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(-) Description

Title :  CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS DNA POLYMERASE/PCNA MONOMER MUTANT COMPLEX
 
Authors :  H. Nishida, Y. Ishino, K. Morikawa
Date :  15 May 09  (Deposition) - 03 Nov 09  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Replication, Dna-Binding, Dna-Directed Dna Polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase, Transferase/Replication Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Nishida, K. Mayanagi, S. Kiyonari, Y. Sato, Y. Ishino, K. Morikawa
Structural Determinant For Switching Between The Polymerase And Exonuclease Modes In The Pcna-Replicative Dna Polymerase Complex
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA POLYMERASE
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: POL, PF0212
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: REPLICATIVE B-TYPE POLYMERASE, PFU POLYMERASE
 
Molecule 2 - DNA POLYMERASE SLIDING CLAMP
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PCN, PF0983
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: DNA CLAMP, PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG, PCNA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 18)

Asymmetric/Biological Unit (1, 18)
No.NameCountTypeFull Name
1MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3A2F)

(-) 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 3A2F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A2F)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PCNA_1PS01251 Proliferating cell nuclear antigen signature 1.PCNA_PYRFU35-58  1B:35-58
2DNA_POLYMERASE_BPS00116 DNA polymerase family B signature.DPOL_PYRFU539-547  1A:539-547

(-) Exons   (0, 0)

(no "Exon" information available for 3A2F)

(-) 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:773
 aligned with DPOL_PYRFU | P61875 from UniProtKB/Swiss-Prot  Length:775

    Alignment length:773
                                    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       760       770   
           DPOL_PYRFU     1 MILDVDYITEEGKPVIRLFKKENGKFKIEHDRTFRPYIYALLRDDSKIEEVKKITGERHGKIVRIVDVEKVEKKFLGKPITVWKLYLEHPQDVPTIREKVREHPAVVDIFEYDIPFAKRYLIDKGLIPMEGEEELKILAFDIETLYHEGEEFGKGPIIMISYADENEAKVITWKNIDLPYVEVVSSEREMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLTIGRDGSEPKMQRIGDMTAVEVKGRIHFDLYHVITRTINLPTYTLEAVYEAIFGKPKEKVYADEIAKAWESGENLERVAKYSMEDAKATYELGKEFLPMEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWENIVYLDFRALYPSIIITHNVSPDTLNLEGCKNYDIAPQVGHKFCKDIPGFIPSLLGHLLEERQKIKTKMKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLYATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGFYKRGFFVTKKRYAVIDEEGKVITRGLEIVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEYKAIGPHVAVAKKLAAKGVKIKPGMVIGYIVLRGDGPISNRAILAEEYDPKKHKYDAEYYIENQVLPAVLRILEGFGYRKEDLRYQKTRQVGLTSWLNIK 773
               SCOP domains d3a2fa1 A:1-347 automated matches                                                                                                                                                                                                                                                                                                                          d3a2fa2 A:348-773 automated matches                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..eeeeeeeee....eeeeee.....eeeeee....hhhhhh..eee....eee.....ee..ee..ee..eeeee....hhhhhhhhhhh....eeeee....hhhhhhhhhh............eeeeeee...............eeeeee..eeeeee........eee..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.............eeeee..eeeee....eeeehhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhh.ee.....hhhhhhhhhh.......ee.....eeeeeeeeee.hhhhhhhhhh..hhhhh.......eee......eee....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeee....hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeeee..eeeee.....eeee.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhheeee...........hhhhhhhhhhhhh........eeeeee......hhh.eee...........hhhhhhhhhhhhhhhhhhhhhh.hhhhhh....ee..hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a2f A   1 mILDVDYITEEGKPVIRLFKKENGKFKIEHDRTFRPYIYALLRDDSKIEEVKKITGERHGKIVRIVDVEKVEKKFLGKPITVWKLYLEHPQDVPTIREKVREHPAVVDIFEYDIPFAKRYLIDKGLIPmEGEEELKILAFDIETLYHEGEEFGKGPIImISYADENEAKVITWKNIDLPYVEVVSSEREmIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLTIGRDGSEPKmQRIGDmTAVEVKGRIHFDLYHVITRTINLPTYTLEAVYEAIFGKPKEKVYADEIAKAWESGENLERVAKYSmEDAKATYELGKEFLPmEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWENIVYLDFRALYPSIIITHNVSPDTLNLEGCKNYDIAPQVGHKFCKDIPGFIPSLLGHLLEERQKIKTKmKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLYATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGFYKRGFFVTKKRYAVIDEEGKVITRGLEIVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEYKAIGPHVAVAKKLAAKGVKIKPGmVIGYIVLRGDGPISNRAILAEEYDPKKHKYDAEYYIENQVLPAVLRILEGFGYRKEDLRYQKTRQVGLTSWLNIK 773
                            |       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       760       770   
                            |                                                                                                                             129-MSE                       159-MSE                        190-MSE                                            241-MSE |                                                               313-MSE         329-MSE                                                                                                                                    468-MSE                                                                                                                                                                                                                               698-MSE                                                                       
                            1-MSE                                                                                                                                                                                                                                               247-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with PCNA_PYRFU | O73947 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
           PCNA_PYRFU     2 PFEIVFEGAKEFAQLIDTASKLIDEAAFKVTEDGISMRAMDPSRVVLIDLNLPSSIFSKYEVVEPETIGVNMDHLKKILKRGKAKDTLILKKGEENFLEITIQGTATRTFRVPLIDVEEMEVDLPELPFTAKVVVLGEVLKDAVKDASLVSDSIKFIARENEFIMKAEGETQEVEIKLTLEDEGLLDIEVQEETKSAYGVSYLSDMVKGLGKADEVTIKFGNEMPMQMEYYIRDEGRLTFLLAPRVE 248
               SCOP domains d3a2fb1 B:2-117 automated matches                                                                                   d3a2fb2 B:118-248 automated matches                                                                                                 SCOP domains
               CATH domains 3a2fB00 B:2-248  [code=3.70.10.10, no name defined]                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhh.....eeeeeee..eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhh......eeeeee....eeeeeee....eeeeee.................eeeeeehhhhhhhhhhhh....eeeeeee..eeeeeee....eeeeeehhhhh.eeeeee...eeeeeehhhhhhhhh......eeeeee.....eeeeeee...eeeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: B:35-58    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a2f B   2 PFEIVFEGAKEFAQLIDTASKLIDEAAFKVTEDGISmRAmDPSRVVLIDLNLPSSIFSKYEVVEPETIGVNLDHLKKILKRGKAKDTLILKKGEENFLEITIQGTATRTFRVPLIDVEEmEVDLPELPFTAKVVVLGEVLKAAVKAASLVSDSIKFIARENEFImKAEGETQEVEIKLTLEDEGLLDIEVQEETKSAYGVSYLSDmVKGLGKADEVTIKFGNEmPmQmEYYIRDEGRLTFLLAPRVE 248
                                    11        21        31      | 41        51        61        71        81        91       101       111       121       131       141       151       161    |  171       181       191       201     | 211       221   | | 231       241       
                                                               38-MSE                                                                            121-MSE                                      166-MSE                                  207-MSE           225-MSE                   
                                                                  41-MSE                                                                                                                                                                                   227-MSE                 
                                                                                                                                                                                                                                                             229-MSE
   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  (3, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A2F)

(-) Gene Ontology  (15, 17)

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.

Chain B   (PCNA_PYRFU | O73947)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030337    DNA polymerase processivity factor activity    An enzyme regulator activity that increases the processivity of polymerization by DNA polymerase, by allowing the polymerase to move rapidly along DNA while remaining topologically bound to it.
biological process
    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:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.

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  3a2f
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  DPOL_PYRFU | P61875
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  PCNA_PYRFU | O73947
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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: 2jgu 4ahc 4ail
        PCNA_PYRFU | O73947: 1ge8 1isq 1iz4 1iz5 5auj

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3A2F)