1SMY

Structural basis for transcription regulation by alarmone ppGpp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.266 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5TMC


Literature

Structural basis for transcription regulation by alarmone ppGpp

Artsimovitch, I.Patlan, V.Sekine, S.Vassylyeva, M.N.Hosaka, T.Ochi, K.Yokoyama, S.Vassylyev, D.G.

(2004) Cell 117: 299-310

  • DOI: 10.1016/s0092-8674(04)00401-5
  • Primary Citation of Related Structures:  
    1SMY

  • PubMed Abstract: 
  • Guanosine-tetraphosphate (ppGpp) is a major regulator of stringent control, an adaptive response of bacteria to amino acid starvation. The 2.7 A resolution structure of the Thermus thermophilus RNA polymerase (RNAP) holoenzyme in complex with ppGpp reveals that ppGpp binds to the same site near the active center in both independent RNAP molecules in the crystal but in strikingly distinct orientations ...

    Guanosine-tetraphosphate (ppGpp) is a major regulator of stringent control, an adaptive response of bacteria to amino acid starvation. The 2.7 A resolution structure of the Thermus thermophilus RNA polymerase (RNAP) holoenzyme in complex with ppGpp reveals that ppGpp binds to the same site near the active center in both independent RNAP molecules in the crystal but in strikingly distinct orientations. Binding is symmetrical with respect to the two diphosphates of ppGpp and is relaxed with respect to the orientation of the nucleotide base. Different modes of ppGpp binding are coupled with asymmetry of the active site configurations. The results suggest that base pairing of ppGpp with cytosines in the nontemplate DNA strand might be an essential component of transcription control by ppGpp. We present experimental evidence highlighting the importance of base-specific contacts between ppGpp and specific cytosine residues during both transcription initiation and elongation.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence 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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UniProt GroupQ5SHR6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta chainC,
I [auth M]
1119Thermus 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
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta' chainD,
J [auth N]
1524Thermus 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
MoleculeChainsSequence LengthOrganismDetailsImage
RNA POLYMERASE OMEGA SUBUNITE,
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
MoleculeChainsSequence LengthOrganismDetailsImage
principal sigma factorF,
L [auth P]
423Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SKW1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SKW1
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4P
Query on G4P

Download Ideal Coordinates CCD File 
ON [auth N],
PN [auth N]
GUANOSINE-5',3'-TETRAPHOSPHATE
C10 H17 N5 O17 P4
BUFLLCUFNHESEH-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AF [auth D],
KN [auth N],
LN [auth N],
ZE [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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],
AG [auth D],
AH [auth D],
AI [auth D],
AJ [auth D],
AK [auth D],
AL [auth E],
AM [auth F],
AN [auth F],
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 D],
BL [auth E],
BM [auth F],
BN [auth F],
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 D],
CL [auth E],
CM [auth F],
CN [auth F],
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 D],
DL [auth E],
DM [auth F],
DN [auth F],
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 D],
EL [auth E],
EM [auth F],
EN [auth F],
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 D],
FL [auth E],
FM [auth F],
FN [auth F],
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 D],
GL [auth E],
GM [auth F],
GN [auth F],
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 D],
HL [auth E],
HM [auth F],
HN [auth F],
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 D],
IL [auth E],
IM [auth F],
IN [auth F],
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 D],
JL [auth E],
JM [auth F],
JN [auth M],
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 D],
KL [auth E],
KM [auth F],
LA [auth A],
LB [auth C],
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 D],
LL [auth E],
LM [auth F],
M [auth A],
MA [auth A],
MB [auth C],
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 D],
ML [auth F],
MM [auth F],
MN [auth N],
N [auth A],
NA [auth A],
NB [auth C],
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 D],
NL [auth F],
NM [auth F],
NN [auth N],
O [auth A],
OA [auth A],
OB [auth C],
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 D],
OL [auth F],
OM [auth F],
P [auth A],
PA [auth B],
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 D],
PL [auth F],
PM [auth F],
Q [auth A],
QA [auth B],
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 D],
QL [auth F],
QM [auth F],
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 D],
RL [auth F],
RM [auth F],
S [auth A],
SA [auth B],
SB [auth C],
SC [auth C],
SD [auth C],
SE [auth C],
SF [auth D],
SG [auth D],
SH [auth D],
SI [auth D],
SJ [auth D],
SK [auth D],
SL [auth F],
SM [auth F],
T [auth A],
TA [auth B],
TB [auth C],
TC [auth C],
TD [auth C],
TE [auth C],
TF [auth D],
TG [auth D],
TH [auth D],
TI [auth D],
TJ [auth D],
TK [auth D],
TL [auth F],
TM [auth F],
U [auth A],
UA [auth B],
UB [auth C],
UC [auth C],
UD [auth C],
UE [auth C],
UF [auth D],
UG [auth D],
UH [auth D],
UI [auth D],
UJ [auth D],
UK [auth D],
UL [auth F],
UM [auth F],
V [auth A],
VA [auth B],
VB [auth C],
VC [auth C],
VD [auth C],
VE [auth C],
VF [auth D],
VG [auth D],
VH [auth D],
VI [auth D],
VJ [auth D],
VK [auth E],
VL [auth F],
VM [auth F],
W [auth A],
WA [auth B],
WB [auth C],
WC [auth C],
WD [auth C],
WE [auth C],
WF [auth D],
WG [auth D],
WH [auth D],
WI [auth D],
WJ [auth D],
WK [auth E],
WL [auth F],
WM [auth F],
X [auth A],
XA [auth B],
XB [auth C],
XC [auth C],
XD [auth C],
XE [auth C],
XF [auth D],
XG [auth D],
XH [auth D],
XI [auth D],
XJ [auth D],
XK [auth E],
XL [auth F],
XM [auth F],
Y [auth A],
YA [auth B],
YB [auth C],
YC [auth C],
YD [auth C],
YE [auth C],
YF [auth D],
YG [auth D],
YH [auth D],
YI [auth D],
YJ [auth D],
YK [auth E],
YL [auth F],
YM [auth F],
Z [auth A],
ZA [auth B],
ZB [auth C],
ZC [auth C],
ZD [auth C],
ZF [auth D],
ZG [auth D],
ZH [auth D],
ZI [auth D],
ZJ [auth D],
ZK [auth E],
ZL [auth F],
ZM [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.266 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 236.35α = 90
b = 236.35β = 90
c = 249.04γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance