Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  YEAST DNA POLYMERASE ETA EXTENDING FROM AN 8-OXOG LESION
 
Authors :  T. D. Silverstein, R. Jain, A. K. Aggarwal
Date :  17 Aug 10  (Deposition) - 22 Dec 10  (Release) - 22 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Protein-Dna Complex, Transferase/Dna, Nucleotidyltransferase, Dna- Directed Dna Polymerase, Dna Repair, Dna Replication, Dna Binding, Nucleotide Binding, Metal Binding, Magnesium Binding, Nucleus, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. D. Silverstein, R. Jain, R. E. Johnson, L. Prakash, S. Prakash, A. K. Aggarwal
Structural Basis For Error-Free Replication Of Oxidatively Damaged Dna By Yeast Dna Polymerase Eta.
Structure V. 18 1463 2010
PubMed-ID: 21070945  |  Reference-DOI: 10.1016/J.STR.2010.08.019

(-) Compounds

Molecule 1 - DNA POLYMERASE ETA
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSL414
    Expression System StrainER2566
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1-513
    GeneDBH1, RAD30, YDR419W
    MutationYES
    Organism CommonBREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymRADIATION-SENSITIVE PROTEIN 30
 
Molecule 2 - 5'-D(*TP*AP*AP*TP*GP*(8OG)P*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)- 3'
    ChainsT
    EngineeredYES
    SyntheticYES
 
Molecule 3 - 5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3'
    ChainsP
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2DCP1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
3DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4MG2Ligand/IonMAGNESIUM ION
5SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:30 , MET A:31 , ASN A:32 , ALA A:33 , PHE A:34 , PHE A:35 , ILE A:60 , ALA A:61 , TYR A:64 , ARG A:67 , ARG A:73 , ASP A:155 , LYS A:279 , MG A:515 , MG A:516 , HOH A:634 , HOH A:643 , HOH A:654 , HOH A:667 , HOH A:708 , HOH A:782 , HOH A:875 , HOH A:1032 , DOC P:11 , HOH P:406 , DT T:4 , DG T:5 , 8OG T:6BINDING SITE FOR RESIDUE DCP A 514
2AC2SOFTWAREASP A:30 , MET A:31 , ASP A:155 , DCP A:514BINDING SITE FOR RESIDUE MG A 515
3AC3SOFTWAREASP A:30 , ASP A:155 , GLU A:156 , DCP A:514 , HOH A:875 , DOC P:11BINDING SITE FOR RESIDUE MG A 516
4AC4SOFTWARESER A:446 , ARG A:456 , HOH A:1044 , DC P:7BINDING SITE FOR RESIDUE SO4 A 517
5AC5SOFTWAREPRO A:209 , GLU A:210 , LYS A:211 , HOH A:575 , HOH A:590 , HOH A:794 , HOH A:891 , HOH A:978 , HOH A:1013BINDING SITE FOR RESIDUE SO4 A 518
6AC6SOFTWARESER A:14 , PRO A:15 , SER A:16 , LYS A:366BINDING SITE FOR RESIDUE SO4 A 519

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:279 -Pro A:280
2Tyr A:494 -Pro A:495

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UMUCPS50173 UmuC domain profile.POLH_YEAST26-309  1A:26-309

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR419W1YDR419W.1IV:1303167-13050651899POLH_YEAST1-6326321A:1-512512

(-) 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:515
 aligned with POLH_YEAST | Q04049 from UniProtKB/Swiss-Prot  Length:632

    Alignment length:515
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507     
           POLH_YEAST     - ---MSKFTWKELIQLGSPSKAYESSLACIAHIDMNAFFAQVEQMRCGLSKEDPVVCVQWNSIIAVSYAARKYGISRMDTIQEALKKCSNLIPIHTAVFKKGEDFWQYHDGCGSWVQDPAKQISVEDHKVSLEPYRRESRKALKIFKSACDLVERASIDEVFLDLGRICFNMLMFDNEYELTGDLKLKDALSNIREAFIGGNYDINSHLPLIPEKIKSLKFEGDVFNPEGRDLITDWDDVILALGSQVCKGIRDSIKDILGYTTSCGLSSTKNVCKLASNYKKPDAQTIVKNDCLLDFLDCGKFEITSFWTLGGVLGKELIDVLDLPHENSIKHIRETWPDNAGQLKEFLDAKVKQSDYDRSTSNIDPLKTADLAEKLFKLSRGRYGLPLSSRPVVKSMMSNKNLRGKSCNSIVDCISWLEVFCAELTSRIQDLEQEYNKIVIPRTVSISLKTKSYEVYRKSGPVAYKGINFQSHELLKVGIKFVTDLDIKGKNKSYYPLTKLSMTITNFDIIDLQ 512
               SCOP domains d3ohba1 A:-2-389 automated matches                                                                                                                                                                                                                                                                                                                                                                      d3ohba2 A:390-512 automated matches                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh..hhhhh....eeeeee.hhhhhhhhhhh.......eeeee..eeeeehhhhhh.......hhhhhhhhh...eeee.eeee.....ee....................eeeehhhhhhhhhhhhhhhhhhh..eeeee..eeeeehhhhhhhhhhhh...eee..eehhhhhhhhhhhhhhh...........hhhhhhh....ee..........hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh.....eeee.hhhhhhhhhh....hhhhh....hhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhhhh.............hhhhhhhhhhhhh................eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeeee.....eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------UMUC  PDB: A:26-309 UniProt: 26-309                                                                                                                                                                                                                                                         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 ---Exon 1.1  PDB: A:1-512 UniProt: 1-632 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Transcript 1
                 3ohb A  -2 DPHMSKFTWKELIQLGSPSKAYESSLACIAHIDMNAFFAQVEQMRCGLSKEDPVVCVQWNSIIAVSYAARKYGISRMDTIQEALKKCSNLIPIHTAVFKKGEDFWQYHDGCGSWVQDPAKQISVEDHKVSLEPYRRESRKALAIFKWACDLVERASIDEVFLDLGRICFNMLMFDNEYELTGDLKLKDALSNIREAFIGGNYDINSHLPLIPEKIKSLKFEGDVFNPEGRDLITDWDDVILALGSQVCKGIRDSIKDILGYTTSCGLSSTKNVCKLASNYKKPDAQTIVKNDCLLDFLDCGKFEITSFWTLGGVLGKELIDVLDLPHENSIKHIRETWPDNAGQLKEFLDAKVKQSDYDRSTSNIDPLKTADLAEKLFKLSRGRYGLPLSSRPVVKSMMSNKNLRGKSCNSIVDCISWLEVFCAELTSRIQDLEQEYNKIVIPRTVSISLKTKSYEVYRKSGPVAYKGINFQSHELLKVGIKFVTDLDIKGKNKSYYPLTKLSMTITNFDIIDLQ 512
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507     

Chain P from PDB  Type:DNA  Length:11
                                           
                 3ohb P   1 GTCCTCCCCTc  11
                                    10|
                                     11-DOC

Chain T from PDB  Type:DNA  Length:13
                                             
                 3ohb T   4 TGgAGGGGAGGAC  16
                              |     13   
                              |          
                              6-8OG      

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (POLH_YEAST | Q04049)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    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:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    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:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0070987    error-free translesion synthesis    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.
    GO:0042276    error-prone translesion synthesis    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites.
    GO:0007064    mitotic sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome are joined along the entire length of the chromosome, from their formation in S phase through metaphase during a mitotic cell cycle. This cohesion cycle is critical for high fidelity chromosome transmission.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005657    replication fork    The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    8OG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DCP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DOC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:279 - Pro A:280   [ RasMol ]  
    Tyr A:494 - Pro A:495   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3ohb
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  POLH_YEAST | Q04049
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.7
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  POLH_YEAST | Q04049
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        POLH_YEAST | Q040491jih 2r8j 2r8k 2wtf 2xgp 2xgq 3mfh 3mfi 3oha

(-) Related Entries Specified in the PDB File

1jih YEAST DNA POLYMERASE ETA APO-ENZYME
3mfh YEAST DNA POLYMERASE ETA IN COMPLEX WITH UNDAMAGED DNA
3mfi YEAST DNA POLYMERASE ETA IN COMPLEX WITH A CIS-SYN THYMIDINE DIMER
3oha YEAST DNA POLYMERASE ETA INSERTING DCTP OPPOSITE AND 8-OXOG LESION