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(-) Description

Title :  POLYMERASE-DAMAGED DNA COMPLEX
 
Authors :  J. Kottur, A. Sharma, D. T. Nair
Date :  13 Apr 14  (Deposition) - 06 May 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,F,G,H
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  F,G,H  (1x)
Keywords :  Polymerase, Dna Polymerase, Translesion Synthesis, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Kottur, A. Sharma, K. R. Gore, N. Narayanan, B. Samanta, P. I. Pradeepkumar, D. T. Nair
Unique Structural Features In Dna Polymerase Iv Enable Efficient Bypass Of The N2 Adduct Induced By The Nitrofurazone Antibiotic
Structure V. 23 56 2015
PubMed-ID: 25497730  |  Reference-DOI: 10.1016/J.STR.2014.10.019

(-) Compounds

Molecule 1 - DNA POLYMERASE IV
    ChainsA, F
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P1
    Expression System StrainC41DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDINB
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12
    SynonymPOL IV
 
Molecule 2 - DNA (5'-D(*TP*CP*TP*(RDG) P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
    ChainsB, G
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsCHEMICALLY SYNTHESIZED DNA OLIGONUCLEOTIDE
    SyntheticYES
 
Molecule 3 - DNA (5'- D(*T*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
    ChainsC, H
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsCHEMICALLY SYNTHESIZED DNA OLIGONUCLEOTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCFGH
Biological Unit 1 (1x)ABC   
Biological Unit 2 (1x)   FGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
10KX2Ligand/Ion2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
2MG4Ligand/IonMAGNESIUM ION
3RDG2Mod. Nucleotide2'-DEOXY-N-(FURAN-2-YLMETHYL)GUANOSINE 5'-(DIHYDROGENPHOSPHATE)
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
10KX1Ligand/Ion2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
2MG-1Ligand/IonMAGNESIUM ION
3RDG1Mod. Nucleotide2'-DEOXY-N-(FURAN-2-YLMETHYL)GUANOSINE 5'-(DIHYDROGENPHOSPHATE)
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
10KX1Ligand/Ion2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
2MG-1Ligand/IonMAGNESIUM ION
3RDG1Mod. Nucleotide2'-DEOXY-N-(FURAN-2-YLMETHYL)GUANOSINE 5'-(DIHYDROGENPHOSPHATE)

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP 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 , LYS A:157 , MG A:402 , MG A:403 , HOH A:504 , HOH A:510 , RDG B:840 , DC C:873BINDING SITE FOR RESIDUE 0KX A 401
2AC2SOFTWAREASP A:8 , MET A:9 , ASP A:103 , 0KX A:401BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWAREASP A:8 , GLU A:104 , 0KX A:401 , DC C:873BINDING SITE FOR RESIDUE MG A 403
4AC4SOFTWAREASP F:8 , MET F:9 , ASP F:10 , CYS F:11 , PHE F:12 , PHE F:13 , SER F:42 , THR F:43 , ARG F:49 , SER F:55 , ASP F:103 , GLU F:104 , LYS F:157 , MG F:402 , MG F:403 , HOH F:507 , HOH F:516 , HOH F:530 , HOH F:546 , RDG G:840 , DC H:873BINDING SITE FOR RESIDUE 0KX F 401
5AC5SOFTWAREASP F:8 , MET F:9 , ASP F:103 , LYS F:157 , 0KX F:401BINDING SITE FOR RESIDUE MG F 402
6AC6SOFTWARESER F:101 , ASP F:103 , GLU F:104 , 0KX F:401 , DC H:873BINDING SITE FOR RESIDUE MG F 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q43)

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q43)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q43)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q43)

(-) 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.hhhhhhhhhh........eeee........eeeehhhhhh.......hhhhhhhh....eee..hhhhhhhhhhhhhhhhhh....eee....eeeee.........hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh....eee....hhhhhhhh.hhhhh...hhhhhhhhhhhh..hhhhhh..hhhhhhhhh...hhhhhhhhh..............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh.........eeeeeeee....eeeeeee....hhhhhhhhhhhhhh.......eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4q43 A   0 GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP 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:DNA  Length:18
                                                  
                 4q43 B 837 TCTgGGGTCCTAGGACCC 854
                               |   846        
                             840-RDG          

Chain C from PDB  Type:DNA  Length:17
                                                 
                 4q43 C 857 CTAGGGTCCTAGGACCC 873
                                   866       

Chain F from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhhhhhhh...eeee.......eeeeehhhhhh......eehhhhhhhh...eee..hhhhhhhhhhhhhhhhhh....eeeee..eeeee.........hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh......eee....hhhhhhhh.hhhhh...hhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee....eeeeeee....hhhhhhhhhhhhhhhhh....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4q43 F   0 GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP 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 G from PDB  Type:DNA  Length:18
                                                  
                 4q43 G 837 TCTgGGGTCCTAGGACCC 854
                               |   846        
                             840-RDG          

Chain H from PDB  Type:DNA  Length:14
                                              
                 4q43 H 860 GGGTCCTAGGACCC 873
                                   869    

   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 4Q43)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q43)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q43)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DPO4_ECOLI | Q471551ok7 1unn 4ir1 4ir9 4irc 4ird 4irk 4q44 4q45 4r8u 5c5j

(-) Related Entries Specified in the PDB File

4q44 4q45