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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST DNA POLYMERASE ALPHA BOUND TO DNA/RNA AND DGTP
 
Authors :  R. L. Perera, L. Pellegrini
Date :  04 Jul 12  (Deposition) - 27 Feb 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,E  (1x)
Biol. Unit 2:  B,D,F  (1x)
Keywords :  Dna Polymerase, Dna Replication, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Perera, R. Torella, S. Klinge, M. L. Kilkenny, J. D. Maman, L. Pellegrini
Mechanism For Priming Dna Synthesis By Yeast Dna Polymerase Alpha
Elife V. 2 00482 2013
PubMed-ID: 23599895  |  Reference-DOI: 10.7554/ELIFE.00482

(-) Compounds

Molecule 1 - DNA POLYMERASE ALPHA CATALYTIC SUBUNIT A
    Chains: A, B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSFDUET-1
    Expression System Strain: BL21(DE3)ROSETTA2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: POLYMERASE DOMAIN, UNP RESIDUES 349-1258
    Gene: CDC17, N2181, POL1, YNL102W
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 2 - DNA (5'- D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*C P*CP*G)-3')
    Chains: C, D
    Engineered: YES
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES
 
Molecule 3 - DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')
    Chains: E, F
    Engineered: YES
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A C E 
Biological Unit 2 (1x):  B D F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1DGT2Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1DGT1Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1DGT1Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:864 , PHE A:865 , ASN A:866 , SER A:867 , LEU A:868 , TYR A:869 , PRO A:870 , ARG A:917 , ASN A:948 , TYR A:951 , GLY A:952 , ASN A:998 , DC C:5 , DC C:6 , DG E:12BINDING SITE FOR RESIDUE DGT A 1301
2AC2SOFTWAREPHE B:865 , SER B:867 , LEU B:868 , TYR B:869 , PRO B:870 , ARG B:917 , LYS B:944 , ASN B:948 , TYR B:951 , GLY B:952 , THR B:997 , ASN B:998 , DC D:5 , DC D:6 , DG F:12BINDING SITE FOR RESIDUE DGT B 1301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FYD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FYD)

(-) 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:848
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee..eeeeeeeee.....eeeeeeee...eeeeeeee....hhhhhhhhhhhhhhhhhh.....eeeeeee..........eeeeeeeeee...................eeeee....hhhhhhhhhh......eeee...........eeeee.hhh.eee........eeeeeeeeeeeee....eeeeeeeeeeeeeee.............eeeeee..........hhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...hhhhhh.............hhhhhhhhhh...eeee..hhhhhhhh......hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhh.....................eee...eeeeee.hhhhhhhhhh...........................hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...eeeee....hhhhhhhhhhhhhhhhhh......eeeeeeeeeeeeee..eeeeeeeee.....eeeeeeee.hhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhheeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeee...hhh.eeehhhhhhhhhh...hhhhhhhh.hhhhhhhhhh.....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fyd A  349 TDTFQMFWLDYCEVNNTLILFGKVKLKDDNCVSAMVQINGLCRELFFLPREGKTPTDIHEEIIPLLMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSRDTIPSDLSSDTFYHVFGGNSNIFESFVIQNRIMGPCWLDIKGADFNSSHCAVEVSVDKPQNITPTTTKTMPNLRCLSLSIQTLMNPKENKQEIVSITLSAYRNISLDSPIPENIKPDDLCTLVRPPQSTSFPLGLAALAKQKLPGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGRRLRRTWPEKFGNMNHFFISDICSGRLICDIANEMGQSLTPKCQSWDLSEMYQVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRIQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSVPPSEVDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDIRQQALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTNSVMIDTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNGTTVLEVKGLDMKRREFCPLSRDVSIHVLNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPAVQVALRMRKAGRVVKAGSVITFVITKSVAERAHALNEVMIKSNNLIPDPQYYLEKQIFAPVERLLERIDSFNVVRLSEALG 1242
                                   358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672   ||  686       696       706       716       726       736       746       756       766       776       786       796       806       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171  ||  1194      1204      1214      1224      1234        
                                                                                                                                                                                       506|                                                                                                                                                                  676|                                                                                                                                   815|                                                                                                                                                                                                                                                                                                                                         1174|                                                      
                                                                                                                                                                                        511                                                                                                                                                                   681                                                                                                                                    841                                                                                                                                                                                                                                                                                                                                          1188                                                      


Chain B from PDB  Type:PROTEIN  Length:848
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee..eeeeeeeee.....eeeeeeee...eeeeeeee....hhhhhhhhhhhhhhhhhh.....eeeeeee..........eeeeeeeeee...................eeeee....hhhhhhhhhh......eeee...........eeeee.hhh.eee........eeeeeeeeeeeee....eeeeeeeeeeeeeee.............eeeeee..........hhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...hhhhhh.............hhhhhhhhhh...eeee..hhhhhhhh......hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhh.....................eee...eeeeee.hhhhhhhhhh...........................hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...eeeee....hhhhhhhhhhhhhhhhhh......eeeeeeeeeeeeee..eeeeeeeee.....eeeeeeee.hhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhheeee.......hhhhhhhhhhhhhhhhhhhh.......eeeeee...hhh.eeehhhhhhhhhh...hhhhhhhh.hhhhhhhhhh.....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fyd B  349 TDTFQMFWLDYCEVNNTLILFGKVKLKDDNCVSAMVQINGLCRELFFLPREGKTPTDIHEEIIPLLMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSRDTIPSDLSSDTFYHVFGGNSNIFESFVIQNRIMGPCWLDIKGADFNSSHCAVEVSVDKPQNITPTTTKTMPNLRCLSLSIQTLMNPKENKQEIVSITLSAYRNISLDSPIPENIKPDDLCTLVRPPQSTSFPLGLAALAKQKLPGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGRRLRRTWPEKFGNMNHFFISDICSGRLICDIANEMGQSLTPKCQSWDLSEMYQVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRIQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSVPPSEVDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDIRQQALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTNSVMIDTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNGTTVLEVKGLDMKRREFCPLSRDVSIHVLNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPAVQVALRMRKAGRVVKAGSVITFVITKSVAERAHALNEVMIKSNNLIPDPQYYLEKQIFAPVERLLERIDSFNVVRLSEALG 1242
                                   358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672   ||  686       696       706       716       726       736       746       756       766       776       786       796       806       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171  ||  1194      1204      1214      1224      1234        
                                                                                                                                                                                       506|                                                                                                                                                                  676|                                                                                                                                   815|                                                                                                                                                                                                                                                                                                                                         1174|                                                      
                                                                                                                                                                                        511                                                                                                                                                                   681                                                                                                                                    841                                                                                                                                                                                                                                                                                                                                          1188                                                      


Chain C from PDB  Type:DNA  Length:16
                                                 
                4fyd C    1 TGTACCCCTGCCCGCC   16
                                    10      


Chain D from PDB  Type:DNA  Length:16
                                                 
                4fyd D    1 TGTACCCCTGCCCGCC   16
                                    10      


Chain E from PDB  Type:DNA/RNA  Length:12
                                             
                4fyd E    1 CGGCGGGCAGGG   12
                                    10  


Chain F from PDB  Type:DNA/RNA  Length:12
                                             
                4fyd F    1 CGGCGGGCAGGG   12
                                    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 4FYD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

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  4fyd
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  DPOA_YEAST | P13382
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOA_YEAST | P13382: 3flo 3oiq 4b08 4c93 4fvm 4fxd

(-) Related Entries Specified in the PDB File

4b08 CRYSTAL STRUCTURE OF YEAST DNA POLYMERASE ALPHA, SELENOMETHIONINE PROTEIN
4fvm CRYSTAL STRUCTURE OF YEAST DNA POLYMERASE ALPHA
4fxd CRYSTAL STRUCTURE OF YEAST DNA POLYMERASE ALPHA BOUND TO DNA/RNA