1SMY

Structural basis for transcription regulation by alarmone ppGpp

• PDB DOI: https://doi.org/10.2210/pdb1SMY/pdb

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


• Deposited: 2004-03-10 Released: 2004-05-18 
• Deposition Author(s): Artsimovitch, I., Patlan, V., Sekine, S., Vassylyeva, M.N., Hosaka, T., Ochi, K., Yokoyama, S., Vassylyev, D.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.266 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.266 (Depositor) 

Starting Model: experimental

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

• PubMed: 15109491 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

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.

Macromolecule Content

• Total Structure Weight: 863.54 kDa 
• Atom Count: 63,021 
• 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 Q9Z9H6 (Thermus thermophilus) Explore Q9Z9H6  Go to UniProtKB:  Q9Z9H6

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 SUBUNIT	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
principal sigma factor	F, L [auth P]	423	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q72L95 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72L95  Go to UniProtKB:  Q72L95

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G4P	ON [auth N], PN [auth N]	GUANOSINE-5',3'-TETRAPHOSPHATE C10 H17 N5 O17 P4 BUFLLCUFNHESEH-UUOKFMHZSA-N
ZN	AF [auth D], KN [auth N], LN [auth N], ZE [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.266 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.266 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 236.35	α = 90
b = 236.35	β = 90
c = 249.04	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: 2004-05-18 
Deposition Author(s): Artsimovitch, I., Patlan, V., Sekine, S., Vassylyeva, M.N., Hosaka, T., Ochi, K., Yokoyama, S., Vassylyev, D.G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• 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
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary