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(-) Description

Title :  POLYMERASE DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS LIGASE D IN COMPLEX WITH AN ANNEALED DOUBLE-STRAND DNA BREAK.
 
Authors :  N. C. Brissett, A. J. Doherty
Date :  05 Sep 13  (Deposition) - 11 Dec 13  (Release) - 08 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,E,F,G,H  (1x)
Biol. Unit 2:  C,D,I,J,K,L  (1x)
Keywords :  Protein-Dna Complex, Transferase-Dna Complex, Nucleotide-Binding, Polymerase, Primase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. C. Brissett, M. J. Martin, E. J. Bartlett, J. Bianchi, L. Blanco, A. J. Doherty
Molecular Basis For Dna Double-Strand Break Annealing And Primer Extension By An Nhej Dna Polymerase.
Cell Rep V. 5 1108 2013
PubMed-ID: 24239356  |  Reference-DOI: 10.1016/J.CELREP.2013.10.016

(-) Compounds

Molecule 1 - DNA LIGASE-LIKE PROTEIN RV0938/MT0965
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: B834(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MT0965, MTCY08D9.01C, MTCY10D7.36C, RV0938
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
 
Molecule 2 - 5'-D(P*DGP*DCP*DGP*DGP*DC)-3'
    Chains: E, G, I, K
    Engineered: YES
    Other Details: SYNTHESISED DNA
    Synthetic: YES
 
Molecule 3 - 5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DGP*DTP*DAP*DC)-3'
    Chains: F, H, J, L
    Engineered: YES
    Other Details: SYNTHESISED DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): AB  EFGH    
Biological Unit 2 (1x):   CD    IJKL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4MKY)

(-) Sites  (0, 0)

(no "Site" information available for 4MKY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MKY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MKY)

(-) 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:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee....eehhhhhhhhhhhhhhhhh.......eeee.........eee...........eeeeeee..eeeeeee..hhhhhhhhhhhh..eeee..eeeee......eeeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhh.....eeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh...ee...hhhhh...eeeehhhhh....ee..............ee...hhhhh......hhhhhhhhhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mky A  10 QRVTLTNADKVLYPATGTTKSDIFDYYAGVAEVMLGHIAGRPATRKRWPNGVDQPAFFEKQLALSAPPWLSRATVAHRSGTTTYPIIDSATGLAWIAQQAALEVHVPQWRFVAEPGSGELNPGPATRLVFDLDPGEGVMMAQLAEVARAVRDLLADIGLVTFPVTSGSKGLHLYTPLDEPVSSRGATVLAKRVAQRLEQAMPALVTSTMTKSLRAGKVFVDWSQNSGSKTTIAPYSLRGRTHPTVAAPRTWAELDDPALRQLSYDEVLTRIARDGDLLERLDAD 293
                                    19        29        39        49        59        69        79       89A        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289    
                                                                                                         89A                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhh.....eeee.........eee...........eeeeeee..eeeeeee..hhhhhhhhhhhh..eeee..eeeee......eeeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhh.....eeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh...ee...hhhhh...eeeehhhhh....ee...........ee.ee.hhhhhh......eehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mky B  10 QRVTLTNADKVLYPATGTTKSDIFDYYAGVAEVMLGHIAGRPATRKRWPNGVDQPAFFEKQLALSAPPWLSRATVAHRSGTTTYPIIDSATGLAWIAQQAALEVHVPQWRFVAEPGSGELNPGPATRLVFDLDPGEGVMMAQLAEVARAVRDLLADIGLVTFPVTSGSKGLHLYTPLDEPVSSRGATVLAKRVAQRLEQAMPALVTSTMTKSLRAGKVFVDWSQNSGSKTTIAPYSLRGRTHPTVAAPRTWAELDDPALRQLSYDEVLTRIARDGDLLERLDA 292
                                    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   


Chain C from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhh....eeee.........eee...........eeeeeee..eeeeeee..hhhhhhhhhhh...eeee..eeeee......eeeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhh.....eeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh...ee...hhhhh...eeeehhhhh....ee..............ee.hhhhhh.......hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mky C  10 QRVTLTNADKVLYPATGTTKSDIFDYYAGVAEVMLGHIAGRPATRKRWPNGVDQPAFFEKQLALSAPPWLSRATVAHRSGTTTYPIIDSATGLAWIAQQAALEVHVPQWRFVAEPGSGELNPGPATRLVFDLDPGEGVMMAQLAEVARAVRDLLADIGLVTFPVTSGSKGLHLYTPLDEPVSSRGATVLAKRVAQRLEQAMPALVTSTMTKSLRAGKVFVDWSQNSGSKTTIAPYSLRGRTHPTVAAPRTWAELDDPALRQLSYDEVLTRIARDGDLLERLDAD 293
                                    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    


Chain D from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee....eehhhhhhhhhhhhhhhhhhh.....eeee.........eee............eeeeee..eeeeee...hhhhhhhhhhh...eeee..eeeee......eeeeeeeeeeeeeee......hhhhhhhhhhhhhhhh.....eeee.....eeeeeeeeeeehhhhhhhhhhhhhhhhhhhh...ee...hhhhh...eeeehhhhh....ee...........ee.ee.hhhhhh......eehhhhhhhhhhhh..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mky D  10 QRVTLTNADKVLYPATGTTKSDIFDYYAGVAEVMLGHIAGRPATRKRWPNGVDQPAFFEKQLALSAPPWLSRATVAHRSGTTTYPIIDSATGLAWIAQQAALEVHVPQWRFVAEPGSGELNPGPATRLVFDLDPGEGVMMAQLAEVARAVRDLLADIGLVTFPVTSGSKGLHLYTPLDEPVSSRGATVLAKRVAQRLEQAMPALVTSTMTKSLRAGKVFVDWSQNSGSKTTIAPYSLRGRTHPTVAAPRTWAELDDPALRQLSYDEVLTRIARDGDLLERLDAD 293
                                    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    


Chain E from PDB  Type:DNA  Length:3
                                   
                 4mky E   1 GCG   3


Chain F from PDB  Type:DNA  Length:10
                                          
                 4mky F   1 GCCGCAGTAC  10
                                    10


Chain G from PDB  Type:DNA  Length:3
                                   
                 4mky G   1 GCG   3


Chain H from PDB  Type:DNA  Length:10
                                          
                 4mky H   1 GCCGCAGTAC  10
                                    10


Chain I from PDB  Type:DNA  Length:3
                                   
                 4mky I   1 GCG   3


Chain J from PDB  Type:DNA  Length:10
                                          
                 4mky J   1 GCCGCAGTAC  10
                                    10


Chain K from PDB  Type:DNA  Length:3
                                   
                 4mky K   1 GCG   3


Chain L from PDB  Type:DNA  Length:10
                                          
                 4mky L   1 GCCGCAGTAC  10
                                    10
   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 4MKY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 53)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LIGD_MYCTO | P9WNV2: 1vs0 2iru 2irx 2iry 2r9l 3pky
        LIGD_MYCTU | P9WNV3: 1vs0 2iru 2irx 2iry 2r9l 3pky

(-) Related Entries Specified in the PDB File

2iru CRYSTAL STRUCTURE OF THE POLYMERASE DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS LIGASE D
2irx CRYSTAL STRUCTURE OF THE POLYMERASE DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS LIGASE D WITH GTP AND MANGANESE.
2iry CRYSTAL STRUCTURE OF THE POLYMERASE DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS LIGASE D WITH DGTP AND MANGANESE.
2r9l POLYMERASE DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS LIGASE D IN COMPLEX WITH DNA
3pky POLYMERASE DOMAIN FROM MYCOBACTERIUM TUBERCULOSIS LIGASE D IN COMPLEX WITH DNA, UTP AND MANGANESE.