PDBsum entry 2h9b

Transcription

PDB id: 2h9b

Contents

Protein chains

216 a.a.

Ligands

SO4 ×7

Metals

_CL ×3

Waters ×741

References listed in PDB file

Key reference

Title

Inducer responses of benm, A lysr-Type transcriptional regulator from acinetobacter baylyi ADP1.

Authors

S.H.Craven, O.C.Ezezika, S.Haddad, R.A.Hall, C.Momany, E.L.Neidle.

Ref.

Mol Microbiol, 2009, 72, 881-894.

PubMed id

19400783

Note: In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above have been manually determined.

Abstract

BenM and CatM control transcription of a complex regulon for aromatic compound degradation. These Acinetobacter baylyi paralogues belong to the largest family of prokaryotic transcriptional regulators, the LysR-type proteins. Whereas BenM activates transcription synergistically in response to two effectors, benzoate and cis,cis-muconate, CatM responds only to cis,cis-muconate. Here, site-directed mutagenesis was used to determine the physiological significance of an unexpected benzoate-binding pocket in BenM discovered during structural studies. Residues in BenM were changed to match those of CatM in this hydrophobic pocket. Two BenM residues, R160 and Y293, were found to mediate the response to benzoate. Additionally, alteration of these residues caused benzoate to inhibit activation by cis,cis-muconate, positioned in a separate primary effector-binding site of BenM. The location of the primary site, in an interdomain cleft, is conserved in diverse LysR-type regulators. To improve understanding of this important family, additional regulatory mutants were analysed. The atomic-level structures were characterized of the effector-binding domains of variants that do not require inducers for activation, CatM(R156H) and BenM(R156H,T157S). These structures clearly resemble those of the wild-type proteins in their activated muconate-bound complexes. Amino acid replacements that enable activation without effectors reside at protein interfaces that may impact transcription through effects on oligomerization.

Secondary reference #1

Title

Distinct effector-Binding sites enable synergistic transcriptional activation by benm, A lysr-Type regulator.

Authors

O.C.Ezezika, S.Haddad, T.J.Clark, E.L.Neidle, C.Momany.

Ref.

J Mol Biol, 2007, 367, 616-629. [DOI no: 10.1016/j.jmb.2006.09.090]

PubMed id

17291527

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a perfect match.

Figure 3.

Figure 5.
Figure 5. Schematic representation of the BenM-EBD effector-binding sites. (a) Muconate in the primary site. Hydrogen bonds (between non-hydrogen atoms) to the effector are shown as broken lines. The distance between the O1 of muconate and the Arg146 N^ε atom is also shown (dash-dot). Helices, colored as in Figure 2, are shown as cylinders. β-Strands were omitted for clarity. (b) Benzoate in the secondary site. H1 is a 3[10]-helix associated with both binding sites. (c) Residues implicated in the charge relay postulated to be responsible for synergistic activation.

The above figures are reproduced from the cited reference with permission from Elsevier