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(-) Description

Title :  DAMAGE DETECTION BY THE UVRABC PATHWAY: CRYSTAL STRUCTURE OF UVRB BOUND TO FLUORESCEIN-ADDUCTED DNA
 
Authors :  T. R. Waters, J. Eryilmaz, S. Geddes, T. E. Barrett
Date :  23 Oct 06  (Deposition) - 16 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym./Biol. Unit :  A,B,D
Keywords :  Protein-Dna Complex, T-Fluorescein, Hairpin, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. R. Waters, J. Eryilmaz, S. Geddes, T. E. Barrett
Damage Detection By The Uvrabc Pathway: Crystal Structure Of Uvrb Bound To Fluorescein-Adducted Dna
Febs Lett. V. 580 6423 2006
PubMed-ID: 17097086  |  Reference-DOI: 10.1016/J.FEBSLET.2006.10.051
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(P*TP*TP*TP*TP*T)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - UVRABC SYSTEM PROTEIN B
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET8C
    Expression System Strain: BL21DE3 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UVRB
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: PROTEIN UVRB, EXCINUCLEASE ABC SUBUNIT B, PROTEIN DINA
 
Molecule 3 - UVRABC SYSTEM PROTEIN B
    Chains: B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET8C
    Expression System Strain: BL21DE3 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 622-659
    Gene: UVRB
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: PROTEIN UVRB, EXCINUCLEASE ABC SUBUNIT B, PROTEIN DINA

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2FLU1Ligand/Ion2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID
3NML1Ligand/IonN-METHYLACETAMIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:11 , GLN A:12 , GLN A:14 , GLN A:17 , ALA A:40 , GLY A:42 , THR A:43 , GLY A:44 , LYS A:45 , THR A:46 , PHE A:47 , PRO A:414 , ARG A:543BINDING SITE FOR RESIDUE ADP A 662
2AC2SOFTWAREDT D:2 , DT D:3BINDING SITE FOR RESIDUE NML D 103
3AC3SOFTWAREGLY A:71 , TYR A:74 , SER A:75 , ASN A:116 , ILE A:119BINDING SITE FOR RESIDUE FLU D 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NMV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NMV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NMV)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UVRPS50151 UVR domain profile.UVRB_BACSU625-660
 		  2A:625-654
B:625-659

(-) Exons   (0, 0)

(no "Exon" information available for 2NMV)

(-) 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:620
 aligned with UVRB_BACSU | P37954 from UniProtKB/Swiss-Prot  Length:661

    Alignment length:652
                                    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       602       612       622       632       642       652  
           UVRB_BACSU     3 DRFELVSKYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNLIKEVNKPTLVIAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSALFERRDVIIIASVSCIYGLGSPEEYREMVVSLRTEMEIERNELLRKLVDIQYARNDIDFQRGTFRVRGDVVEIFPASRDEHCVRVEFFGDEIERIREVDALTGEILGDRDHVAIFPASHFVTRAEKMEKAIQNIEKELEEQLKVMHENGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPPGSTPYTLLDYFPDDFMIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRLPSALDNRPLRFEEFEKHMHNIVYVSATPGPYEIEHTDEMVEQIIRPTGLLDPLIDVRPIEGQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIMYADKITKSMEIAINETKRRREQQERFNEEHGITPKTINKEIRDVIRATVAAEDKAEYKTKAAPKLSKMTKKERQKVVEQMEHEMKEAAKALDFERAAELRDLL 654
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2nmvA0 1 A:3-89,A:117-148,A:320-338,A:388-410                                          ---------------------------2nmvA01                         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------2nmvA01            -------------------------------------------------2nmvA01                --2nmvA04 A:413-589 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                          ---------------------------------- CATH domains
               Pfam domains -------ResIII-2nmvA02 A:10-132                                                                                                    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Helicase_C-2nmvA01 A:463-545                                                       -----UvrB-2nmvA03 A:551-589                 ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ......-......hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh...eeeee...eeeee..ee......ee..eeeehhhhhhhhhhhhhhhhhh..eeeee.hhhhh...hhhhhhhhheeee.....hhhhhhhhhhh...ee........eeeee..eeee.......eeeeeee....eeeeeeee.....eeeee.eeee........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.........hhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhh...eeeee....hhhhhhhh...eee..........eeeee...hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh...eeee............eeeeee.hhhhh....hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.......-------------------------------hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UVR  PDB: A:625-654            PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nmv A   3 DRFELV-KYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNLIKEVNKPTLVIAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDASINDEIDKLRHSATSALFERRDVIIIASVSCIYGLGSPEEYREMVVSLRTEMEIERNELLRKLVDIQYARNDIDFQRGTFRVRGDVVEIFPASRDEHCVRVEFFGDEIERIREVDALTGEILGDRDHVAIFPASHFVTRAEKMEKAIQNIEKELEEQLKVMHENGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLTLRPPGSTPYTLLDYFPDDFMIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRLPSALDNRPLRFEEFEKHMHNIVYVSATPGPYEIEHTDEMVEQIIRPTGLLDPLIDVRPIEGQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIMYADKITKSMEIAINETKRRREQQERFNEEHGITPKTIN-------------------------------KKERQKVVEQMEHEMKEAAKALDFERAAELRDLL 654
                                 | |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      |  -         -         -       622       632       642       652  
                                 8 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                589                             621                                 
                                  10                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:38
 aligned with UVRB_BACSU | P37954 from UniProtKB/Swiss-Prot  Length:661

    Alignment length:38
                                   631       641       651        
           UVRB_BACSU   622 KERQKVVEQMEHEMKEAAKALDFERAAELRDLLLELKA 659
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
           Pfam domains (1) ---UVR-2nmvB01 B:625-659               Pfam domains (1)
           Pfam domains (2) ---UVR-2nmvB02 B:625-659               Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE ---UVR  PDB: B:625-659                 PROSITE
                 Transcript -------------------------------------- Transcript
                 2nmv B 622 KERQKVVEQMEHEMKEAAKALDFERAAELRDLLLELKA 659
                                   631       641       651        


Chain D from PDB  Type:DNA  Length:5
                                     
                 2nmv D   1 TTTTT   5
   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 2NMV)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (4, 5)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: UVR] (3)
(-)
Family: UVR (3)
(-)
Bacillus subtilis (2)
3aUVR-2nmvB01B:625-659
3bUVR-2nmvB02B:625-659
(-)
Clan: no clan defined [family: UvrB] (1)

(-) 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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  2nmv
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  UVRB_BACSU | P37954
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 Related Entries

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

UniProtKB/Swiss-Prot
        UVRB_BACSU | P37954: 2d7d 3v4r

(-) Related Entries Specified in the PDB File

2d7d THE SAME PROTEIN COMPLEXED WITH FLUORESCEIN ADDUCTED PENTATHYMINE