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(-) Description

Title :  CRYSTAL STRUCTURE OF DNA-DIRECTED DNA POLYMERASE
 
Authors :  D. U. Kim, H. S. Cho
Date :  15 Feb 07  (Deposition) - 22 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna-Directed Dna Polymerase, Pfu, Nuclease, Hydrolase, Transferase, Dna-Binding, Endonuclease, Dna Replication, Nucleotidyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. W. Kim, D. U. Kim, J. K. Kim, L. W. Kang, H. S. Cho
Crystal Structure Of Pfu, The High Fidelity Dna Polymerase From Pyrococcus Furiosus.
Int. J. Biol. Macromol. V. 42 356 2008
PubMed-ID: 18355915  |  Reference-DOI: 10.1016/J.IJBIOMAC.2008.01.010

(-) Compounds

Molecule 1 - DNA POLYMERASE
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(BE3)
    Expression System Taxid: 511693
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: PFU POLYMERASE, DNA POLYMERASE PFU

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:4 , VAL A:5 , GLU A:251 , ASP A:343BINDING SITE FOR RESIDUE MN A1758
2AC2SOFTWAREASP A:141 , ILE A:142 , GLU A:143 , ASP A:315BINDING SITE FOR RESIDUE MN A1759

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:429 -A:443
2A:507 -A:510

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JGU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_BPS00116 DNA polymerase family B signature.DPOL_PYRFU539-547  1A:539-547

(-) Exons   (0, 0)

(no "Exon" information available for 2JGU)

(-) 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:712
 aligned with DPOL_PYRFU | P61875 from UniProtKB/Swiss-Prot  Length:775

    Alignment length:758
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       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       670       680       690       700       710       720       730       740       750        
           DPOL_PYRFU     1 MILDVDYITEEGKPVIRLFKKENGKFKIEHDRTFRPYIYALLRDDSKIEEVKKITGERHGKIVRIVDVEKVEKKFLGKPITVWKLYLEHPQDVPTIREKVREHPAVVDIFEYDIPFAKRYLIDKGLIPMEGEEELKILAFDIETLYHEGEEFGKGPIIMISYADENEAKVITWKNIDLPYVEVVSSEREMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLTIGRDGSEPKMQRIGDMTAVEVKGRIHFDLYHVITRTINLPTYTLEAVYEAIFGKPKEKVYADEIAKAWESGENLERVAKYSMEDAKATYELGKEFLPMEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWENIVYLDFRALYPSIIITHNVSPDTLNLEGCKNYDIAPQVGHKFCKDIPGFIPSLLGHLLEERQKIKTKMKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLYATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGFYKRGFFVTKKRYAVIDEEGKVITRGLEIVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEYKAIGPHVAVAKKLAAKGVKIKPGMVIGYIVLRGDGPISNRAILAEEYDPKKHKYDAEYYIENQVLPAVLRILEGFGYRKEDLRY 758
               SCOP domains d2jgua1 A:1-347 automated matches                                                                                                                                                                                                                                                                                                                          d2jgua2 A:348-758 automated matches                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------DNA_pol_B_exo1-2jguA02 A:127-278                                                                                                                        ----------------------------------------------------------------------DNA_pol_B-2jguA01 A:349-758                                                                                                                                                                                                                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------DNA_pol_B_exo1-2jguA03 A:127-278                                                                                                                        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeeeeeee....eeeeeeee....eeeeee.....eeeeee.hhhhhhh...................eeeeee..eeeeeeeee.........hhhhhhh...eeeee....hhhhhhhhhh............eeeeeee...............eeeee....eeeee........eee..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhh.................eeee....eeee....eeeehhhhhh........hhhhhhhhhhh........hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhhh................eeeeeeeee.hhhhhhhhhh..hhhh........eee......eee....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..eeeee.......hhhhhhhhhhhhhhh.......eeeeeeeeeeeeee..eeeeee....eeee...------hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.............----------------..........................------------------------.hhhhhhhhhhhhhhhhhhh...hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jgu A   1 MILDVDYITEEGKPVIRLFKKENGKFKIEHDRTFRPYIYALLRDDSKIEEVKKITGERHGKIVRIVDVEKVEKKFLGKPITVWKLYLEHPQDVPTLREKVREHPAVVDIFEYDIPFAKRYLIDKGLIPMEGEEELKILAFDIETLYHEGEEFGKGPIIMISYADENEARVITWKNIDLPYVESVSTEKEMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLTIGRDGSEPKMQRIGDMTAVEVKGRIHFDLYHVIRTTINLPTYTLEAVYEAIFGKPKEKVYADEIAKAWESGENLERVAKYSMEDAKATYELGKEFLPMEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWENIVYLDYKSLYPSIIITHNVSPDTLNLEGCKNYDIAPQVGHKFCKDIPGFIPSLLGHLLEERQKIKTKMKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLYATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGFYKRGFFVTKKRYAVIDEEGKVITRGLE------SEIAKETQARVLETILKHGDVEEAVRIVKEVIQKLANYEIPPEKLA----------------PHVAVAKKLAAKGVKIKPGMVIGYIV------------------------DAEYYIENQVLPAVLRILEGFGYRKEDLRY 758
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       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 |       -       680       690       700   |     -         -       730       740       750        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           610    617                                          662              679                      704                      729
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: DNA_pol_B-like (44)
(-)
Clan: RNase_H (288)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPOL_PYRFU | P61875)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    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:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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: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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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  2jgu
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  DPOL_PYRFU | P61875
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  2.7.7.7
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOL_PYRFU | P61875: 3a2f 4ahc 4ail

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2JGU)