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(-) Description

Title :  STRUCTURE OF MSDPO4
 
Authors :  D. T. Nair, A. Sharma
Date :  22 Jan 12  (Deposition) - 22 Aug 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Y-Family, Dna Polymerase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Sharma, V. Subramanian, D. T. Nair
The Pad Region In The Mycobacterial Dinb Homologue Mspoliv Exhibits Positional Heterogeneity.
Acta Crystallogr. , Sect. D V. 68 960 2012
PubMed-ID: 22868761  |  Reference-DOI: 10.1107/S0907444912017623

(-) Compounds

Molecule 1 - DNA POLYMERASE IV 1
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4P1
    Expression System StrainC41DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDINB, DINB1, MSMEG_1014, MSMEG_2294
    Organism ScientificMYCOBACTERIUM SMEGMATIS
    Organism Taxid246196
    StrainMC2 155
    SynonymPOL IV 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

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

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(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:159 -Pro A:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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:232
 aligned with A0QR77_MYCS2 | A0QR77 from UniProtKB/TrEMBL  Length:356

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
         A0QR77_MYCS2     2 TKWVLHVDLDQFLASVELRRRPDLRGQPVIVGGSGDPSEPRKVVTCASYEAREFGVHAGMPLRAAARRCPDATFLPSDPAAYDEASEQVMGLLRDLGHPLEVWGWDEAYLGADLPDESDPVEVAERIRTVVAAETGLSCSVGISDNKQRAKVATGFAKPAGIYVLTEANWMTVMGDRPPDALWGVGPKTTKKLAAMGITTVADLAVTDPSVLTTAFGPSTGLWLLLLAKGGGDTEVSS 239
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhhhhhhhhhhh...eeeee.------..eeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh....eeee...eeeeeee.....hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eee....hhhhhhh..hhhhh...hhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dez A   2 TKWVLHVDLDQFLASVELRRRPDLRGQPVIVGGS------RKVVTCASYEAREFGVHAGMPLRAAARRCPDATFLPSDPAAYDEASEQVMGLLRDLGHPLEVWGWDEAYLGADLPDESDPVEVAERIRTVVAAETGLSCSVGISDNKQRAKVATGFAKPAGIYVLTEANWMTVMGDRPPDALWGVGPKTTKKLAAMGITTVADLAVTDPSVLTTAFGPSTGLWLLLLAKGGGDTEVSS 239
                                    11        21        31   |     -|       51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
                                                            35     42                                                                                                                                                                                                     

   Legend:   → Mismatch (orange background)
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  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 4DEZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (A0QR77_MYCS2 | A0QR77)
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:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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.
    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:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
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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