PDBsum entry 1mj2

Transcription/DNA

PDB id: 1mj2

Contents

Protein chains

104 a.a. *

DNA/RNA

Ligands

SAM ×4

Metals

_CA

Waters ×220

* Residue conservation analysis

PDB id:

1mj2

Name:

Transcription/DNA

Title:

Methionine repressor mutant (q44k) plus corepressor (s-adenosyl methionine) complexed to a consensus operator sequence

Structure:

DNA (5'- d( Tp Tp Ap Gp Ap Cp Gp Tp Cp Tp Ap Gp Ap Cp Gp Tp Cp Tp A)-3'). Chain: f, g. Engineered: yes. Protein (methionine repressor). Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

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

Biol. unit:

Dimer (from PDB file)

Resolution:

2.40Å R-factor: 0.212 R-free: 0.260

Authors:

C.W.Garvie,S.E.V.Phillips

Key ref:

C.W.Garvie and S.E.Phillips (2000). Direct and indirect readout in mutant Met repressor-operator complexes. Structure, 8, 905-914. PubMed id: 10986458

Date:

27-Jan-98 Release date: 02-Aug-99

Protein chains

P0A8U6  (METJ_ECOLI) -  Met repressor from Escherichia coli (strain K12)

Seq: 105 a.a.

Struc: 104 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

T-T-A-G-A-C-G-T-C-T-A-G-A-C-G-T-C-T-A 19 bases

T-T-A-G-A-C-G-T-C-T-A-G-A-C-G-T-C-T-A 19 bases

Enzyme reactions

• Enzyme class: E.C.?

Structure 8:905-914 (2000)

PubMed id: 10986458

Direct and indirect readout in mutant Met repressor-operator complexes.

C.W.Garvie, S.E.Phillips.

ABSTRACT

BACKGROUND: The methionine repressor, MetJ, represses the transcription of genes involved in methionine biosynthesis by binding to arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. Naturally occurring operators differ from the consensus sequence to a greater extent as the number of metboxes increases. MetJ, while accommodating this sequence variation in natural operators, is very sensitive to particular base changes, even where bases are not directly contacted in the crystal structure of a complex formed between the repressor and consensus operator. RESULTS: Here we report the high-resolution structure of a MetJ mutant, Q44K, bound to the consensus operator sequence (Q44Kwt19) and two related sequences containing mutations at sites believed to be important for indirect readout at non-contacted bases. The overall structure of the Q44Kwt19 complex is very similar to the wild-type complex, but there are small variations in sugar-phosphate backbone conformation and direct contacts to the DNA bases. The mutant complexes show a mixture of direct and indirect readout of sequence variations, with differences in direct contacts and DNA conformation. CONCLUSIONS: Comparison of the wild-type and mutant repressor-operator complexes shows that the repressor makes sufficiently strong interactions with the sugar-phosphate backbone to accommodate some variation in operator sequence with minor changes in direct bases contacts. The reduction in repressor affinity for the two mutant repressor complexes can be partially attributed to a loss in direct contacts to the DNA. In one case, however, the replacement of a flexible TA base-step leads to an unfavourable DNA conformation that reduces the stability of the repressor-operator complex.