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(-) Description

Title :  TERNARY CRYSTAL STRUCTURE OF YEAST DNA POLYMERASE EPSILON WITH TEMPLATE G
 
Authors :  R. Jain, K. R. Rajashankar, A. Buku, R. E. Johnson, L. Prakash, S. Prakas A. K. Aggarwal
Date :  10 Mar 14  (Deposition) - 30 Apr 14  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Dna Polymerase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Jain, K. R. Rajashankar, A. Buku, R. E. Johnson, L. Prakash, S. Prakash, A. K. Aggarwal
Crystal Structure Of Yeast Dna Polymerase Epsilon Catalytic Domain.
Plos One V. 9 94835 2014
PubMed-ID: 24733111  |  Reference-DOI: 10.1371/JOURNAL.PONE.0094835

(-) Compounds

Molecule 1 - DNA POLYMERASE EPSILON CATALYTIC SUBUNIT A
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: BAKER'S YEAST
    Expression System Taxid: 4932
    Fragment: CATALYTIC DOMAIN (UNP RESIDUES 1-1187)
    Gene: POL2, DUN2, YNL262W, N0825
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: DNA POLYMERASE II SUBUNIT A
 
Molecule 2 - 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'
    Chains: P
    Engineered: YES
    Other Details: PRIMER DNA STRAND
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'
    Chains: T
    Engineered: YES
    Other Details: TEMPLATE DNA STRAND
    Synthetic: YES

 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
1CA4Ligand/IonCALCIUM ION
2DCP1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
3DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4EDO1Ligand/Ion1,2-ETHANEDIOL
5NA1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:640 , VAL A:641 , SER A:643 , MET A:644 , TYR A:645 , ARG A:781 , LYS A:785 , LYS A:824 , ASN A:828 , TYR A:831 , ASP A:877 , CA A:1202 , CA A:1203 , HOH A:1345 , DOC P:12 , DG T:4 , DG T:5BINDING SITE FOR RESIDUE DCP A 1201
2AC2SOFTWAREASP A:640 , VAL A:641 , ASP A:877 , DCP A:1201 , CA A:1203BINDING SITE FOR RESIDUE CA A 1202
3AC3SOFTWAREASP A:640 , ASP A:877 , DCP A:1201 , CA A:1202 , DOC P:12BINDING SITE FOR RESIDUE CA A 1203
4AC4SOFTWAREASP A:290 , HOH A:1365BINDING SITE FOR RESIDUE CA A 1204
5AC5SOFTWAREARG A:968 , LYS A:1156 , DG T:10BINDING SITE FOR RESIDUE NA A 1205
6AC6SOFTWAREDG T:9 , HOH T:213 , HOH T:214 , HOH T:215BINDING SITE FOR RESIDUE CA T 101
7AC7SOFTWAREDG T:13 , DG T:14BINDING SITE FOR RESIDUE EDO T 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Arg A:663 -Asp A:664
2Tyr A:747 -His A:748
3Asp A:802 -Lys A:803
4Arg A:806 -Asp A:807
5Gly A:948 -Pro A:949
6Lys A:1096 -Pro A:1097

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PTF)

(-) 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:1112
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.............hhhhhhhh..eeeeeeeeeeeee.......eeeeeeeeee....eeeeeee...eeeeee....hhhhhhhhhhhhh........eeee......hhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhh.......hhhh.eeeee....hhhhhhhhhh......eeee....eee...........eeeeeeee..............eeeeeeee..eeeeee...........ee.........eeee....hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..hhhhhhh.ee.....ee....eeeehhhhhhhhh..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..............ee..eeeeeeee....eee...eeee....eeee.hhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhh.eeee.eeeeeeee.hhhhhhhhhhh.hhh.ee.....eeeeeeeeeee...hhhhhhhhhhhhh...ee.........ee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeee.....eeeee.....eeeeehhhhhhhhhhhhhh.eeeeeeeee....eeeeeee....eeeeeee.eeee.............eeee.....eeeee........eehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.eeee...hhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.......hhhh.eee.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ptf A   30 YALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLTNMHATLVSQETNQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLFEARKLLRPILQDNARNIYNKVDAKHLIEDIREYDVPYHVRVSIDKDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFPDSAVDQIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDETLRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGHVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKVTNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASMYPNIMTTNRLQPDSIKAERDARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKNKFSKKKVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENPFYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALVERVGRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQKFTNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKRYAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYSAVASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSITTARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIPIKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGVSNPVPRVEHPDWLKRKIA 1185
                                    39        49        59        69        79        89||     118       128       138       148       158       168       178       188       198       208     ||223||     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       600       610       620       630       640       650       660   ||  683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183  
                                                                                       90|                                                                                                     214| 224|                                                                                                                                                                                                                                                                                                                                                                                                                                             664|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
                                                                                       110                                                                                                      220  232                                                                                                                                                                                                                                                                                                                                                                                                                                              678                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           


Chain P from PDB  Type:DNA  Length:11
                                            
                4ptf P    2 TCCTCCCCTAc   12
                                    11|
                                     12-DOC


Chain T from PDB  Type:DNA  Length:15
                                                
                4ptf T    1 TAAGGTAGGGGAGGA   15
                                    10
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4PTF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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    Gly A:948 - Pro A:949   [ RasMol ]  
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