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(-) Description

Title :  CRYSTAL STRUCTURE OF DEINOCOCCUS RADIODURANS UVRD IN COMPLEX WITH DNA, FORM 1
 
Authors :  M. Stelter, S. Acajjaoui, S. Mcsweeney, J. Timmins
Date :  20 Aug 13  (Deposition) - 30 Oct 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,D,X,Y
Keywords :  Hydrolase-Dna Complex, Dna Repair, Dna Helicases, Nucleotide Excision Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Stelter, S. Acajjaoui, S. Mcsweeney, J. Timmins
Structural And Mechanistic Insight Into Dna Unwinding By Deinococcus Radiodurans Uvrd.
Plos One V. 8 77364 2013
PubMed-ID: 24143224  |  Reference-DOI: 10.1371/JOURNAL.PONE.0077364

(-) Compounds

Molecule 1 - DNA HELICASE II
    Chains: A, D
    EC Number: 3.6.4.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET151D
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL TRUNCATION, RESIDUES 1-665
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Synonym: UVRD
 
Molecule 2 - FOR25
    Chains: Y
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - REV25
    Chains: X
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ADXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2GOL2Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4NA2Ligand/IonSODIUM ION
5NO34Ligand/IonNITRATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:17 , ALA A:34 , GLY A:35 , SER A:36 , GLY A:37 , LYS A:38 , THR A:39 , ARG A:40 , GLN A:258 , TYR A:290 , ARG A:291 , GLU A:577 , ARG A:617 , MG A:1666 , NO3 A:1667 , HOH A:2006 , HOH A:2007 , HOH A:2037BINDING SITE FOR RESIDUE ANP A1665
02AC2SOFTWARETHR A:39 , ANP A:1665 , HOH A:2005 , HOH A:2006 , HOH A:2007BINDING SITE FOR RESIDUE MG A1666
03AC3SOFTWAREALA A:12 , ANP A:1665BINDING SITE FOR RESIDUE NO3 A1667
04AC4SOFTWAREASP A:391 , ALA A:542BINDING SITE FOR RESIDUE GOL A1668
05AC5SOFTWAREASP A:231 , ASN A:233 , TYR A:261 , ARG A:264 , ALA A:266 , HOH A:2023 , DT X:24BINDING SITE FOR RESIDUE NO3 A1669
06AC6SOFTWAREGLY A:58 , GLU A:59 , ILE A:60 , TRP A:88 , LYS A:220BINDING SITE FOR RESIDUE NA A1670
07AC7SOFTWAREGLN D:17 , ALA D:34 , GLY D:35 , SER D:36 , GLY D:37 , LYS D:38 , THR D:39 , ARG D:40 , GLN D:258 , TYR D:290 , ARG D:291 , GLU D:577 , ARG D:617 , MG D:1666 , NO3 D:1667 , HOH D:2006 , HOH D:2008 , HOH D:2040BINDING SITE FOR RESIDUE ANP D1665
08AC8SOFTWARETHR D:39 , ANP D:1665 , HOH D:2006 , HOH D:2007 , HOH D:2008BINDING SITE FOR RESIDUE MG D1666
09AC9SOFTWAREGLN D:11 , ALA D:12 , LEU D:13 , ANP D:1665BINDING SITE FOR RESIDUE NO3 D1667
10BC1SOFTWAREASP D:391 , ALA D:542 , ARG D:552BINDING SITE FOR RESIDUE GOL D1668
11BC2SOFTWAREASP D:231 , ASN D:233 , TYR D:261 , ARG D:264 , ALA D:266 , HOH D:2030 , DT Y:24BINDING SITE FOR RESIDUE NO3 D1669
12BC3SOFTWAREPRO D:57 , GLY D:58 , GLU D:59 , ILE D:60 , TRP D:88 , LYS D:220BINDING SITE FOR RESIDUE NA D1670

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C2U)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg D:420 -Pro D:421

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C2U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C2U)

(-) Exons   (0, 0)

(no "Exon" information available for 4C2U)

(-) 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:658
 aligned with Q9RTI9_DEIRA | Q9RTI9 from UniProtKB/TrEMBL  Length:745

    Alignment length:661
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663 
         Q9RTI9_DEIRA     4 SAGPDLLQALNPTQAQAADHFTGPALVIAGAGSGKTRTLIYRIAHLIGHYGVHPGEILAVTFTNKAAAEMRERAGHLVPGAGDLWMSTFHSAGVRILRTYGEHIGLRRGFVIYDDDDQLDIIKEVMGSIPGIGAETQPRVIRGIIDRAKSNLWTPDDLDRSREPFISGLPRDAAAEAYRRYEVRKKGQNAIDFGDLITETVRLFKEVPGVLDKVQNKAKFIHVDEYQDTNRAQYELTRLLASRDRNLLVVGDPDQSIYKFRGADIQNILDFQKDYPDAKVYMLEHNYRSSARVLEAANKLIENNTERLDKTLKPVKEAGQPVTFHRATDHRAEGDYVADWLTRLHGEGRAWSEMAILYRTNAQSRVIEESLRRVQIPARIVGGVGFYDRREIRDILAYARLALNPADDVALRRIIGRPRRGIGDTALQKLMEWARTHHTSVLTACANAAEQNILDRGAHKATEFAGLMEAMSEAADNYEPAAFLRFVMETSGYLDLLRQEGQEGQVRLENLEELVSAAEEWSQDEANVGGSIADFLDDAALLSSVDDMRTKAENKGAPEDAVTLMTLHNAKGLEFPVVFIVGVEQGLLPSKGAIAEGPSGIEEERRLFYVGITRAMERLLMTAAQNRMQFGKTNAAEDSAFLEDIEGLFDTVDPYGQPIEY 664
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhh...hhh.eeee..hhhhhhhhhhhhhh...hhhhheeehhhhhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhh....---..hhhhhhhhhhhhhhhh.hhhhhhh....ee..eehhhhhhhhhhhhhhhhhh.ee..hhhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh....eeeeehhhhh.hhhhh..hhhhhhhhhhh...eee........hhhhhhhhhhhhh....................eeeee.hhhhhhhhhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh....hhhhhhhhh.......eeeee.hhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee.eee....eee...hhhhhhh....ee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c2u A   4 SAGPDLLQALNPTQAQAADHFTGPALVIAGAGSGKTRTLIYRIAHLIGHYGVHPGEILAVTFTNKAAAEMRERAGHLVPGAGDLWMSTFHSAGVRILRTYGEHIGLRRGFVIYDDDDQLDIIKEVMGSIPG---ETQPRVIRGIIDRAKSNLWTPDDLDRSREPFISGLPRDAAAEAYRRYEVRKKGQNAIDFGDLITETVRLFKEVPGVLDKVQNKAKFIHVDEYQDTNRAQYELTRLLASRDRNLLVVGDPDQSIYKFRGADIQNILDFQKDYPDAKVYMLEHNYRSSARVLEAANKLIENNTERLDKTLKPVKEAGQPVTFHRATDHRAEGDYVADWLTRLHGEGRAWSEMAILYRTNAQSRVIEESLRRVQIPARIVGGVGFYDRREIRDILAYARLALNPADDVALRRIIGRPRRGIGDTALQKLMEWARTHHTSVLTACANAAEQNILDRGAHKATEFAGLMEAMSEAADNYEPAAFLRFVMETSGYLDLLRQEGQEGQVRLENLEELVSAAEEWSQDEANVGGSIADFLDDAALLSSVDDMRTKAENKGAPEDAVTLMTLHNAKGLEFPVVFIVGVEQGLLPSKGAIAEGPSGIEEERRLFYVGITRAMERLLMTAAQNRMQFGKTNAAEDSAFLEDIEGLFDTVDPYGQPIEY 664
                                    13        23        33        43        53        63        73        83        93       103       113       123       133|   |  143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663 
                                                                                                                                                            134 138                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:658
 aligned with Q9RTI9_DEIRA | Q9RTI9 from UniProtKB/TrEMBL  Length:745

    Alignment length:661
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663 
         Q9RTI9_DEIRA     4 SAGPDLLQALNPTQAQAADHFTGPALVIAGAGSGKTRTLIYRIAHLIGHYGVHPGEILAVTFTNKAAAEMRERAGHLVPGAGDLWMSTFHSAGVRILRTYGEHIGLRRGFVIYDDDDQLDIIKEVMGSIPGIGAETQPRVIRGIIDRAKSNLWTPDDLDRSREPFISGLPRDAAAEAYRRYEVRKKGQNAIDFGDLITETVRLFKEVPGVLDKVQNKAKFIHVDEYQDTNRAQYELTRLLASRDRNLLVVGDPDQSIYKFRGADIQNILDFQKDYPDAKVYMLEHNYRSSARVLEAANKLIENNTERLDKTLKPVKEAGQPVTFHRATDHRAEGDYVADWLTRLHGEGRAWSEMAILYRTNAQSRVIEESLRRVQIPARIVGGVGFYDRREIRDILAYARLALNPADDVALRRIIGRPRRGIGDTALQKLMEWARTHHTSVLTACANAAEQNILDRGAHKATEFAGLMEAMSEAADNYEPAAFLRFVMETSGYLDLLRQEGQEGQVRLENLEELVSAAEEWSQDEANVGGSIADFLDDAALLSSVDDMRTKAENKGAPEDAVTLMTLHNAKGLEFPVVFIVGVEQGLLPSKGAIAEGPSGIEEERRLFYVGITRAMERLLMTAAQNRMQFGKTNAAEDSAFLEDIEGLFDTVDPYGQPIEY 664
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhh...hhh.eeee..hhhhhhhhhhhhhh...hhhhheeehhhhhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhh....---..hhhhhhhhhhhhhhhh.hhhhhhh....ee..eehhhhhhhhhhhhhhhhhh.ee..hhhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh....eeeeehhhhh.hhhhh..hhhhhhhhhhh...eee...ee...hhhhhhhhhhhhh..........ee........eeeee.hhhhhhhhhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhh.........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh....hhhhhhhhh.......eeeee.hhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee.eee....eee...hhhhhhh....eee.....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c2u D   4 SAGPDLLQALNPTQAQAADHFTGPALVIAGAGSGKTRTLIYRIAHLIGHYGVHPGEILAVTFTNKAAAEMRERAGHLVPGAGDLWMSTFHSAGVRILRTYGEHIGLRRGFVIYDDDDQLDIIKEVMGSIPG---ETQPRVIRGIIDRAKSNLWTPDDLDRSREPFISGLPRDAAAEAYRRYEVRKKGQNAIDFGDLITETVRLFKEVPGVLDKVQNKAKFIHVDEYQDTNRAQYELTRLLASRDRNLLVVGDPDQSIYKFRGADIQNILDFQKDYPDAKVYMLEHNYRSSARVLEAANKLIENNTERLDKTLKPVKEAGQPVTFHRATDHRAEGDYVADWLTRLHGEGRAWSEMAILYRTNAQSRVIEESLRRVQIPARIVGGVGFYDRREIRDILAYARLALNPADDVALRRIIGRPRRGIGDTALQKLMEWARTHHTSVLTACANAAEQNILDRGAHKATEFAGLMEAMSEAADNYEPAAFLRFVMETSGYLDLLRQEGQEGQVRLENLEELVSAAEEWSQDEANVGGSIADFLDDAALLSSVDDMRTKAENKGAPEDAVTLMTLHNAKGLEFPVVFIVGVEQGLLPSKGAIAEGPSGIEEERRLFYVGITRAMERLLMTAAQNRMQFGKTNAAEDSAFLEDIEGLFDTVDPYGQPIEY 664
                                    13        23        33        43        53        63        73        83        93       103       113       123       133|   |  143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663 
                                                                                                                                                            134 138                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              


Chain X from PDB  Type:DNA  Length:24
                                                        
                 4c2u X   1 ACGACCTGCGAGCACTGCTTTTTT  24
                                    10        20    


Chain Y from PDB  Type:DNA  Length:23
                                                       
                 4c2u Y   2 CAGTGCTCGCAGGTCGTTTTTTT  24
                                    11        21
   Legend:   → Mismatch (orange background)
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  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 4C2U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C2U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C2U)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,D   (Q9RTI9_DEIRA | Q9RTI9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004003    ATP-dependent DNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.

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 Related Entries

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

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        Q9RTI9_DEIRA | Q9RTI9: 4c2t 4c30

(-) Related Entries Specified in the PDB File

4c2t CRYSTAL STRUCTURE OF FULL LENGTH DEINOCOCCUS RADIODURANS UVRD IN COMPLEX WITH DNA