PDBsum entry: 1lb2

Gene regulation/DNA

PDB-id: 1lb2

Asymmetric unit

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Description

Header details

Header records

References

PROCHECK

Protein chains

201 a.a. *

72 a.a. *

66 a.a. *

DNA/RNA

Ligands

CMP

Waters ×32

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit, decamer
- as defined in PDB file (see also PQS)

PDB id:

1lb2

Name:

Gene regulation/DNA

Title:

Structure of the e. Coli alpha c-terminal domain of RNA polymerase in complex with cap and DNA

Structure:

5'- d( Cp Tp Tp Tp Tp Tp Tp Cp Cp Tp Ap Ap Ap Ap Tp Gp Tp Gp Ap T)-3'. Chain: k. Engineered: yes. 5'- d( Cp Tp Ap Gp Ap Tp Cp Ap Cp Ap Tp Tp Tp Tp Ap Gp Gp Ap Ap Ap Ap Ap Ap G)-3'. Chain: j.

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biological unit:

Decamer (from PDB file)

UniProt:

Chain A: P0ACJ8 (CRP_ECOLI)

Seq:	210 a.a.
Struc:	201 a.a.

Chain B: P0A7Z4 (RPOA_ECOLI)

Seq:
Struc:
	Seq:	329 a.a.
	Struc:	72 a.a.

Chain E: P0A7Z4 (RPOA_ECOLI)

Seq:

Struc:

Seq:

329 a.a.

Struc:

66 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

Chains B, E: E.C.2.7.7.6   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1) (see diagram below)

Resolution:

3.10Å

R-factor:

0.211

R-free:

0.244

Authors:

B.Benoff,H.Yang,C.L.Lawson,G.Parkinson,J.Liu,E.Blatter, Y.W.Ebright,H.M.Berman,R.H.Ebright

Key ref:

B.Benoff et al. (2002). Structural basis of transcription activation: the CAP-alpha CTD-DNA complex.. Science, 297, 1562-1566. [PubMed id: 12202833] [DOI: 10.1126/science.1076376]

Date:

01-Apr-02

Release date:

06-Sep-02

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Surface

Key reference

DOI no: 10.1126/science.1076376

Science 297:1562-1566 (2002)

PubMed id: 12202833

Structural basis of transcription activation: the CAP-alpha CTD-DNA complex.

B.Benoff, H.Yang, C.L.Lawson, G.Parkinson, J.Liu, E.Blatter, Y.W.Ebright, H.M.Berman, R.H.Ebright.

ABSTRACT

The Escherichia coli catabolite activator protein (CAP) activates transcription at P(lac), P(gal), and other promoters through interactions with the RNA polymerase alpha subunit carboxyl-terminal domain (alphaCTD). We determined the crystal structure of the CAP-alphaCTD-DNA complex at a resolution of 3.1 angstroms. CAP makes direct protein-protein interactions with alphaCTD, and alphaCTD makes direct protein-DNA interactions with the DNA segment adjacent to the DNA site for CAP. There are no large-scale conformational changes in CAP and alphaCTD, and the interface between CAP and alphaCTD is small. These findings are consistent with the proposal that activation involves a simple "recruitment" mechanism.

Selected figure(s)

Figure 2.
Fig. 2. CAP- CTD^CAP,DNA-DNA(interactions representative of those at a class I or class II CAP-dependent promoter). (A) Stereo view of interactions among CAP, CTD^CAP,DNA, and DNA (two orthogonal views). AR1 of CAP is in blue; the 287 determinant (CAP contact), 265 determinant (DNA contact), and the 261 determinant (proposed 70 contact) of CTD^CAP,DNA are in yellow, red, and gray-white, respectively. (B) Interactions between AR1 of CAP and residues 285 to 288 of the 287 determinant of CTD^CAP,DNA. Hydrogen bonds are in magenta. (C) Interactions between the COOH-terminal residue of CAP (Arg209) and residues 315 and 317 of the 287 determinant of CTD^CAP,DNA. Hydrogen bonds are in magenta. C-TER, COOH-terminus. (D) Interactions between CTD^CAP,DNA and DNA (view along DNA minor-groove axis). Water-mediated hydrogen bonds involving the Arg265 side-chain guanidinium, DNA bases, and an experimentally defined water molecule (sphere near center) are in cyan. The network of hydrogen bonds buttressing the Arg265 side-chain guanidinium relative to the phosphate backbones of the two DNA strands is in yellow. Other hydrogen bonds are in magenta. (E) Summary of interactions between CTD^CAP,DNA and DNA. Colors are as in (D). G, Gly; K, Lys; N, Asn; R, Arg; S, Ser; and V, Val.

Figure 3.
Fig. 3. CTD^DNA-DNA (interactions representative of those at an UP element subsite-dependent promoter). (A) Stereo view comparing interactions between CTD^DNA and DNA (dark green and gray) and interactions between CTD^CAP-DNA and DNA (light green and gray) (RMSD = 0.74 Å for 72 C and 10 P atoms). (B) Interactions between CTD^DNA and DNA. View and colors are as in Fig. 2D. No water molecules were observed in the CTD^DNA-DNA interface in this structure at 3.1 Å. However, the positions of the Arg265 side-chain guanidinium and DNA bases are compatible with the establishment of water-mediated hydrogen bonds identical to those at the CTD^CAP,DNA-DNA interface (Fig. 2D) (39). (C) Summary of interactions between CTD^DNA and DNA. Colors are as in Fig. 2, D and E.

The above figures are reprinted by permission from the AAAs: Science (2002, 297, 1562-1566) copyright 2002.

Figures were selected by the author.