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(-) Description

Title :  STRUCTURAL BASIS OF DNA DAMAGE RECOGNITION AND PROCESSING BY UVRB: CRYSTAL STRUCTURE OF A UVRB/DNA COMPLEX
 
Authors :  J. J. Truglio, C. Kisker
Date :  13 Dec 05  (Deposition) - 14 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Protein-Dna Complex, Uvrb, Uvrc, Uvrd, Uvra, Ner, Nucleotide Excision Repair, Dna Repair, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Truglio, E. Karakas, B. Rhau, H. Wang, M. J. Dellavecchia, B. Van Houten, C. Kisker
Structural Basis For Dna Recognition And Processing By Uvrb
Nat. Struct. Mol. Biol. V. 13 360 2006
PubMed-ID: 16532007  |  Reference-DOI: 10.1038/NSMB1072

(-) Compounds

Molecule 1 - 5'-D(P*CP*GP*GP*CP*TP*CP*CP*AP*TP*CP*TP*CP*TP*AP*CP*CP*GP*C P*AP*A)-3'
    Chains: C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - UVRABC SYSTEM PROTEIN B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UVRB
    Organism Scientific: BACILLUS CALDOTENAX
    Organism Taxid: 1395
    Synonym: UVRB PROTEIN, EXCINUCLEASE ABC SUBUNIT B

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1FLQ1Ligand/IonN-[6-(ACETYLAMINO)HEXYL]-3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-6-CARBOXAMIDE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FLQ-1Ligand/IonN-[6-(ACETYLAMINO)HEXYL]-3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-6-CARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FLQ1Ligand/IonN-[6-(ACETYLAMINO)HEXYL]-3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-6-CARBOXAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:65 , ASN B:66 , PRO B:345 , GLN B:346 , ASN B:503 , LEU B:505 , DC C:4 , DT C:5 , DT C:13 , DA C:14BINDING SITE FOR RESIDUE FLQ C 473

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FDC)

(-) Exons   (0, 0)

(no "Exon" information available for 2FDC)

(-) Sequences/Alignments

Asymmetric 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:505
 aligned with UVRB_BACCA | P56981 from UniProtKB/Swiss-Prot  Length:658

    Alignment length:593
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591   
           UVRB_BACCA     2 VEGRFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPHNAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLRVGMEIERNALLRRLVDIQYDRNDIDFRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGKVLGEREHVAIFPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPYTLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEHSPGVVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNRKHGIVPRTVKKEIRD 594
               SCOP domains -d2fdca1 A:2-414 Nucleotide excision repair enzyme UvrB                                                                                                                                                                                                                                                                                                                                                                      d2fdca2 A:415-594 Nucleotide excision repair enzyme UvrB                                                                                                                             SCOP domains
               CATH domains 2fdcA01 A:1-89,A:120-148,A:323-338,A:388-410                                             ------------------------------2fdcA01                      -----------                                                                                  --------------------------------------------------------------------------------2fdcA01         -------------------------------------------------2fdcA01                ---2fdcA03 A:414-594 P-loop containing nucleotide triphosphate hyd      rolases                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh...eeeee...eeeee..eee....eee..eeeehhhhhhhhhhhhhhhhhh..eeeee.hhhh.ee.hhhhhhh...----------------------------------------------------------------------------------.........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh........ee.hhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhh.eeeee....hhhhhhh....eee..........eeeee...hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...eee..------hhhhhhhhhhhh...eeee............eeeeeee.........hhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fdc A   1 VEGRFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPHNAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVV----------------------------------------------------------------------------------IFPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPYTLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEHSPGVVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLH------ERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNRKHGIVPRTVKKEIRD 594
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        |-         -         -         -         -         -         -         -         - |     251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471    |    - |     491       501       511       521       531       541       551       561       571       581       591   
                                                                                                                                                                                        159                                                                                243                                                                                                                                                                                                                                      476    483                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:585
 aligned with UVRB_BACCA | P56981 from UniProtKB/Swiss-Prot  Length:658

    Alignment length:593
                                                                                                                                                                                                                        191                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                                      190 |                                                                                                                                                                                                                                                                                                                                                                                                                  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181        |-|      200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590   
           UVRB_BACCA     2 VEGRFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPHNAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLRVGMEIERNALLRRLVDIQYDRNDIDFR-GTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGKVLGEREHVAIFPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPYTLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEHSPGVVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNRKHGIVPRTVKKEIR 593
               SCOP domains -d2fdcb1 B:2-414 Nucleotide excision repair enzyme UvrB                                                                                                                                                                                                                                                                                                                                                                       d2fdcb2 B:415-593 Nucleotide excision repair enzyme UvrB                                                                                                                            SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2fdcB04 B:414-593 P-loop containing nucleotide triphosphate hyd        rolases                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhh...eeeee...eeeee..eee....eee..eeee.hhhhhhhhhhhhhhhhh..eeeee.hhhh.ee.hhhhhhhh.eeee.......hhhhhhhhhh..ee........eeee....eeee........eeeeee..eeeeee..............eeee........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh........ee.hhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhh..eeeee....hhhhhhhh...eee..........eeeee...hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh..eee..--------..hhhhhhh....eeee............eeeeee..........hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fdc B   1 VEGRFQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKTLAGQLYSELKEFFPHNAVEYFVSYYDYYQPEAYVPQTDTYIEKDAKINDEIDKLRHSATSALFERRDVIIVASVSCIYGLGSPEEYRELVVSLRVGMEIERNALLRRLVDIQYDRNDIDFRRGTFRVRGDVVEIFPASRDEHCIRVEFFGDEIERIREVDALTGEVLGEREHVAIFPASHFVTREEKMRLAIQNIEQELEERLAELRAQGKLLEAQRLEQRTRYDLEMMREMGFCSGIENYSRHLALRPPGSTPYTLLDYFPDDFLIIVDESHVTLPQLRGMYNGDRARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSATPGPYELEHSPGVVEQIIRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLH--------IEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNRKHGIVPRTVKKEIR 593
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470     |   -    |  490       500       510       520       530       540       550       560       570       580       590   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     476      485                                                                                                            


Chain C from PDB  Type:DNA  Length:12
                                            
                 2fdc C   1 CGGCTTACCGCA  19
                                ||  17  
                                5|      
                                13      


Chain D from PDB  Type:DNA  Length:5
                                     
                 2fdc D  15 CCGCA  19
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FDC)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  2fdc
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  UVRB_BACCA | P56981
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 Related Entries

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

UniProtKB/Swiss-Prot
        UVRB_BACCA | P56981: 1d9x 1d9z 1t5l

(-) Related Entries Specified in the PDB File

1d9x CRYSTAL STRUCTURE OF WILD TYPE UVRB
1d9z CRYSTAL STRUCTURE OF WILD TYPE UVRB BOUND TO ATP
1qoj CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN (DOMAIN 4) OF UVRB
1t5l CRYSTAL STRUCTURE OF THE Y96A MUTANT UVRB REVEALING DOMAIN 2.
1yd1 CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF UVRC BOUND TO MAGNESIUM