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(-) Description

Title :  THE SLIDING CLAMP OF MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH A NATURAL PRODUCT.
 
Authors :  P. Lukat, A. Kling, D. W. Heinz, R. Mueller
Date :  03 Feb 15  (Deposition) - 03 Jun 15  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transferase, Dnan, Dna Polymerase, Mycobacterium Tuberculosis, Tuberculosis, Natural Product, Sliding Clamp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kling, P. Lukat, D. V. Almeida, A. Bauer, E. Fontaine, S. Sordello, N. Zaburannyi, J. Herrmann, S. C. Wenzel, C. Konig, N. C. Ammerman, M. B. Barrio, K. Borchers, F. Bordon-Pallier, M. Bronstrup, G. Courtemanche, M. Gerlitz, M. Geslin, P. Hammann, D. W. Heinz, H. Hoffmann, S. Klieber, M. Kohlmann, M. Kurz, C. Lair, H. Matter, E. Nuermberger, S. Tyagi, L. Fraisse, J. H. Grosset, S. Lagrange, R. Muller
Antibiotics. Targeting Dnan For Tuberculosis Therapy Using Novel Griselimycins.
Science V. 348 1106 2015
PubMed-ID: 26045430  |  Reference-DOI: 10.1126/SCIENCE.AAA4690

(-) Compounds

Molecule 1 - DNA POLYMERASE III SUBUNIT BETA
    Chains: A, B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP008_DNANMTB
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS H37RV
    Organism Taxid: 83332
 
Molecule 2 - GRISELIMYCIN
    Chains: C, D
    Organism Scientific: STREPTOMYCES CAELICUS
    Organism Taxid: 1520516

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 16)

Asymmetric/Biological Unit (7, 16)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2BU31Ligand/Ion(R,R)-2,3-BUTANEDIOL
3MLU2Mod. Amino AcidN-METHYL-D-LEUCINE
4MP84Mod. Amino Acid(4R)-4-METHYL-L-PROLINE
5MVA4Mod. Amino AcidN-METHYLVALINE
6NZC2Mod. Amino AcidN-METHYLIDENE-L-THREONINE
7TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:135 , THR A:160 , SER A:194 , ALA A:195 , SER A:196 , ARG A:225 , HOH A:2116BINDING SITE FOR RESIDUE BU3 A1403
2AC2SOFTWAREVAL A:188 , GLU A:190 , THR A:389 , ASP A:390 , TYR A:391 , ASP B:199BINDING SITE FOR RESIDUE TRS A1404
3AC3SOFTWAREGLU A:142 , ARG A:183 , PHE A:184 , ARG A:185 , SER A:194 , SER A:222 , LYS A:260 , GLN A:263 , LEU A:264 , MET A:396 , PRO A:397 , VAL A:398 , ARG A:399 , HOH A:2111 , HOH A:2131 , HOH A:2221 , HOH A:2222 , HOH A:2226 , HOH A:2227 , HOH A:2228BINDING SITE FOR CHAIN C OF GRISELIMYCIN
4AC4SOFTWAREGLU B:142 , THR B:181 , ARG B:183 , PHE B:184 , ARG B:185 , LYS B:260 , LEU B:264 , LYS B:361 , PRO B:362 , MET B:396 , PRO B:397 , VAL B:398 , ARG B:399 , HOH B:2048 , HOH B:2128BINDING SITE FOR CHAIN D OF GRISELIMYCIN

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AGU)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:382 -Pro A:383
2Leu B:33 -Pro B:34
3Gly B:382 -Pro B:383

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AGU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AGU)

(-) Exons   (0, 0)

(no "Exon" information available for 5AGU)

(-) 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:373
                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeehhhhhhhhhhhhhhhhhh.eeeeeee..eeeeee....eeeeeee..eeee.eeeeeehhhhhhhhhhh...eeeeee...eeeeee..eeeeee..hhhhh........eeeeeehhhhhhhhhhhhh.......hhhh.eeeeeee..eeeeeee...eeeeeeee.ee.....eeeeeeehhhhhhhhh......eeeee..hhhhh....eeeeee..eeeeee........hhhhh..ee.eeeeeehhhhhhhhhhhh.....eeeeee..eeeeeeee...eeeeeeee.eee...eeeeehhhhhhhhhhh....eeeeee......eeeeee.......ee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5agu A  12 DLTFRLLRESFADAVSWVAKNLPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEIVSPGSVLVSGRLLSDITRALPNKPVDVHVEGNRVALTCGNARFSLPTMPVEDYPTLPTLPEETGLLPAELFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVRELKWSASSPDIEAAVLVPAKTLAEAAKAGIGGSDVRLSLGTGPGVGKDGLLGISGNGKRSTTRLLDAEFPKFRQLLPTEHTAVATMDVAELIEAIKLVALVAAQVRMEFADGSVRLSAGADDVGRAEEDLVVDYAGEPLTIAFNPTYLTDGLSSLRSERVSFGFTTAGKPALLRPVSGNGNGPFPAVSTDYVYLLMPVRLP 401
                                    21        31 ||     47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287   ||  300       310       320       330       340       350       360       370|      388       398   
                                                33|                                                                                                                                                                                                                                                        291|                                                                        370|                      
                                                 40                                                                                                                                                                                                                                                         295                                                                         379                      


Chain B from PDB  Type:PROTEIN  Length:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeehhhhhhhhhhhhhh...hhhh.eeeeeee..eeeeeee...eeeeeeee.eeee.eeeeeehhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh..........eeeehhhhhhhhhhhhh.......hhhh.eeeeeee..eeeeeee...eeeeeeee.ee.....eeeeeeehhhhhhhhhhh...eeeee..hhhhh....eeeeee..eeeeee........hhhhh..ee.eeeeeehhhhhhhhhhhhhhhhhhh.eeeeee..eeeeeeee...eeeeeeee.eee...eeeeehhhhhhhhhhhh...eeeeee......eeeeee.......ee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5agu B  12 DLTFRLLRESFADAVSWVAKNLPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEIVSPGSVLVSGRLLSDITRALPNKPVDVHVEGNRVALTCGNARFSLPTMPVEDYPTLPTLPEETGLLPAELFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVRELKWSASSPDIEAAVLVPAKTLAEAAKAGGGSDVRLSLGTGPGVGKDGLLGISGNGKRSTTRLLDAEFPKFRQLLPTEHTAVATMDVAELIEAIKLVALVADRGAQVRMEFADGSVRLSAGADDVGRAEEDLVVDYAGEPLTIAFNPTYLTDGLSSLRSERVSFGFTTAGKPALLRPVSGDGNGPFPAVSTDYVYLLMPVRLP 401
                                    21        31  ||    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214   ||  225       235       245       255       265       275       285       295       305       315       325       335       345       355       365     ||383       393        
                                                 34|                                                                                                                                                                                 218|                                                                                                                                                    371|                     
                                                  38                                                                                                                                                                                  220                                                                                                                                                     380                     


Chain C from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5agu C   1 xvptLpLvPxG  11
                            |||| | |10 
                            1-ACE| | | 
                             2-MVA | | 
                              3-MP8| | 
                               4-NZC | 
                                 6-MP8 
                                   8-MVA
                                    10-MLU


Chain D from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5agu D   1 xvptLpLvPxG  11
                            |||| | |10 
                            |||| | | | 
                            1-ACE| | | 
                             2-MVA | | 
                              3-MP8| | 
                               4-NZC | 
                                 6-MP8 
                                   8-MVA
                                    10-MLU
   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 5AGU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AGU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AGU)

(-) Gene Ontology  (12, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPO3B_MYCTU | P9WNU1: 3p16 3rb9 5agv
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(-) Related Entries Specified in the PDB File

5agv THE SLIDING CLAMP OF MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH A NATURAL PRODUCT.
5ah2 THE SLIDING CLAMP OF MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH A NATURAL PRODUCT.
5ah4 THE SLIDING CLAMP OF MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH A NATURAL PRODUCT.