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(-) Description

Title :  STRUCTURE OF POLYMERASE-DNA COMPLEX, DNA
 
Authors :  D. T. Nair, A. Sharma
Date :  14 Jan 13  (Deposition) - 17 Apr 13  (Release) - 29 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A,B,C,F,G,H
Biol. Unit 1:  B,C,G  (1x)
Biol. Unit 2:  A,F,H  (1x)
Keywords :  Dna Polymerase, Y-Family, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Sharma, J. Kottur, N. Narayanan, D. T. Nair
A Strategically Located Serine Residue Is Critical For The Mutator Activity Of Dna Polymerase Iv From Escherichia Coli
Nucleic Acids Res. V. 41 5104 2013
PubMed-ID: 23525461  |  Reference-DOI: 10.1093/NAR/GKT146

(-) Compounds

Molecule 1 - DNA POLYMERASE IV
    Chains: B, A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C41DE3
    Expression System Taxid: 562
    Gene: B0231, DINB, DINP, JW0221
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: POL IV
 
Molecule 2 - DNA (5'- D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
    Chains: C, F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*CP*TP*A*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3')
    Chains: G, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCFGH
Biological Unit 1 (1x):  BC G 
Biological Unit 2 (1x): A  F H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1DCP2Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2DOC2Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1DCP1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1DCP1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:8 , MET B:9 , ASP B:10 , CYS B:11 , PHE B:12 , PHE B:13 , SER B:42 , THR B:43 , SER B:55 , ASP B:103 , GLU B:104 , LYS B:157 , MG B:402 , HOH B:530 , DA C:840 , DOC G:873BINDING SITE FOR RESIDUE DCP B 401
2AC2SOFTWAREASP B:8 , MET B:9 , ASP B:103 , GLU B:104 , DCP B:401BINDING SITE FOR RESIDUE MG B 402
3AC3SOFTWAREASP A:8 , MET A:9 , ASP A:10 , CYS A:11 , PHE A:12 , PHE A:13 , SER A:42 , THR A:43 , ARG A:49 , ASP A:103 , GLU A:104 , LYS A:157 , MG A:402 , HOH A:507 , HOH A:514 , HOH A:523 , HOH A:547 , HOH A:548 , DA F:840 , DG F:841 , DOC H:873 , HOH H:905BINDING SITE FOR RESIDUE DCP A 401
4AC4SOFTWAREASP A:8 , MET A:9 , ASP A:103 , DCP A:401BINDING SITE FOR RESIDUE MG A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IRK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys B:157 -Pro B:158
2Lys A:157 -Pro A:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IRK)

(-) 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:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhhhhhhh...eeee........eeeehhhhhh.......hhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh....eeeee..eeeee.........hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhh.......eee....hhhhhhhh.hhhhh...hhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee....eeeeeee....hhhhhhhhhhhhhhhhh....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4irk A   0 GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALALCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCGDVQACDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP 341
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  


Chain B from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhhhhhhh...eeee........eeeehhhhhhh......hhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhh..eeeee..eeeee.........hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh......eee....hhhhhhhh.hhhhh...hhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhh...............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh........eeeeeeee....eeeeeee....hhhhhhhhhhhhhhhhh....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4irk B   0 GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALALCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCGDVQACDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP 341
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  


Chain C from PDB  Type:DNA  Length:18
                                                  
                 4irk C 837 TCTAGGGTCCTAGGACCC 854
                                   846        


Chain F from PDB  Type:DNA  Length:18
                                                  
                 4irk F 837 TCTAGGGTCCTAGGACCC 854
                                   846        


Chain G from PDB  Type:DNA  Length:14
                                              
                 4irk G 860 GGGTCCTAGGACCc 873
                                   869   |
                                       873-DOC


Chain H from PDB  Type:DNA  Length:14
                                              
                 4irk H 860 GGGTCCTAGGACCc 873
                                   869   |
                                       873-DOC
   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 4IRK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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  4irk
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  DPO4_ECOLI | Q47155
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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
        DPO4_ECOLI | Q47155: 1ok7 1unn 4ir1 4ir9 4irc 4ird 4q43 4q44 4q45 4r8u 5c5j

(-) Related Entries Specified in the PDB File

4ir1 4ir9 4irc 4ird