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(-) Description

Title :  PYROCOCCUS ABYSSI B FAMILY DNA POLYMERASE BOUND TO A DSDNA, IN EDITION MODE
 
Authors :  J. Gouge, M. Delarue
Date :  15 Jun 12  (Deposition) - 29 Aug 12  (Release) - 17 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Dna Polymerase, Dna Binding, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Gouge, C. Ralec, G. Henneke, M. Delarue
Molecular Recognition Of Canonical And Deaminated Bases By P. Abyssi Family B Dna Polymerase.
J. Mol. Biol. V. 423 315 2012
PubMed-ID: 22902479  |  Reference-DOI: 10.1016/J.JMB.2012.07.025

(-) Compounds

Molecule 1 - TEMPLATE STRAND
    Chains: T
    Engineered: YES
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES
 
Molecule 2 - PRIMER STRAND
    Chains: P
    Engineered: YES
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES
 
Molecule 3 - DNA POLYMERASE 1
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: POLI, POL, PYRAB17200, PAB1128
    Mutation: YES
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 272844
    Strain: GE5 / ORSAY
    Synonym: PAB POLYMERASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1DU1Mod. Residue
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:141 , GLU A:143 , ASP A:315 , HOH A:944 , HOH A:946 , HOH A:948BINDING SITE FOR RESIDUE MG A 801
2AC2SOFTWAREHOH A:901 , HOH A:903 , HOH A:904 , HOH A:908 , HOH A:913 , HOH A:943BINDING SITE FOR RESIDUE MG A 802
3AC3SOFTWAREASP A:6 , TYR A:7 , HOH A:904 , HOH A:1012 , DG T:1 , HOH T:101BINDING SITE FOR RESIDUE MES A 803

(-) 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 4FLY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FLY)

(-) 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:755
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee..eeeeeeeeee..eeeeeee.....eeeeee.hhhhhhhhh..eeee..eeee..eeeeeeeee..eeeeeeeee....hhhhhhhhhhhhh..eeeee....hhhhhhhhhh............eeeeeeee............eeeeeeee..eeeeee........eee..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.............eeeee..eeeee....eeeehhhhhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhh........hhhhhhhhhhh..........eeeeeeee...hhhhhhhhh..............eee......eee....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeee....hhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeee..eeeee.....eeee.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhheeee...hhhhh...hhhhhhhhhhhhh........eeeeee.....hhhh.eee.hhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fly A  -1 AGMIIDADYITEDGKPIIRIFKKEKGEFKVEYDRTFRPYIYALLKDDSAIDEVKKITAERHGKIVRITEVEKVQKKFLGRPIEVWKLYLEHPQDVPAIREKIREHPAVVDIFEYDIPFAKRYLIDKGLTPMEGNEELTFLAVDIETLYHEGEEFGKGPIIMISYADEEGAKVITWKSIDLPYVEVVSSEREMIKRLVKVIREKDPDVIITYNGDNFAFPYLLKRAEKLGIKLPLGRDNSEPKMQRMGDSLAVEIKGRIHFDLFPVIRRTINLPTYTLEAVYEAIFGKSKEKVYAHEIAEAWETGKGLERVAKYSMEDAKVTFELGKEFFPMEAQLARLVGQPVWDVSRSSTGNLVEWFLLRKAYERNELAPNKPDEREYERRLRESYEKEPEKGLWEGIVSLDFRSLYPSIIITHNVSPDTLNRENCKEYDVAPQVGHRFCKDFPGFIPSLLGNLLEERQKIKKRMKESKDPVEKKLLDYRQRAIKILANSYYGYYGYAKARWYCKECAESVTAWGRQYIDLVRRELESRGFKVLYIDTDGLYATIPGAKHEEIKEKALKFVEYINSKLPGLLELEYEGFYARGFFVTKKKYALIDEEGKIVTRGLEIVRRDWSEIAKETQAKVLEAILKHGNVDEAVKIVKEVTEKLSKYEIPPEKLVIYEQITRPLSEYKAIGPHVAVAKRLAAKGVKVKPGMVIGYIVLRGDGPISKRAIAIEEFDPKKHKYDAEYYIENQVLPAVERILRAFGYRKEDLKY 757
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752     
                                                                                                                                                                                                                                                                                                                                                                                                                             386|                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                              391                                                                                                                                                                                                                                                                                                                                                                              


Chain P from PDB  Type:DNA  Length:8
                                        
                 4fly P   1 CGATCACG   8


Chain T from PDB  Type:DNA  Length:13
                                             
                 4fly T   1 GxGTACGTGATCG  13
                             |      10   
                             2-DU
   Legend:   → Mismatch (orange background)
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  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 4FLY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  4fly
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  DPOL_PYRAB | P0CL77
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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_PYRAB | P0CL77: 4flt 4flu 4flv 4flw 4flx 4flz 4fm0 4fm1 4fm2

(-) Related Entries Specified in the PDB File

4flt 4flu 4flv 4flw 4flx 4flz 4fm0 4fm1 4fm2