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(-) Description

Title :  CRYSTAL STRUCTURE OF A POLC-TYPE DNA POLYMERASE III EXONUCLEASE DOMAIN FROM THERMOTOGA MARITIMA
 
Authors :  J. B. Bonanno, M. Rutter, K. T. Bain, M. Izuka, V. Sridhar, D. Smith, S. Wa J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center Structural Genomics (Nysgxrc)
Date :  05 Mar 07  (Deposition) - 20 Mar 07  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Exonuclease, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. B. Bonanno, M. Rutter, K. T. Bain, M. Izuka, V. Sridhar, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of A Polc-Type Dna Polymerase Iii Exonuclease Domain From Thermotoga Maritima
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA POLYMERASE III POLC-TYPE
    Atcc43589
    ChainsA, B
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidMODIFIED PET26
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET
    Expression System Vector TypePLASMID
    FragmentEXONUCLEASE DOMAIN
    GenePOLC, TM_0576
    Organism ScientificTHERMOTOGA MARITIMA MSB8
    Organism Taxid243274
    StrainMSB8, DSM 3109, JCM 10099
    SynonymPOLIII

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2P1J)

(-) Sites  (0, 0)

(no "Site" information available for 2P1J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P1J)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:495 -Pro A:496
2Met A:519 -Met A:520

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P1J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P1J)

(-) Exons   (0, 0)

(no "Exon" information available for 2P1J)

(-) 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:164
 aligned with DPO3_THEMA | Q9ZHF6 from UniProtKB/Swiss-Prot  Length:1367

    Alignment length:164
                                   366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516    
           DPO3_THEMA   357 TFVVLDFETTGLDPQVDEIIEIGAVKIQGGQIVDEYHTLIKPSREISRKSSEITGITQEMLENKRSIEEVLPEFLGFLEDSIIVAHNANFDYRFLRLWIKKVMGLDWERPYIDTLALAKSLLKLRSYSLDSVVEKLGLGPFRHHRALDDARVTAQVFLRFVEMM 520
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2p1jA01 A:357-494  [code=3.30.420.10, no name defined]                                                                                    2p1jA02 A:495-520          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.........eeeeeeeeee..eeeeeeeee.......hhhhhhhhh.hhhhhh...hhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh......eeehhhhhhhhh.....hhhhhhhhh.......hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p1j A 357 TFVVLDFETTGLDPQVDEIIEIGAVKIQGGQIVDEYHTLIKPSREISRKSSEITGITQEMLENKRSIEEVLPEFLGFLEDSIIVAHNANFDYRFLRLWIKKVMGLDWERPYIDTLALAKSLLKLRSYSLDSVVEKLGLGPFRHHRALDDARVTAQVFLRFVEMM 520
                                   366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516    

Chain B from PDB  Type:PROTEIN  Length:171
 aligned with DPO3_THEMA | Q9ZHF6 from UniProtKB/Swiss-Prot  Length:1367

    Alignment length:171
                                   366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526 
           DPO3_THEMA   357 TFVVLDFETTGLDPQVDEIIEIGAVKIQGGQIVDEYHTLIKPSREISRKSSEITGITQEMLENKRSIEEVLPEFLGFLEDSIIVAHNANFDYRFLRLWIKKVMGLDWERPYIDTLALAKSLLKLRSYSLDSVVEKLGLGPFRHHRALDDARVTAQVFLRFVEMMKKIGITK 527
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2p1jB01 B:357-494  [code=3.30.420.10, no name defined]                                                                                    2p1jB02 B:495-520         ------- CATH domains
           Pfam domains (1) PHP-2p1jB01 B:357-522                                                                                                                                                 ----- Pfam domains (1)
           Pfam domains (2) PHP-2p1jB02 B:357-522                                                                                                                                                 ----- Pfam domains (2)
           Pfam domains (3) --RNase_T-2p1jB03 B:359-513                                                                                                                                  -------------- Pfam domains (3)
           Pfam domains (4) --RNase_T-2p1jB04 B:359-513                                                                                                                                  -------------- Pfam domains (4)
         Sec.struct. author .eeeeeeee.........eeeeeeeeee..eeeeeeeee.......hhhhhhhhh.hhhhhh...hhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh......eeehhhhhhhhh.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p1j B 357 TFVVLDFETTGLDPQVDEIIEIGAVKIQGGQIVDEYHTLIKPSREISRKSSEITGITQEMLENKRSIEEVLPEFLGFLEDSIIVAHNANFDYRFLRLWIKKVMGLDWERPYIDTLALAKSLLKLRSYSLDSVVEKLGLGPFRHHRALDDARVTAQVFLRFVEMMKKEGHHH 527
                                   366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526 

   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 2P1J)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Family: PHP (10)
1aPHP-2p1jB01B:357-522
1bPHP-2p1jB02B:357-522
(-)
Clan: RNase_H (288)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DPO3_THEMA | Q9ZHF6)
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: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:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    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: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:0006261    DNA-dependent DNA replication    A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  Cis Peptide Bonds
    Gly A:495 - Pro A:496   [ RasMol ]  
    Met A:519 - Met A:520   [ RasMol ]  
 

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