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(-) Description

Title :  THE SLIDING CLAMP OF MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH A NATURAL PRODUCT.
 
Authors :  P. Lukat, A. Kling, D. W. Heinz, R. Mueller
Date :  04 Feb 15  (Deposition) - 03 Jun 15  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  C,D,G,H  (1x)
Biol. Unit 2:  A,B,E,F  (1x)
Keywords :  Transferase-Antibiotic Complex, Dnan, Dna Polymerase, Tuberculosis (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. Koenig, N. C. Ammermann, M. B. Barrio, K. Borchers, F. Bordon-Pallier, M. Broenstrup, 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. Mueller
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, C, D
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP008_DNANMSM
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 1772
    Strain: MC(2)155
 
Molecule 2 - GRISELIMYCIN
    Chains: E, F, G, H
    Organism Scientific: STREPTOMYCES CAELICUS
    Organism Taxid: 1520516

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x):   CD  GH
Biological Unit 2 (1x): AB  EF  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 30)

Asymmetric Unit (6, 30)
No.NameCountTypeFull Name
1ACE4Mod. Amino AcidACETYL GROUP
2MLU4Mod. Amino AcidN-METHYL-D-LEUCINE
3MP88Mod. Amino Acid(4R)-4-METHYL-L-PROLINE
4MVA8Mod. Amino AcidN-METHYLVALINE
5NA2Ligand/IonSODIUM ION
6NZC4Mod. Amino AcidN-METHYLIDENE-L-THREONINE
Biological Unit 1 (5, 14)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2MLU2Mod. Amino AcidN-METHYL-D-LEUCINE
3MP84Mod. Amino Acid(4R)-4-METHYL-L-PROLINE
4MVA4Mod. Amino AcidN-METHYLVALINE
5NA-1Ligand/IonSODIUM ION
6NZC2Mod. Amino AcidN-METHYLIDENE-L-THREONINE
Biological Unit 2 (5, 14)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2MLU2Mod. Amino AcidN-METHYL-D-LEUCINE
3MP84Mod. Amino Acid(4R)-4-METHYL-L-PROLINE
4MVA4Mod. Amino AcidN-METHYLVALINE
5NA-1Ligand/IonSODIUM ION
6NZC2Mod. Amino AcidN-METHYLIDENE-L-THREONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:307 , ALA A:308 , ARG A:315 , ALA A:316 , HOH A:2228BINDING SITE FOR RESIDUE NA A1398
2AC2SOFTWARELEU C:44 , SER C:55 , GLU C:64 , HOH C:2020 , HOH C:2183BINDING SITE FOR RESIDUE NA C1398
3AC3SOFTWAREMET A:161 , ARG A:181 , PHE A:182 , ARG A:183 , PRO A:257 , LEU A:262 , MET A:391 , PRO A:392 , VAL A:393 , ARG A:394 , HOH A:2267 , HOH A:2271 , HOH A:2272 , HOH A:2273 , TYR D:59 , ASP D:123BINDING SITE FOR CHAIN E OF GRISELIMYCIN
4AC4SOFTWAREMET B:161 , ARG B:181 , PHE B:182 , ARG B:183 , PRO B:257 , LEU B:262 , MET B:391 , PRO B:392 , VAL B:393 , ARG B:394 , HOH B:2188 , ILE C:37 , TYR C:59 , ASP C:123 , ARG C:250BINDING SITE FOR CHAIN F OF GRISELIMYCIN
5AC5SOFTWARETHR B:36 , ILE B:37 , PRO B:38 , TYR B:59 , ASP B:123 , ARG B:250 , ARG C:181 , PHE C:182 , ARG C:183 , GLN C:261 , LEU C:262 , MET C:391 , PRO C:392 , VAL C:393 , ARG C:394 , HOH C:2181BINDING SITE FOR CHAIN G OF GRISELIMYCIN
6AC6SOFTWARETHR A:36 , ILE A:37 , TYR A:59 , ASP A:123 , ARG A:250 , MET D:161 , ARG D:181 , PHE D:182 , ARG D:183 , LEU D:262 , MET D:391 , PRO D:392 , VAL D:393 , ARG D:394 , HOH D:2121 , HOH D:2124BINDING SITE FOR CHAIN H OF GRISELIMYCIN

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AH2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:377 -Pro A:378
2Gly B:377 -Pro B:378
3Gly C:377 -Pro C:378
4Gly D:377 -Pro D:378

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AH2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AH2)

(-) Exons   (0, 0)

(no "Exon" information available for 5AH2)

(-) 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:380
                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhhhhhh.......hhhh.eeeeee....eeeeee...eeeeeee..eeee.eeeeeehhhhhhhhhhh....eeeeee..eeeeee..eeeeee...............eeeeeehhhhhhhhhhhhh....hhhh.eeeeeee..eeeeeee...eeeeeeee.ee.....eeeeeeehhhhhhhhhhh....eeeee..hhhhh....eeeeee..eeeeee.......hhhhhh..ee.eeeeeehhhhhhhhhhhhhhhhhhh.eeeeee..eeeeeeee...eeeeeeee.eeee..eeeeehhhhhhhhhhhhh..eeeeee......eeeee........ee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ah2 A   9 TDLKFRVVREDFADAVAWVARSLPTRPTIPVLAGVLLTGTDEGLTISGFDYEVSAEVKVSAEIASAGSVLVSGRLLSDITKALPAKPVEVSVEGTRVSLTCGSARFSLPTLAVEDYPALPALPEETGVIASDLFAEAIGQVAVAAGRLPMLTGIRVEISGESVVLAATDRFRLAVRELTWVTTAGDVEAAVLVPAKTLAEAAKAGTDGNQVHLALGSGASVGKDGLLGIRSEGKRSTTRLLDAEFPKFRQLLPAEHTAVATIGVAELTEAIKRVALVADRGAQIRMEFSDDTLKLSAGADDVGRAEEDLPVDFAGEPLTIAFNPTYLTDGLGSLHSERVTFGFTTPSRPAVLRPAGEGGSGPFPAAKTDYVYLLMPVRLP 396
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148      |161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361      |376       386       396
                                                                                                                                                                            155|                                                                                                                                                                                                              368|                      
                                                                                                                                                                             159                                                                                                                                                                                                               374                      


Chain B from PDB  Type:PROTEIN  Length:377
                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhhhhhhhh....hhhh.eeeeee....eeeeee...eeeeeee..eeee.eeeeeehhhhhhhhhhh....eeeeee..eeeeee..eeeeee...............eeeeeehhhhhhhhhhhhh....hhhh.eeeeeee..eeeeeee...eeeeeeee.ee.....eeeeeeehhhhhhhhhhhh...eeeee...........eeeeee..eeeeee........hhhhh..ee.eeeeeehhhhhhhhhhhhhhhhhhh.eeeeee..eeeeeeee...eeeeeeee.eeee..eeeeehhhhhhhhhhh....eeeeee......eeeee......ee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ah2 B   9 TDLKFRVVREDFADAVAWVARSLPTPTIPVLAGVLLTGTDEGLTISGFDYEVSAEVKVSAEIASAGSVLVSGRLLSDITKALPAKPVEVSVEGTRVSLTCGSARFSLPTLAVEDYPALPALPEETGVIASDLFAEAIGQVAVAAGRLPMLTGIRVEISGESVVLAATDRFRLAVRELTWVTTAGDVEAAVLVPAKTLAEAAKAGTDGNQVHLALGSGASVGKDGLLGIRSEGKRSTTRLLDAEFPKFRQLLPAEHTAVATIGVAELTEAIKRVALVADRGAQIRMEFSDDTLKLSAGADDVGRAEEDLPVDFAGEPLTIAFNPTYLTDGLGSLHSERVTFGFTTPSRPAVLRPAGGSGPFPAAKTDYVYLLMPVRLP 396
                                    18        28    ||  39        49        59        69        79        89        99       109       119       129       139       149     ||162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362    || 379       389       
                                                   33|                                                                                                                     155|                                                                                                                                                                                                             367|                     
                                                    35                                                                                                                      159                                                                                                                                                                                                              375                     


Chain C from PDB  Type:PROTEIN  Length:382
                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhhhhh......hhhh.eeeeee....eeeeee...eeeeeee..eeee.eeeeeehhhhhhhhh......eeeeee..eeeeee..eeeeee...............eeeeeehhhhhhhhhhhhh.......hhhh.eeeeeee..eeeeeee...eeeeeeee.ee.....eeeeeeehhhhhhhhhhh....eeeee..hhhhh....eeeeee..eeeeee........hhhhh..ee.eeeeeehhhhhhhhhhhhhhh....eeeee...eeeeeeee...eeeeeeee.eeee..eeeeehhhhhhhhhh.....eeeeee......eeeee........ee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ah2 C   8 LTDLKFRVVREDFADAVAWVARSLPTPTIPVLAGVLLTGTDEGLTISGFDYEVSAEVKVSAEIASAGSVLVSGRLLSDITKALPAKPVEVSVEGTRVSLTCGSARFSLPTLAVEDYPALPALPEETGVIASDLFAEAIGQVAVAAGRDDTLPMLTGIRVEISGESVVLAATDRFRLAVRELTWVTTAGDVEAAVLVPAKTLAEAAKAGTDGNQVHLALGSGASVGKDGLLGIRSEGKRSTTRLLDAEFPKFRQLLPAEHTAVATIGVAELTEAIKRVALVADRAQIRMEFSDDTLKLSAGADDVGRAEEDLPVDFAGEPLTIAFNPTYLTDGLGSLHSERVTFGFTTPSRPAVLRPAGEGGSGPFPAAKTDYVYLLMPVRLP 396
                                    17        27     || 38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288  ||   299       309       319       329       339       349       359       374       384       394  
                                                    33|                                                                                                                                                                                                                                                             291|                                                                        368|                      
                                                     35                                                                                                                                                                                                                                                              293                                                                         374                      


Chain D from PDB  Type:PROTEIN  Length:379
                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhhhhh.......hhhh.eeeeee....eeeeee...eeeeeee..eeee.eeeeeehhhhhhhhhhh...eeeeeee..eeeeee..eeeeee...............eeeeeehhhhhhhhhhhhh.....hhhh.eeeeeee..eeeeeee...eeeeeeee.ee.....eeeeeeehhhhhhhhhh....eeeee..hhhhh....eeeeee..eeeeee........hhhhh..ee.eeeeeehhhhhhhhhhhhhhhhhhh.eeeeee..eeeeeeee...eeeeeeee.eeee..eeeeehhhhhhhhhh.....eeeeee......eeeee......ee.....eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ah2 D   9 TDLKFRVVREDFADAVAWVARSLPTRPTIPVLAGVLLTGTDEGLTISGFDYEVSAEVKVSAEIASAGSVLVSGRLLSDITKALPAKPVEVSVEGTRVSLTCGSARFSLPTLAVEDYPALPALPEETGVIASDLFAEAIGQVAVAAGRDLPMLTGIRVEISGESVVLAATDRFRLAVRELTWVTTAGDVEAAVLVPAKTLAEAAKAGTGNQVHLALGSGASVGKDGLLGIRSEGKRSTTRLLDAEFPKFRQLLPAEHTAVATIGVAELTEAIKRVALVADRGAQIRMEFSDDTLKLSAGADDVGRAEEDLPVDFAGEPLTIAFNPTYLTDGLGSLHSERVTFGFTTPSRPAVLRPAGGSGPFPAAKTDYVYLLMPVRLPG 397
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       160       170       180       190       200       210      |221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    || 378       388         
                                                                                                                                                                             156|                                                       217|                                                                                                                                                366|                       
                                                                                                                                                                              159                                                        219                                                                                                                                                 374                       


Chain E 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
                 5ah2 E   1 xvptLpLvPxG  11
                            |||| | |10 
                            1-ACE| | | 
                             2-MVA | | 
                              3-MP8| | 
                               4-NZC | 
                                 6-MP8 
                                   8-MVA
                                    10-MLU


Chain F 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
                 5ah2 F   1 xvptLpLvPxG  11
                            |||| | |10 
                            |||| | | | 
                            1-ACE| | | 
                             2-MVA | | 
                              3-MP8| | 
                               4-NZC | 
                                 6-MP8 
                                   8-MVA
                                    10-MLU


Chain G 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
                 5ah2 G   1 xvptLpLvPxG  11
                            |||| | |10 
                            |||| | | | 
                            1-ACE| | | 
                             2-MVA | | 
                              3-MP8| | 
                               4-NZC | 
                                 6-MP8 
                                   8-MVA
                                    10-MLU


Chain H 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
                 5ah2 H   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)
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  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 5AH2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AH2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AH2)

(-) Gene Ontology  (10, 10)

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  Cis Peptide Bonds
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  5ah2
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 Related Entries

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

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        A0QND6_MYCS2 | A0QND6: 5ah4

(-) Related Entries Specified in the PDB File

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