  (Release) - 10 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Helicase Motifs And A Beta-Hairpin, Dna Helicase, Uvra, Atp Hydrolysis, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. P. Webster, R. Jukes, V. S. Zamfir, C. W. Kay, C. Bagneris, T. Barrett
Crystal Structure Of The Uvrb Dimer: Insights Into The Nature And Functioning Of The Uvrab Damage Engagement And Uvrb-Dna Complexes.
Nucleic Acids Res. V. 40 8743 2012
PubMed-ID: 22753105  |  Reference-DOI: 10.1093/NAR/GKS633

(-) Compounds

Molecule 1 - UVRABC SYSTEM PROTEIN B
    Chains: A, B
    EC Number: 3.1.21.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 8C
    Expression System Strain: BL21 DE3 PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BSU35170, DINA, UVR, UVRB
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: PROTEIN UVRB, EXCINUCLEASE ABC SUBUNIT B, PROTEIN DINA
 
Molecule 2
    Chains: C, D
    Engineered: YES
    Other Details: SYNTHESISED DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:11 , GLN A:12 , GLN A:17 , GLY A:42 , GLY A:44 , LYS A:45 , THR A:46 , PHE A:47 , GLU A:76 , ARG A:543BINDING SITE FOR RESIDUE ADP A 701
2AC2SOFTWAREGLY B:42 , GLY B:44 , LYS B:45 , THR B:46BINDING SITE FOR RESIDUE ADP B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V4R)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys B:32 -Lys B:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V4R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V4R)

(-) Exons   (0, 0)

(no "Exon" information available for 3V4R)

(-) 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:586
 aligned with UVRB_BACSU | P37954 from UniProtKB/Swiss-Prot  Length:661

    Alignment length:588
                                    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        
           UVRB_BACSU     3 DRFELVSKYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNLIKEVNKPTLVIAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSALFERRDVIIIASVSCIYGLGSPEEYREMVVSLRTEMEIERNELLRKLVDIQYARNDIDFQRGTFRVRGDVVEIFPASRDEHCVRVEFFGDEIERIREVDALTGEILGDRDHVAIFPASHFVTRAEKMEKAIQNIEKELEEQLKVMHENGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPPGSTPYTLLDYFPDDFMIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRLPSALDNRPLRFEEFEKHMHNIVYVSATPGPYEIEHTDEMVEQIIRPTGLLDPLIDVRPIEGQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIMYADKITKSMEIAINETKRRREQQERFNEEHGITPKTINK 590
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh...eeeee...eeeee..eee....eee..eeeehhhhhhhhhhhhhhhhhh..eeeee.hhhhh...hhhhhhhh.eeee.....hhhhhhhhhhh...ee........eeee...eeeee.--...eeeeeee....eeeeeeee.......eee.eeee...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.........hhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhh...eeeeee...hhhhhhhh...eee..........eeeee...hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh..eee.......hhhhhhhhhhhhh...eee.............eeeeeee.....hhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v4r A   3 DRFELVSKYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNLIKEVNKPTLVIAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSALFERRDVIIIASVSCIYGLGSPEEYREMVVSLRTEMEIERNELLRKLVDIQYARNDIDFQRGTFRVRGDVVEIFP--RDEHCVRVEFFGDEIERIREVDALTGEILGDRDHVAIFPASHFVTRAEKMEKAIQNIEKELEEQLKVMHENGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPPGSTPYTLLDYFPDDFMIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRLPSALDNRPLRFEEFEKHMHNIVYVSATPGPYEIEHTDEMVEQIIRPTGLLDPLIDVRPIEGQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIMYADKITKSMEIAINETKRRREQQERFNEEHGITPKTINK 590
                                    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        
                                                                                                                                                                                                                                   204  |                                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                      207                                                                                                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:579
 aligned with UVRB_BACSU | P37954 from UniProtKB/Swiss-Prot  Length:661

    Alignment length:587
                                    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       
           UVRB_BACSU     3 DRFELVSKYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNLIKEVNKPTLVIAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSALFERRDVIIIASVSCIYGLGSPEEYREMVVSLRTEMEIERNELLRKLVDIQYARNDIDFQRGTFRVRGDVVEIFPASRDEHCVRVEFFGDEIERIREVDALTGEILGDRDHVAIFPASHFVTRAEKMEKAIQNIEKELEEQLKVMHENGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPPGSTPYTLLDYFPDDFMIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRLPSALDNRPLRFEEFEKHMHNIVYVSATPGPYEIEHTDEMVEQIIRPTGLLDPLIDVRPIEGQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIMYADKITKSMEIAINETKRRREQQERFNEEHGITPKTIN 589
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh...eeeee...eeeee..eee....eee..eeeehhhhhhhhhhhhhhhhhh..eeeee.hhhhh...hhhhhhhhheeee.....hhhhhhhhhhhh..ee........ee.....eeee.......eeeeeeee..eeeeeeeee.......eee.eeee....--------.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.........hhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhh...eeeeee...hhhhhhhh...eee..........eeeee...hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhh...eeee............eeeeeee.....hhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v4r B   3 DRFELVSKYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNLIKEVNKPTLVIAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSALFERRDVIIIASVSCIYGLGSPEEYREMVVSLRTEMEIERNELLRKLVDIQYARNDIDFQRGTFRVRGDVVEIFPASRDEHCVRVEFFGDEIERIREVDALTGEILGDRDHVAIFPAS--------MEKAIQNIEKELEEQLKVMHENGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPPGSTPYTLLDYFPDDFMIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRLPSALDNRPLRFEEFEKHMHNIVYVSATPGPYEIEHTDEMVEQIIRPTGLLDPLIDVRPIEGQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIMYADKITKSMEIAINETKRRREQQERFNEEHGITPKTIN 589
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242    |    -   |   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       
                                                                                                                                                                                                                                                                              247      256                                                                                                                                                                                                                                                                                                                                             


Chain C from PDB  Type:DNA  Length:7
                                       
                 3v4r C   2 ACTGTTT   8


Chain D from PDB  Type:DNA  Length:7
                                       
                 3v4r D   2 ACTGTTT   8
   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  (0, 0)

(no "SCOP Domain" information available for 3V4R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V4R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V4R)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (UVRB_BACSU | P37954)
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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  3v4r
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  UVRB_BACSU | P37954
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  3.1.21.5
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 Related Entries

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

UniProtKB/Swiss-Prot
        UVRB_BACSU | P37954: 2d7d 2nmv

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3V4R)