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(-) Description

Title :  STRUCTURE OF FAMILY X DNA POLYMERASE FROM DEINOCOCCUS RADIODURANS
 
Authors :  N. Leulliot, L. Cladiere, F. Lecointe, D. Durand, U. Hubscher, H. Van Tilbeurgh
Date :  27 Jan 09  (Deposition) - 10 Feb 09  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.46
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Saxs, Dna Repair, Dna Polymerase, Dna Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Leulliot, L. Cladiere, F. Lecointe, D. Durand, U. Hubscher, H. Van Tilbeurgh
The Family X Dna Polymerase From Deinococcus Radioduran Adopts A Non-Standard Extended Conformation.
J. Biol. Chem. V. 284 11992 2009
PubMed-ID: 19251692  |  Reference-DOI: 10.1074/JBC.M809342200

(-) Compounds

Molecule 1 - POLYMERASE X
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1HG2Ligand/IonMERCURY (II) ION
2ZN7Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:339 , HIS A:364 , HIS A:518BINDING SITE FOR RESIDUE ZN A1565
2AC2SOFTWAREHIS A:332 , HIS A:334 , GLU A:401 , ASP A:516 , ZN A:1567BINDING SITE FOR RESIDUE ZN A1566
3AC3SOFTWAREGLU A:401 , HIS A:428 , HIS A:456 , ZN A:1566BINDING SITE FOR RESIDUE ZN A1567
4AC4SOFTWAREPHE B:431 , ALA B:469BINDING SITE FOR RESIDUE ZN A1569
5AC5SOFTWAREASP B:339 , HIS B:364 , HIS B:518BINDING SITE FOR RESIDUE ZN B1565
6AC6SOFTWAREHIS B:332 , HIS B:334 , GLU B:401 , ASP B:516 , ZN B:1567BINDING SITE FOR RESIDUE ZN B1566
7AC7SOFTWAREGLU B:401 , HIS B:428 , HIS B:456 , ZN B:1566BINDING SITE FOR RESIDUE ZN B1567
8AC8SOFTWAREGLY B:204 , PRO B:206 , CYS B:237 , ALA B:238BINDING SITE FOR RESIDUE HG B1568
9AC9SOFTWAREGLY A:204 , PRO A:206 , CYS A:237BINDING SITE FOR RESIDUE HG A1568

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W9M)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ser A:251 -Gly A:252
2Asp A:496 -Leu A:497
3Leu B:27 -Gly B:28
4Ser B:251 -Gly B:252
5Asp B:496 -Leu B:497

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W9M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W9M)

(-) Exons   (0, 0)

(no "Exon" information available for 2W9M)

(-) 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:541
 aligned with Q9RX48_DEIRA | Q9RX48 from UniProtKB/TrEMBL  Length:572

    Alignment length:557
                                    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       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       
         Q9RX48_DEIRA     8 PSRHRLVHALERTADLLDILGGEDFKSRAYRSAARSLEELNEETPELLAREFTGIPKVGKGIAAELSDFARSGTFAPLEAAAGQLPPGLLDLLGVRGLGPKKIRSLWLAGIDSLERLREAAESGELAGLKGFGAKSAATILENVVFLFEARQRQSLRAGLAVAEELAGALTDLSPAPAGDVRRGLETVRAAELTVTGTPDDVLARLPELTVQGDGVLSGDYEGVPVEIACAPAEARGALDLLRSGEHFAGQVQAAAQARGFTLTAGGLSRGDEVLPTPTEAVVFHALDLPFRPAEYREPEHDDLWQTLPDPAELVTVGDLRGMIHTHSTWSDGGASIREMAEATLTLGHEFLGTADHSRAAYYANGLTIERLREQLKEIRELQRAGLPIVAGSEVDILDDGSLDFPDDVLGELDYVVVSVHSNFTLDAARQTERLIRAVSHPLVTVLGHATGRLLLRRPGYALDLDAVLGACEANGTVVEINANAARLDLDWREALRWRERLKFAINTDAHVPGGLRDARYGVMQARKAGLTPAHVVNSLGRAEFLDFVARQRAARG 564
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh---..hhhhhhhhhhhhhh..----------.......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh.eehhhhhhh..ee..eeeeee.hhhhhhhhh...ee.---.eeeee..eeeeeeee...hhhhhhhhh.hhhhhhhhhhhhhh...eee..eeee..eee...hhhhhhhhh.....hhhhhhhhhh.......hhhhh.hhhhh.eeeee.........hhhhhhhhhhhh...eeee.ee...hhhhh..hhhhhhhhhhhhhhhhhh...ee.eeeee.........hhhhhh...eeeee.......hhhhhhhhhhhhhh.....ee................hhhhhhhhhhhhh.eeeee........hhhhhhhhh....eeee....hhhhhhhhhhhhhhhhhh..hhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w9m A   8 PSRHRLVHALERTADLLDIL---DFKSRAYRSAARSLEELN----------FTGIPKVGKGIAAELSDFARSGTFAPLEAAAGQLPPGLLDLLGVRGLGPKKIRSLWLAGIDSLERLREAAESGELAGLKGFGAKSAATILENVVFLFEARQRQSLRAGLAVAEELAGALTDLSPAPAGDVRRGLETVRAAELTVTGTPDDVLARLPELTVQ---VLSGDYEGVPVEIACAPAEARGALDLLRSGEHFAGQVQAAAQARGFTLTAGGLSRGDEVLPTPTEAVVFHALDLPFRPAEYREPEHDDLWQTLPDPAELVTVGDLRGMIHTHSTWSDGGASIREMAEATLTLGHEFLGTADHSRAAYYANGLTIERLREQLKEIRELQRAGLPIVAGSEVDILDDGSLDFPDDVLGELDYVVVSVHSNFTLDAARQTERLIRAVSHPLVTVLGHATGRLLLRRPGYALDLDAVLGACEANGTVVEINANAARLDLDWREALRWRERLKFAINTDAHVPGGLRDARYGVMQARKAGLTPAHVVNSLGRAEFLDFVARQRAARG 564
                                    17        27   |    37        47|        - |      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       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       
                                              27  31               48         59                                                                                                                                                             219 223                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:559
 aligned with Q9RX48_DEIRA | Q9RX48 from UniProtKB/TrEMBL  Length:572

    Alignment length:559
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555         
         Q9RX48_DEIRA     6 DAPSRHRLVHALERTADLLDILGGEDFKSRAYRSAARSLEELNEETPELLAREFTGIPKVGKGIAAELSDFARSGTFAPLEAAAGQLPPGLLDLLGVRGLGPKKIRSLWLAGIDSLERLREAAESGELAGLKGFGAKSAATILENVVFLFEARQRQSLRAGLAVAEELAGALTDLSPAPAGDVRRGLETVRAAELTVTGTPDDVLARLPELTVQGDGVLSGDYEGVPVEIACAPAEARGALDLLRSGEHFAGQVQAAAQARGFTLTAGGLSRGDEVLPTPTEAVVFHALDLPFRPAEYREPEHDDLWQTLPDPAELVTVGDLRGMIHTHSTWSDGGASIREMAEATLTLGHEFLGTADHSRAAYYANGLTIERLREQLKEIRELQRAGLPIVAGSEVDILDDGSLDFPDDVLGELDYVVVSVHSNFTLDAARQTERLIRAVSHPLVTVLGHATGRLLLRRPGYALDLDAVLGACEANGTVVEINANAARLDLDWREALRWRERLKFAINTDAHVPGGLRDARYGVMQARKAGLTPAHVVNSLGRAEFLDFVARQRAARG 564
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHP-2w9mB01 B:329-504                                                                                                                                                           ------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHP-2w9mB02 B:329-504                                                                                                                                                           ------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.......hhhhhhhh........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh.eehhhhhhh..ee..eeeeee.hhhhhhhhh...ee....eeeeee..eeeeeeee...hhhhhhhhh.hhhhhhhhhhhhhh...eee..eeee..eee...hhhhhhhhh.....hhhhhhhhhh.......hhhhh.hhhhh.eeeee.........hhhhhhhhhhhh...eeee.ee...hhhhh..hhhhhhhhhhhhhhhhhh...ee.eeeee.........hhhhhh...eeeee.......hhhhhhhhhhhhhh.....ee................hhhhhhhhhhhhh.eeeee........hhhhhhhhh....eeee....hhhhhhhhhhhhhhhhhh..hhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w9m B   6 DAPSRHRLVHALERTADLLDILGGEDFKSRAYRSAARSLEELNEETPELLAREFTGIPKVGKGIAAELSDFARSGTFAPLEAAAGQLPPGLLDLLGVRGLGPKKIRSLWLAGIDSLERLREAAESGELAGLKGFGAKSAATILENVVFLFEARQRQSLRAGLAVAEELAGALTDLSPAPAGDVRRGLETVRAAELTVTGTPDDVLARLPELTVQGDGVLSGDYEGVPVEIACAPAEARGALDLLRSGEHFAGQVQAAAQARGFTLTAGGLSRGDEVLPTPTEAVVFHALDLPFRPAEYREPEHDDLWQTLPDPAELVTVGDLRGMIHTHSTWSDGGASIREMAEATLTLGHEFLGTADHSRAAYYANGLTIERLREQLKEIRELQRAGLPIVAGSEVDILDDGSLDFPDDVLGELDYVVVSVHSNFTLDAARQTERLIRAVSHPLVTVLGHATGRLLLRRPGYALDLDAVLGACEANGTVVEINANAARLDLDWREALRWRERLKFAINTDAHVPGGLRDARYGVMQARKAGLTPAHVVNSLGRAEFLDFVARQRAARG 564
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555
   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 2W9M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W9M)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Amidohydrolase (126)
(-)
Family: PHP (10)
(-)
Deinococcus radiodurans (1)
1aPHP-2w9mB01B:329-504
1bPHP-2w9mB02B:329-504

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9RX48_DEIRA | Q9RX48)
molecular function
    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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    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.

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  2w9m
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 Related Entries

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