2A69

Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin

• PDB DOI: https://doi.org/10.2210/pdb2A69/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus
• Mutation(s): No 


• Deposited: 2005-07-02 Released: 2005-09-20 
• Deposition Author(s): Artsimovitch, I., Vassylyeva, M.N., Svetlov, D., Svetlov, V., Perederina, A., Igarashi, N., Matsugaki, N., Wakatsuki, S., Tahirov, T.H., Vassylyev, D.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.267 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 

Starting Model: experimental

Literature

Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.

Artsimovitch, I., Vassylyeva, M.N., Svetlov, D., Svetlov, V., Perederina, A., Igarashi, N., Matsugaki, N., Wakatsuki, S., Tahirov, T.H., Vassylyev, D.G.

(2005) Cell 122: 351-363

• PubMed: 16096056 
• DOI: https://doi.org/10.1016/j.cell.2005.07.014
• Primary Citation of Related Structures:  
  2A68, 2A69, 2A6E


• PubMed Abstract: 
  

  Rifamycins, the clinically important antibiotics, target bacterial RNA polymerase (RNAP). A proposed mechanism in which rifamycins sterically block the extension of nascent RNA beyond three nucleotides does not alone explain why certain RNAP mutations confer resistance to some but not other rifamycins. Here we show that unlike rifampicin and rifapentin, and contradictory to the steric model, rifabutin inhibits formation of the first and second phosphodiester bonds. We report 2.5 A resolution structures of rifabutin and rifapentin complexed with the Thermus thermophilus RNAP holoenzyme. The structures reveal functionally important distinct interactions of antibiotics with the initiation sigma factor. Strikingly, both complexes lack the catalytic Mg2+ ion observed in the apo-holoenzyme, whereas an increase in Mg2+ concentration confers resistance to rifamycins. We propose that a rifamycin-induced signal is transmitted over approximately 19 A to the RNAP active site to slow down catalysis. Based on structural predictions, we designed enzyme substitutions that apparently interrupt this allosteric signal.

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Organizational Affiliation: 

Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B1C1D1E1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B1C1D1E1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 867.12 kDa 
• Atom Count: 60,572 
• Modelled Residue Count: 6,818 
• Deposited Residue Count: 7,590 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase alpha chain	A, B, G [auth K], H [auth L]	315	Thermus thermophilus	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for Q5SHR6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHR6  Go to UniProtKB:  Q5SHR6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase beta chain	C, I [auth M]	1,119	Thermus thermophilus	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for Q8RQE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RQE9  Go to UniProtKB:  Q8RQE9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase beta' chain	D, J [auth N]	1,524	Thermus thermophilus	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RQE8  Go to UniProtKB:  Q8RQE8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase omega chain	E, K [auth O]	99	Thermus thermophilus	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RQE7  Go to UniProtKB:  Q8RQE7

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor rpoD	F, L [auth P]	423	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SKW1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKW1  Go to UniProtKB:  Q5SKW1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RPT	FL [auth M], OB [auth C]	RIFAPENTINE C47 H64 N4 O12 WDZCUPBHRAEYDL-GZAUEHORSA-N
ZN	KE [auth D], LE [auth D], TN [auth N], UN [auth N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AA [auth A], AB [auth B], AC [auth C], AD [auth C], AE [auth C], AF [auth D], AG [auth D], AH [auth D], AI [auth D], AJ [auth F], AK [auth K], AL [auth L], AM [auth M], AN [auth M], AO [auth N], AP [auth N], AQ [auth N], AR [auth N], AS [auth P], BA [auth A], BB [auth B], BC [auth C], BD [auth C], BE [auth C], BF [auth D], BG [auth D], BH [auth D], BI [auth D], BJ [auth F], BK [auth K], BL [auth L], BM [auth M], BN [auth M], BO [auth N], BP [auth N], BQ [auth N], BR [auth N], BS [auth P], CA [auth A], CB [auth B], CC [auth C], CD [auth C], CE [auth C], CF [auth D], CG [auth D], CH [auth D], CI [auth D], CJ [auth F], CK [auth K], CL [auth L], CM [auth M], CN [auth M], CO [auth N], CP [auth N], CQ [auth N], CR [auth N], CS [auth P], DA [auth A], DB [auth B], DC [auth C], DD [auth C], DE [auth C], DF [auth D], DG [auth D], DH [auth D], DI [auth D], DJ [auth F], DK [auth K], DL [auth L], DM [auth M], DN [auth M], DO [auth N], DP [auth N], DQ [auth N], DR [auth N], DS [auth P], EA [auth A], EB [auth B], EC [auth C], ED [auth C], EE [auth C], EF [auth D], EG [auth D], EH [auth D], EI [auth D], EJ [auth F], EK [auth K], EL [auth L], EM [auth M], EN [auth M], EO [auth N], EP [auth N], EQ [auth N], ER [auth N], ES [auth P], FA [auth A], FB [auth B], FC [auth C], FD [auth C], FE [auth C], FF [auth D], FG [auth D], FH [auth D], FI [auth D], FJ [auth F], FK [auth K], FM [auth M], FN [auth M], FO [auth N], FP [auth N], FQ [auth N], FR [auth N], FS [auth P], GA [auth A], GB [auth B], GC [auth C], GD [auth C], GE [auth C], GF [auth D], GG [auth D], GH [auth D], GI [auth D], GJ [auth F], GK [auth K], GL [auth M], GM [auth M], GN [auth M], GO [auth N], GP [auth N], GQ [auth N], GR [auth N], GS [auth P], HA [auth A], HB [auth B], HC [auth C], HD [auth C], HE [auth C], HF [auth D], HG [auth D], HH [auth D], HI [auth D], HJ [auth F], HK [auth K], HL [auth M], HM [auth M], HN [auth M], HO [auth N], HP [auth N], HQ [auth N], HR [auth N], HS [auth P], IA [auth A], IB [auth B], IC [auth C], ID [auth C], IE [auth C], IF [auth D], IG [auth D], IH [auth D], II [auth D], IJ [auth F], IK [auth K], IL [auth M], IM [auth M], IN [auth M], IO [auth N], IP [auth N], IQ [auth N], IR [auth N], IS [auth P], JA [auth A], JB [auth B], JC [auth C], JD [auth C], JE [auth C], JF [auth D], JG [auth D], JH [auth D], JI [auth D], JJ [auth F], JK [auth K], JL [auth M], JM [auth M], JN [auth M], JO [auth N], JP [auth N], JQ [auth N], JR [auth O], JS [auth P], KA [auth A], KB [auth B], KC [auth C], KD [auth C], KF [auth D], KG [auth D], KH [auth D], KI [auth D], KJ [auth F], KK [auth K], KL [auth M], KM [auth M], KN [auth M], KO [auth N], KP [auth N], KQ [auth N], KR [auth O], KS [auth P], LA [auth A], LB [auth B], LC [auth C], LD [auth C], LF [auth D], LG [auth D], LH [auth D], LI [auth D], LJ [auth F], LK [auth K], LL [auth M], LM [auth M], LN [auth M], LO [auth N], LP [auth N], LQ [auth N], LR [auth O], M [auth A], MA [auth A], MB [auth B], MC [auth C], MD [auth C], ME [auth D], MF [auth D], MG [auth D], MH [auth D], MI [auth D], MJ [auth F], MK [auth K], ML [auth M], MM [auth M], MN [auth M], MO [auth N], MP [auth N], MQ [auth N], MR [auth O], N [auth A], NA [auth A], NB [auth B], NC [auth C], ND [auth C], NE [auth D], NF [auth D], NG [auth D], NH [auth D], NI [auth D], NJ [auth F], NK [auth K], NL [auth M], NM [auth M], NN [auth M], NO [auth N], NP [auth N], NQ [auth N], NR [auth O], O [auth A], OA [auth A], OC [auth C], OD [auth C], OE [auth D], OF [auth D], OG [auth D], OH [auth D], OI [auth E], OJ [auth F], OK [auth L], OL [auth M], OM [auth M], ON [auth M], OO [auth N], OP [auth N], OQ [auth N], OR [auth O], P [auth A], PA [auth A], PB [auth C], PC [auth C], PD [auth C], PE [auth D], PF [auth D], PG [auth D], PH [auth D], PI [auth E], PJ [auth F], PK [auth L], PL [auth M], PM [auth M], PN [auth M], PO [auth N], PP [auth N], PQ [auth N], PR [auth O], Q [auth A], QA [auth A], QB [auth C], QC [auth C], QD [auth C], QE [auth D], QF [auth D], QG [auth D], QH [auth D], QI [auth E], QJ [auth F], QK [auth L], QL [auth M], QM [auth M], QN [auth M], QO [auth N], QP [auth N], QQ [auth N], QR [auth O], R [auth A], RA [auth A], RB [auth C], RC [auth C], RD [auth C], RE [auth D], RF [auth D], RG [auth D], RH [auth D], RI [auth E], RJ [auth F], RK [auth L], RL [auth M], RM [auth M], RN [auth M], RO [auth N], RP [auth N], RQ [auth N], RR [auth P], S [auth A], SA [auth A], SB [auth C], SC [auth C], SD [auth C], SE [auth D], SF [auth D], SG [auth D], SH [auth D], SI [auth E], SJ [auth F], SK [auth L], SL [auth M], SM [auth M], SN [auth M], SO [auth N], SP [auth N], SQ [auth N], SR [auth P], T [auth A], TA [auth B], TB [auth C], TC [auth C], TD [auth C], TE [auth D], TF [auth D], TG [auth D], TH [auth D], TI [auth F], TJ [auth F], TK [auth L], TL [auth M], TM [auth M], TO [auth N], TP [auth N], TQ [auth N], TR [auth P], U [auth A], UA [auth B], UB [auth C], UC [auth C], UD [auth C], UE [auth D], UF [auth D], UG [auth D], UH [auth D], UI [auth F], UJ [auth F], UK [auth L], UL [auth M], UM [auth M], UO [auth N], UP [auth N], UQ [auth N], UR [auth P], V [auth A], VA [auth B], VB [auth C], VC [auth C], VD [auth C], VE [auth D], VF [auth D], VG [auth D], VH [auth D], VI [auth F], VJ [auth K], VK [auth L], VL [auth M], VM [auth M], VN [auth N], VO [auth N], VP [auth N], VQ [auth N], VR [auth P], W [auth A], WA [auth B], WB [auth C], WC [auth C], WD [auth C], WE [auth D], WF [auth D], WG [auth D], WH [auth D], WI [auth F], WJ [auth K], WK [auth L], WL [auth M], WM [auth M], WN [auth N], WO [auth N], WP [auth N], WQ [auth N], WR [auth P], X [auth A], XA [auth B], XB [auth C], XC [auth C], XD [auth C], XE [auth D], XF [auth D], XG [auth D], XH [auth D], XI [auth F], XJ [auth K], XK [auth L], XL [auth M], XM [auth M], XN [auth N], XO [auth N], XP [auth N], XQ [auth N], XR [auth P], Y [auth A], YA [auth B], YB [auth C], YC [auth C], YD [auth C], YE [auth D], YF [auth D], YG [auth D], YH [auth D], YI [auth F], YJ [auth K], YK [auth L], YL [auth M], YM [auth M], YN [auth N], YO [auth N], YP [auth N], YQ [auth N], YR [auth P], Z [auth A], ZA [auth B], ZB [auth C], ZC [auth C], ZD [auth C], ZE [auth D], ZF [auth D], ZG [auth D], ZH [auth D], ZI [auth F], ZJ [auth K], ZK [auth L], ZL [auth M], ZM [auth M], ZN [auth N], ZO [auth N], ZP [auth N], ZQ [auth N], ZR [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.267 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 239.5	α = 90
b = 239.5	β = 90
c = 253.1	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-20 
Deposition Author(s): Artsimovitch, I., Vassylyeva, M.N., Svetlov, D., Svetlov, V., Perederina, A., Igarashi, N., Matsugaki, N., Wakatsuki, S., Tahirov, T.H., Vassylyev, D.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-09-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary