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(-) Description

Title :  YEAST DNA POLYMERASE ETA IN COMPLEX WITH C8-2-ACETYLAMINOFLUORENE CONTAINING DNA
 
Authors :  S. Scheider, K. Lammens, S. Schorr, K. P. Hopfner, T. Carell
Date :  07 Jun 10  (Deposition) - 03 Nov 10  (Release) - 15 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,P,Q,T,U
Biol. Unit 1:  B,Q,U  (1x)
Biol. Unit 2:  A,P,T  (1x)
Keywords :  Transferase-Dna Complex, Translesion Dna Synthesis, Dna-Binding, Dna Damage (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Schorr, S. Schneider, K. Lammens, K. P. Hopfner, T. Carell
Mechanism Of Replication Blocking And Bypass Of Y-Family Polymerase Eta By Bulky Acetylaminofluorene Dna Adducts.
Proc. Natl. Acad. Sci. Usa V. 107 20720 2010
PubMed-ID: 21076032  |  Reference-DOI: 10.1073/PNAS.1008894107

(-) Compounds

Molecule 1 - DNA POLYMERASE ETA
    ChainsA, B
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI,
    Expression System PlasmidPDEST007
    Expression System StrainROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-513
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymRADIATION-SENSITIVE PROTEIN 30
 
Molecule 2 - 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
    ChainsP, Q
    SyntheticYES
 
Molecule 3 - 5'-D(*CP*8FG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
    ChainsT, U
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABPQTU
Biological Unit 1 (1x) B Q U
Biological Unit 2 (1x)A P T 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
18FG2Mod. NucleotideN-(5'-PHOSPHO-2'-DEOXYGUANOSIN-8-YL)-2-ACETYLAMINOFLUORENE
2CA8Ligand/IonCALCIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
18FG1Mod. NucleotideN-(5'-PHOSPHO-2'-DEOXYGUANOSIN-8-YL)-2-ACETYLAMINOFLUORENE
2CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
18FG1Mod. NucleotideN-(5'-PHOSPHO-2'-DEOXYGUANOSIN-8-YL)-2-ACETYLAMINOFLUORENE
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:155 , CA A:1512BINDING SITE FOR RESIDUE CA A1511
2AC2SOFTWAREASP A:30 , ASP A:155 , GLU A:156 , CA A:1511BINDING SITE FOR RESIDUE CA A1512
3AC3SOFTWARETHR A:231 , ASP A:289 , HOH A:2026BINDING SITE FOR RESIDUE CA A1513
4AC4SOFTWAREASN A:32 , THR A:259 , THR A:260 , SER A:261 , PRO A:280 , ASP A:281BINDING SITE FOR RESIDUE CA A1514
5AC5SOFTWAREASP B:30 , ASP B:155 , GLU B:156 , CA B:1512BINDING SITE FOR RESIDUE CA B1511
6AC6SOFTWAREASP B:155 , GLU B:156 , CA B:1511BINDING SITE FOR RESIDUE CA B1512
7AC7SOFTWARELYS B:3 , THR B:231 , ASP B:289BINDING SITE FOR RESIDUE CA B1513
8AC8SOFTWAREGLY B:98 , GLU B:417BINDING SITE FOR RESIDUE CA B1514

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:279 -Pro A:280
2Tyr A:494 -Pro A:495
3Lys B:279 -Pro B:280
4Tyr B:494 -Pro B:495

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UMUCPS50173 UmuC domain profile.POLH_YEAST26-309
 
  2A:26-309
B:26-309
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UMUCPS50173 UmuC domain profile.POLH_YEAST26-309
 
  1-
B:26-309
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UMUCPS50173 UmuC domain profile.POLH_YEAST26-309
 
  1A:26-309
-

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR419W1YDR419W.1IV:1303167-13050651899POLH_YEAST1-6326322A:1-510
B:1-510
510
510

(-) 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:511
 aligned with POLH_YEAST | Q04049 from UniProtKB/Swiss-Prot  Length:632

    Alignment length:511
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509 
           POLH_YEAST     - -MSKFTWKELIQLGSPSKAYESSLACIAHIDMNAFFAQVEQMRCGLSKEDPVVCVQWNSIIAVSYAARKYGISRMDTIQEALKKCSNLIPIHTAVFKKGEDFWQYHDGCGSWVQDPAKQISVEDHKVSLEPYRRESRKALKIFKSACDLVERASIDEVFLDLGRICFNMLMFDNEYELTGDLKLKDALSNIREAFIGGNYDINSHLPLIPEKIKSLKFEGDVFNPEGRDLITDWDDVILALGSQVCKGIRDSIKDILGYTTSCGLSSTKNVCKLASNYKKPDAQTIVKNDCLLDFLDCGKFEITSFWTLGGVLGKELIDVLDLPHENSIKHIRETWPDNAGQLKEFLDAKVKQSDYDRSTSNIDPLKTADLAEKLFKLSRGRYGLPLSSRPVVKSMMSNKNLRGKSCNSIVDCISWLEVFCAELTSRIQDLEQEYNKIVIPRTVSISLKTKSYEVYRKSGPVAYKGINFQSHELLKVGIKFVTDLDIKGKNKSYYPLTKLSMTITNFDIID 510
               SCOP domains d2xgpa1 A:0-389 automated matches                                                                                                                                                                                                                                                                                                                                                                     d2xgpa2 A:390-510 automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhh...........eeeee..hhhhhhhhhhh.......eeeee..eeeeehhhhhh.......hhhhhhhhhh..eeee..eee...........................eee.hhhhhhhhhhhhhhhhhhh..eeeee..eeeeehhhhhhhhhhhh...eee..eehhhhhhhhhhhhhhh......eee..hhhhhhh....ee..........hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhh...eeee.hhhhhhhhhh....hhhhh....hhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh................eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee.....eeeeeee........hhhhhhhhhhhhhhhhhhhh.........eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------UMUC  PDB: A:26-309 UniProt: 26-309                                                                                                                                                                                                                                                         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 -Exon 1.1  PDB: A:1-510 UniProt: 1-632 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Transcript 1
                 2xgp A   0 RMSKFTWKELIQLGSPSKAYESSLACIAHIDMNAFFAQVEQMRCGLSKEDPVVCVQWNSIIAVSYAARKYGISRMDTIQEALKKCSNLIPIHTAVFKKGEDFWQYHDGCGSWVQDPAKQISVEDHKVSLEPYRRESRKALKIFKSACDLVERASIDEVFLDLGRICFNMLMFDNEYELTGDLKLKDALSNIREAFIGGNYDINSHLPLIPEKIKSLKFEGDVFNPEGRDLITDWDDVILALGSQVCKGIRDSIKDILGYTTSCGLSSTKNVCKLASNYKKPDAQTIVKNDCLLDFLDCGKFEITSFWTLGGVLGKELIDVLDLPHENSIKHIRETWPDNAGQLKEFLDAKVKQSDYDRSTSNIDPLKTADLAEKLFKLSRGRYGLPLSSRPVVKSMMSNKNLRGKSCNSIVDCISWLEVFCAELTSRIQDLEQEYNKIVIPRTVSISLKTKSYEVYRKSGPVAYKGINFQSHELLKVGIKFVTDLDIKGKNKSYYPLTKLSMTITNFDIID 510
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509 

Chain B from PDB  Type:PROTEIN  Length:512
 aligned with POLH_YEAST | Q04049 from UniProtKB/Swiss-Prot  Length:632

    Alignment length:512
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508  
           POLH_YEAST     - --MSKFTWKELIQLGSPSKAYESSLACIAHIDMNAFFAQVEQMRCGLSKEDPVVCVQWNSIIAVSYAARKYGISRMDTIQEALKKCSNLIPIHTAVFKKGEDFWQYHDGCGSWVQDPAKQISVEDHKVSLEPYRRESRKALKIFKSACDLVERASIDEVFLDLGRICFNMLMFDNEYELTGDLKLKDALSNIREAFIGGNYDINSHLPLIPEKIKSLKFEGDVFNPEGRDLITDWDDVILALGSQVCKGIRDSIKDILGYTTSCGLSSTKNVCKLASNYKKPDAQTIVKNDCLLDFLDCGKFEITSFWTLGGVLGKELIDVLDLPHENSIKHIRETWPDNAGQLKEFLDAKVKQSDYDRSTSNIDPLKTADLAEKLFKLSRGRYGLPLSSRPVVKSMMSNKNLRGKSCNSIVDCISWLEVFCAELTSRIQDLEQEYNKIVIPRTVSISLKTKSYEVYRKSGPVAYKGINFQSHELLKVGIKFVTDLDIKGKNKSYYPLTKLSMTITNFDIID 510
               SCOP domains d2xgpb1 B:-1-389 automated matches                                                                                                                                                                                                                                                                                                                                                                     d2xgpb2 B:390-510 automated matches                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------IMS-2xgpB01 B:29-276                                                                                                                                                                                                                                    ----------------------------------------------------------------------------------------IMS_C-2xgpB03 B:365-500                                                                                                                 ---------- Pfam domains (1)
           Pfam domains (2) ------------------------------IMS-2xgpB02 B:29-276                                                                                                                                                                                                                                    ----------------------------------------------------------------------------------------IMS_C-2xgpB04 B:365-500                                                                                                                 ---------- Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhh..hhhhh....eeeee..hhhhhhhhhhh.......eeeee..eeeeehhhhhh.......hhhhhhh.....eeee..eee.....ee................hhh.eee.hhhhhhhhhhhhhhhhhhh..eeeee..eeeeehhhhhhhhhhhh.........hhhhhhhhhhhhhhhh...........hhhhh......ee..........hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhh...eeee.hhhhhhhhhh....hhhhh....hhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhhh..............hhhhhhhhhhhhh................eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.....eeeeeee........hhhhhhhhhhhhhhhhhhhh.........eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------UMUC  PDB: B:26-309 UniProt: 26-309                                                                                                                                                                                                                                                         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 --Exon 1.1  PDB: B:1-510 UniProt: 1-632 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Transcript 1
                 2xgp B  -1 GRMSKFTWKELIQLGSPSKAYESSLACIAHIDMNAFFAQVEQMRCGLSKEDPVVCVQWNSIIAVSYAARKYGISRMDTIQEALKKCSNLIPIHTAVFKKGEDFWQYHDGCGSWVQDPAKQISVEDHKVSLEPYRRESRKALKIFKSACDLVERASIDEVFLDLGRICFNMLMFDNEYELTGDLKLKDALSNIREAFIGGNYDINSHLPLIPEKIKSLKFEGDVFNPEGRDLITDWDDVILALGSQVCKGIRDSIKDILGYTTSCGLSSTKNVCKLASNYKKPDAQTIVKNDCLLDFLDCGKFEITSFWTLGGVLGKELIDVLDLPHENSIKHIRETWPDNAGQLKEFLDAKVKQSDYDRSTSNIDPLKTADLAEKLFKLSRGRYGLPLSSRPVVKSMMSNKNLRGKSCNSIVDCISWLEVFCAELTSRIQDLEQEYNKIVIPRTVSISLKTKSYEVYRKSGPVAYKGINFQSHELLKVGIKFVTDLDIKGKNKSYYPLTKLSMTITNFDIID 510
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508  

Chain P from PDB  Type:DNA  Length:9
                                         
                 2xgp P   5 GTGGATGAG  13

Chain Q from PDB  Type:DNA  Length:9
                                         
                 2xgp Q   5 GTGGATGAG  13

Chain T from PDB  Type:DNA  Length:11
                                           
                 2xgp T   4 CgCTCATCCAC  14
                             |      13 
                             5-8FG     

Chain U from PDB  Type:DNA  Length:10
                                          
                 2xgp U   5 gCTCATCCAC  14
                            |       14
                            5-8FG     

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XGP)

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1jih YEAST DNA POLYMERASE ETA
2wtf DNA POLYMERASE ETA IN COMPLEX WITH THE CIS -DIAMMINEPLATINUM (II) 1,3-GTG INTRASTRAND CROSS-LINK
2xgq STRUCTURE OF YEAST DNA POLYMERASE ETA IN COMPLEX WITH C8-N-ACETYL-2-AMINOANTHRACENE CONTAINING DNA