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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 :  2.70
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 - 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
 
Molecule 2 - PRIMER STRAND
    Chains: P
    Engineered: YES
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES
 
Molecule 3 - TEMPLATE STRAND
    Chains: T
    Engineered: YES
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES

 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
1GOL1Ligand/IonGLYCEROL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:141 , ILE A:142 , GLU A:143 , ASP A:315 , DG P:11BINDING SITE FOR RESIDUE MG A 801
2AC2SOFTWAREGLU A:251 , HOH A:1125 , HOH A:1126 , HOH A:1235 , HOH A:1237BINDING SITE FOR RESIDUE MG A 802
3AC3SOFTWAREASP A:6 , TYR A:7 , HOH A:1236 , DG T:1BINDING SITE FOR RESIDUE MES A 803
4AC4SOFTWAREASP A:113 , ASN A:351 , GLU A:354 , TRP A:355 , LEU A:358 , LYS A:371 , ARG A:504 , DG T:3BINDING SITE FOR RESIDUE GOL A 804

(-) 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 4FLV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FLV)

(-) 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:757
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..eeeeeeeeee..eeeeeee.....eeeeee.hhhhhhhhh..eeee..eeee..eeeeeeeee..eeeeeeeee....hhhhhhhhhhhh...eeeee....hhhhhhhhhh............eeeeeeee............eeeeeeee..eeeeee........eee..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh............eeeee..eeeee....eeeehhhhhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh............eeeeeeee...hhhhhhhhh..............eee......eee....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeee....hhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeee..eeeee.....eeee.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhheeee...hhhhh...hhhhhhhhhhhhh........eeeeee.....hhhh.eee.hhh.......hhhhhhhhhhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4flv A  -2 HAGMIIDADYITEDGKPIIRIFKKEKGEFKVEYDRTFRPYIYALLKDDSAIDEVKKITAERHGKIVRITEVEKVQKKFLGRPIEVWKLYLEHPQDVPAIREKIREHPAVVDIFEYDIPFAKRYLIDKGLTPMEGNEELTFLAVDIETLYHEGEEFGKGPIIMISYADEEGAKVITWKSIDLPYVEVVSSEREMIKRLVKVIREKDPDVIITYNGDNFAFPYLLKRAEKLGIKLPLGRDNSEPKMQRMGDSLAVEIKGRIHFDLFPVIRRTINLPTYTLEAVYEAIFGKSKEKVYAHEIAEAWETGKGLERVAKYSMEDAKVTFELGKEFFPMEAQLARLVGQPVWDVSRSSTGNLVEWFLLRKAYERNELAPNKPDEREYERRLRESYEGKEPEKGLWEGIVSLDFRSLYPSIIITHNVSPDTLNRENCKEYDVAPQVGHRFCKDFPGFIPSLLGNLLEERQKIKKRMKESKDPVEKKLLDYRQRAIKILANSYYGYYGYAKARWYCKECAESVTAWGRQYIDLVRRELESRGFKVLYIDTDGLYATIPGAKHEEIKEKALKFVEYINSKLPGLLELEYEGFYARGFFVTKKKYALIDEEGKIVTRGLEIVRRDWSEIAKETQAKVLEAILKHGNVDEAVKIVKEVTEKLSKYEIPPEKLVIYEQITRPLSEYKAIGPHVAVAKRLAAKGVKVKPGMVIGYIVLRGDGPISKRAIAIEEFDPKKHKYDAEYYIENQVLPAVERILRAFGYRKEDLKY 757
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387|      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       
                                                                                                                                                                                                                                                                                                                                                                                                                               387|                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                391                                                                                                                                                                                                                                                                                                                                                                              


Chain P from PDB  Type:DNA  Length:11
                                           
                 4flv P   1 CGATCACGGGG  11
                                    10 


Chain T from PDB  Type:DNA  Length:13
                                             
                 4flv T   1 GGGTACGTGATCG  13
                                    10
   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 4FLV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4flw 4flx 4fly 4flz 4fm0 4fm1 4fm2

(-) Related Entries Specified in the PDB File

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