PDBsum entry: 1smy

Transferase

PDB id: 1smy

Contents

Protein chains

229 a.a. *

1119 a.a. *

1392 a.a. *

95 a.a. *

345 a.a. *

Ligands

G4P ×2

Metals

_MG ×362

_ZN ×4

Waters ×9031

* Residue conservation analysis

PDB id:

1smy

Name:

Transferase

Title:

Structural basis for transcription regulation by alarmone ppgpp

Structure:

DNA-directed RNA polymerase alpha chain. Chain: a, b, k, l. Synonym: rnap alpha subunit, transcriptase alpha chain, RNA polymerase alpha subunit. DNA-directed RNA polymerase beta chain. Chain: c, m. Synonym: rnap beta subunit, transcriptase beta chain, RNA polymerase beta subunit. DNA-directed RNA polymerase beta' chain.

Source:

Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274

Biol. unit:

Hexamer (from PQS)

Resolution:

2.70Å R-factor: 0.186 R-free: 0.266

Authors:

I.Artsimovitch,V.Patlan,S.Sekine,M.N.Vassylyeva,T.Hosaka, K.Ochi,S.Yokoyama,D.G.Vassylyev,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

I.Artsimovitch et al. (2004). Structural basis for transcription regulation by alarmone ppGpp. Cell, 117, 299-310. PubMed id: 15109491 DOI: 10.1016/S0092-8674(04)00401-5

Date:

10-Mar-04 Release date: 18-May-04

Protein chains

Q9Z9H6  (RPOA_THETH) -  DNA-directed RNA polymerase subunit alpha

Seq: 315 a.a.

Struc: 229 a.a.

Protein chains

Q8RQE9  (RPOB_THET8) -  DNA-directed RNA polymerase subunit beta

Seq: 1119 a.a.

Struc: 1119 a.a.

Protein chains

Q8RQE8  (RPOC_THET8) -  DNA-directed RNA polymerase subunit beta'

Seq: 1524 a.a.

Struc: 1392 a.a.

Protein chains

Q8RQE7  (RPOZ_THET8) -  DNA-directed RNA polymerase subunit omega

Seq: 99 a.a.

Struc: 95 a.a.*

Protein chains

Q9WX78  (Q9WX78_THETH) -  RNA polymerase sigma factor

Seq: 423 a.a.

Struc: 345 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, K, L, M, N, O: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)

Nucleoside triphosphate (Bound ligand (Het Group name = G4P) matches with 41.00% similarity) + RNA(n) = diphosphate + RNA(n+1)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: RNA polymerase complex (1 term)
• Biological process: regulation of transcription (6 terms)
• Biochemical function: transferase activity (9 terms)

reference

DOI no: 10.1016/S0092-8674(04)00401-5

Cell 117:299-310 (2004)

PubMed id: 15109491

Structural basis for transcription regulation by alarmone ppGpp.

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

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.

Selected figure(s)

Figure 2.
Figure 2. ppGpp Binding Site(A) Overall stereo view of the ppGpp bound to the RNAP (the RNAP1 molecule was used). ppGpp is shown as pink sticks. The protein surface is colored according to the electrostatic potentials (positive, negative, and neutral are dark blue, red, and white, respectively).(B and C) Stereo view of the active center and ppGpp binding site in RNAP1 and RNAP2, respectively. ppGpp are shown in 5′ (pink) (B) and 3′ (blue) (C) orientations. Mg^2+ ions and their coordination bonds are shown as large magenta spheres and cyan dashed sticks, respectively. Water molecules coordinating Mg^2+ ions are shown as small red spheres. Hydrogen bonds are represented by dashed black lines.

Figure 5.
Figure 5. A Model of the Open ComplexT and NT strands are in magenta and cyan, respectively. (A) Overall stereo view. RNAP is represented by the surface of the electrostatic potentials, as in Figure 3A. ppGpp is blue. σND1 and σND2 are the two N-terminal σ subunit domains. Tyr β′1093 (yellow) stacks on the dwDNA T base at the entrance of the active site. (B) Enlarged stereo view of the open complex in the vicinity of the active and ppGpp binding sites. ppGpp (blue) in the 3′ orientation forms a putative base pair (red dashes) with the NT cytosine.

The above figures are reprinted by permission from Cell Press: Cell (2004, 117, 299-310) copyright 2004.

Figures were selected by the author.