2A68

Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic rifabutin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

Starting Model: experimental
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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

  • 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.

    • Organizational Affiliation: 

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase alpha chainA,
B,
G [auth K],
H [auth L]		315Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5SHR6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Go to UniProtKB:  Q5SHR6
Entity Groups  
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UniProt GroupQ5SHR6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta chainC,
I [auth M]		1,119Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta' chainD,
J [auth N]		1,524Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase omega chainE,
K [auth O]		99Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor rpoDF,
L [auth P]		423Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SKW1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RBT
Query on RBT
Download Ideal Coordinates CCD File 
KN [auth M],
OB [auth C]		RIFABUTIN
C46 H62 N4 O11
ATEBXHFBFRCZMA-VXTBVIBXSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
CQ [auth N],
DQ [auth N],
SE [auth D],
TE [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
AC [auth C]
AD [auth C]
AE [auth C]
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 D],
AK [auth D],
AL [auth F],
AM [auth K],
AN [auth L],
AO [auth M],
AP [auth M],
AQ [auth M],
AR [auth N],
AS [auth N],
AT [auth N],
AU [auth N],
AV [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 D],
BK [auth E],
BL [auth F],
BM [auth K],
BN [auth L],
BO [auth M],
BP [auth M],
BQ [auth M],
BR [auth N],
BS [auth N],
BT [auth N],
BU [auth N],
BV [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 D],
CK [auth E],
CL [auth F],
CM [auth K],
CN [auth L],
CO [auth M],
CP [auth M],
CR [auth N],
CS [auth N],
CT [auth N],
CU [auth N],
CV [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 D],
DK [auth E],
DL [auth F],
DM [auth K],
DN [auth L],
DO [auth M],
DP [auth M],
DR [auth N],
DS [auth N],
DT [auth N],
DU [auth N],
DV [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 D],
EK [auth E],
EL [auth F],
EM [auth K],
EN [auth L],
EO [auth M],
EP [auth M],
EQ [auth N],
ER [auth N],
ES [auth N],
ET [auth N],
EU [auth N],
EV [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 D],
FK [auth E],
FL [auth F],
FM [auth K],
FN [auth L],
FO [auth M],
FP [auth M],
FQ [auth N],
FR [auth N],
FS [auth N],
FT [auth N],
FU [auth N],
FV [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 D],
GK [auth E],
GL [auth F],
GM [auth K],
GN [auth L],
GO [auth M],
GP [auth M],
GQ [auth N],
GR [auth N],
GS [auth N],
GT [auth N],
GU [auth N],
GV [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 D],
HK [auth E],
HL [auth F],
HM [auth K],
HN [auth L],
HO [auth M],
HP [auth M],
HQ [auth N],
HR [auth N],
HS [auth N],
HT [auth N],
HU [auth N],
HV [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 D],
IK [auth E],
IL [auth F],
IM [auth K],
IN [auth L],
IO [auth M],
IP [auth M],
IQ [auth N],
IR [auth N],
IS [auth N],
IT [auth N],
IU [auth O],
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 D],
JK [auth E],
JL [auth F],
JM [auth K],
JN [auth L],
JO [auth M],
JP [auth M],
JQ [auth N],
JR [auth N],
JS [auth N],
JT [auth N],
JU [auth O],
KA [auth A],
KB [auth B],
KC [auth C],
KD [auth C],
KE [auth C],
KF [auth D],
KG [auth D],
KH [auth D],
KI [auth D],
KJ [auth D],
KK [auth E],
KL [auth F],
KM [auth K],
KO [auth M],
KP [auth M],
KQ [auth N],
KR [auth N],
KS [auth N],
KT [auth N],
KU [auth O],
LA [auth A],
LB [auth B],
LC [auth C],
LD [auth C],
LE [auth C],
LF [auth D],
LG [auth D],
LH [auth D],
LI [auth D],
LJ [auth D],
LK [auth F],
LL [auth F],
LM [auth L],
LN [auth M],
LO [auth M],
LP [auth M],
LQ [auth N],
LR [auth N],
LS [auth N],
LT [auth N],
LU [auth O],
M [auth A],
MA [auth A],
MB [auth B],
MC [auth C],
MD [auth C],
ME [auth C],
MF [auth D],
MG [auth D],
MH [auth D],
MI [auth D],
MJ [auth D],
MK [auth F],
ML [auth F],
MM [auth L],
MN [auth M],
MO [auth M],
MP [auth M],
MQ [auth N],
MR [auth N],
MS [auth N],
MT [auth N],
MU [auth O],
N [auth A],
NA [auth A],
NB [auth B],
NC [auth C],
ND [auth C],
NE [auth C],
NF [auth D],
NG [auth D],
NH [auth D],
NI [auth D],
NJ [auth D],
NK [auth F],
NL [auth F],
NM [auth L],
NN [auth M],
NO [auth M],
NP [auth M],
NQ [auth N],
NR [auth N],
NS [auth N],
NT [auth N],
NU [auth O],
O [auth A],
OA [auth A],
OC [auth C],
OD [auth C],
OE [auth C],
OF [auth D],
OG [auth D],
OH [auth D],
OI [auth D],
OJ [auth D],
OK [auth F],
OL [auth F],
OM [auth L],
ON [auth M],
OO [auth M],
OP [auth M],
OQ [auth N],
OR [auth N],
OS [auth N],
OT [auth N],
OU [auth P],
P [auth A],
PA [auth A],
PB [auth C],
PC [auth C],
PD [auth C],
PE [auth C],
PF [auth D],
PG [auth D],
PH [auth D],
PI [auth D],
PJ [auth D],
PK [auth F],
PL [auth F],
PM [auth L],
PN [auth M],
PO [auth M],
PP [auth M],
PQ [auth N],
PR [auth N],
PS [auth N],
PT [auth N],
PU [auth P],
Q [auth A],
QA [auth A],
QB [auth C],
QC [auth C],
QD [auth C],
QE [auth C],
QF [auth D],
QG [auth D],
QH [auth D],
QI [auth D],
QJ [auth D],
QK [auth F],
QL [auth K],
QM [auth L],
QN [auth M],
QO [auth M],
QP [auth M],
QQ [auth N],
QR [auth N],
QS [auth N],
QT [auth N],
QU [auth P],
R [auth A],
RA [auth B],
RB [auth C],
RC [auth C],
RD [auth C],
RE [auth C],
RF [auth D],
RG [auth D],
RH [auth D],
RI [auth D],
RJ [auth D],
RK [auth F],
RL [auth K],
RM [auth L],
RN [auth M],
RO [auth M],
RP [auth M],
RQ [auth N],
RR [auth N],
RS [auth N],
RT [auth N],
RU [auth P],
S [auth A],
SA [auth B],
SB [auth C],
SC [auth C],
SD [auth C],
SF [auth D],
SG [auth D],
SH [auth D],
SI [auth D],
SJ [auth D],
SK [auth F],
SL [auth K],
SM [auth L],
SN [auth M],
SO [auth M],
SP [auth M],
SQ [auth N],
SR [auth N],
SS [auth N],
ST [auth N],
SU [auth P],
T [auth A],
TA [auth B],
TB [auth C],
TC [auth C],
TD [auth C],
TF [auth D],
TG [auth D],
TH [auth D],
TI [auth D],
TJ [auth D],
TK [auth F],
TL [auth K],
TM [auth L],
TN [auth M],
TO [auth M],
TP [auth M],
TQ [auth N],
TR [auth N],
TS [auth N],
TT [auth N],
TU [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 D],
UJ [auth D],
UK [auth F],
UL [auth K],
UM [auth L],
UN [auth M],
UO [auth M],
UP [auth M],
UQ [auth N],
UR [auth N],
US [auth N],
UT [auth N],
UU [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 D],
VJ [auth D],
VK [auth F],
VL [auth K],
VM [auth L],
VN [auth M],
VO [auth M],
VP [auth M],
VQ [auth N],
VR [auth N],
VS [auth N],
VT [auth N],
VU [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 D],
WJ [auth D],
WK [auth F],
WL [auth K],
WM [auth L],
WN [auth M],
WO [auth M],
WP [auth M],
WQ [auth N],
WR [auth N],
WS [auth N],
WT [auth N],
WU [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 D],
XJ [auth D],
XK [auth F],
XL [auth K],
XM [auth L],
XN [auth M],
XO [auth M],
XP [auth M],
XQ [auth N],
XR [auth N],
XS [auth N],
XT [auth N],
XU [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 D],
YJ [auth D],
YK [auth F],
YL [auth K],
YM [auth L],
YN [auth M],
YO [auth M],
YP [auth M],
YQ [auth N],
YR [auth N],
YS [auth N],
YT [auth N],
YU [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 D],
ZJ [auth D],
ZK [auth F],
ZL [auth K],
ZM [auth L],
ZN [auth M],
ZO [auth M],
ZP [auth M],
ZQ [auth N],
ZR [auth N],
ZS [auth N],
ZT [auth N],
ZU [auth P]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 239.5α = 90
b = 239.5β = 90
c = 253.1γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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