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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST DNA POLYMERASE ALPHA BOUND TO DNA/RNA
 
Authors :  R. L. Perera, R. Torella, S. Klinge, M. L. Kilkenny, J. D. Maman, L. Pelle
Date :  03 Jul 12  (Deposition) - 27 Feb 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
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-Rna 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
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 2 - DNA (5'-D(*TP*TP*TP*TP*CP*GP*CP*TP*GP*CP*CP*CP*GP*CP*CP*T)- 3')
    Chains: C, D
    Engineered: YES
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(*AP*GP*GP*CP*GP*GP*GP*CP*AP*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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4FXD)

(-) Sites  (0, 0)

(no "Site" information available for 4FXD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FXD)

(-) 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..............hhhhhhhhhhhhhh..eeee..hhhhhhh.......hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhh.............eee...eeeee..hhhhhhhhhh...........................hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeee....hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeeeeeeee.....eeeeeeee.hhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhheeeee............hhhhhhhhhhhhhh......eeeeeee........eeehhhhhhhhhh...hhhhhhhh.hhhhhhhhh......hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fxd A  351 TFQMFWLDYCEVNNTLILFGKVKLKDDNCVSAMVQINGLCRELFFLPREGKTPTDIHEEIIPLLMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSRDTIPSDLSSDTFYHVFGGNSNIFESFVIQNRIMGPCWLDIKGADFNSIRNASHCAVEVSVDKPQNITPTTTKTMPNLRCLSLSIQTLMNPKENKQEIVSITLSAYRNISLDSPIPENIKPDDLCTLVRPPQSTSFPLGLAALAKQKLPGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGRRLRRTWPEKFGRGNSNMNHFFISDICSGRLICDIANEMGQSLTPKCQSWDLSEMYQVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRIQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSVPPSEVDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDIRQQALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTDSVMIDTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNGTTVLEVKGLDMKRREFCPLSRDVSIHVLNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPAVQVALRMRKAGRVVKAGSVITFVITKLSVAERAHALNEVMIKSNNLIPDPQYYLEKQIFAPVERLLERIDSFNVVRLSEALG 1242
                                   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       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810    || 852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172 ||   1194      1204      1214      1224      1234        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          815|                                                                                                                                                                                                                                                                                                                                  1174|                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           848                                                                                                                                                                                                                                                                                                                                   1187                                                       


Chain B from PDB  Type:PROTEIN  Length:807
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               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..............hhhhhhhhhhhhhh..eeee..hhhhhhh.......hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhh.............eee...eeeee..hhhhhhhhhh...........................hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeee....hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeeeee....eeeee.hhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhheee..eeeee........eeehhhhhhhhhh...hhhhhhhh.hhhhhhhhh......hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fxd B  351 TFQMFWLDYCEVNNTLILFGKVKLKDDNCVSAMVQINGLCRELFFLPREGKTPTDIHEEIIPLLMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSRDTIPSDLSSDTFYHVFGGNSNIFESFVIQNRIMGPCWLDIKGADFNSIRNASHCAVEVSVDKPQNITPTTTKTMPNLRCLSLSIQTLMNPKENKQEIVSITLSAYRNISLDSPIPENIKPDDLCTLVRPPQSTSFPLGLAALAKQKLPGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGRRLRRTWPEKFGRGNSNMNHFFISDICSGRLICDIANEMGQSLTPKCQSWDLSEMYQVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRIQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSVPPSEVDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDIRQQALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTDSVMIDTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNTTVLEVKGLDMKRREFCPLSRDVSIHVLNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKVITFVITKLSVAERAHALNEVMIKSNNLIPDPQYYLEKQIFAPVERLLERIDSFNVVRLSEALG 1242
                                   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       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810    || 852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052  ||  1069      1079      1089      1099      1109      1119      1129  ||  1173||    1195      1205      1215      1225      1235       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          815|                                                                                                                                                                                                           1055|                                                                 1132|   1174|                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           848                                                                                                                                                                                                            1063                                                                  1167    1187                                                       


Chain C from PDB  Type:DNA  Length:8
                                         
                4fxd C    1 CTGCCCGC    8


Chain D from PDB  Type:DNA  Length:8
                                         
                4fxd D    1 CTGCCCGC    8


Chain E from PDB  Type:RNA  Length:8
                                         
                4fxd E    1 GCGGGCAG    8


Chain F from PDB  Type:RNA  Length:8
                                         
                4fxd F    1 GCGGGCAG    8
   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 4FXD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

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 Related Entries

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        DPOA_YEAST | P13382: 3flo 3oiq 4b08 4c93 4fvm 4fyd

(-) 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
4fyd CRYSTAL STRUCTURE OF YEAST DNA POLYMERASE ALPHA BOUND TO DNA/RNA AND DGTP