PDBsum entry 1mh3

Sugar binding, DNA binding protein

PDB id: 1mh3

Contents

Protein chain

421 a.a. *

Waters ×230

* Residue conservation analysis

PDB id:

1mh3

Name:

Sugar binding, DNA binding protein

Title:

Maltose binding-a1 homeodomain protein chimera, crystal form i

Structure:

Maltose binding-a1 homeodomain protein chimera. Chain: a. Synonym: mata1 homeodomain-maltose binding protein chimera. Engineered: yes. Mutation: yes. Other_details: chimera consisting of residues 1-366 (sequence database residues 27-392) of maltose-binding periplasmic protein, a 5 alanine linker, and residues 477-526 (sequence database residues 77- 126) of homeobox of mating-type protein a-1.

Source:

Escherichia coli, saccharomyces cerevisiae. , Baker's yeast. Organism_taxid: 562, 4932. Strain: ,. Expressed in: escherichia coli. Expression_system_taxid: 562. Linker

Resolution:

2.10Å R-factor: 0.232 R-free: 0.262

Authors:

A.Ke,C.Wolberger

Key ref:

A.Ke and C.Wolberger (2003). Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera. Protein Sci, 12, 306-312. PubMed id: 12538894 DOI: 10.1110/ps.0219103

Date:

19-Aug-02 Release date: 18-Sep-02

Protein chain

P0AEX9  (MALE_ECOLI) -  Maltose/maltodextrin-binding periplasmic protein from Escherichia coli (strain K12)

Seq: 396 a.a.

Struc: 421 a.a.*

Protein chain

P0CY11  (HMRA1_YEAST) -  Silenced mating-type protein A1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 126 a.a.

Struc: 421 a.a.*

* PDB and UniProt seqs differ at 82 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1110/ps.0219103

Protein Sci 12:306-312 (2003)

PubMed id: 12538894

Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera.

A.Ke, C.Wolberger.

ABSTRACT

The Yeast MATa1 and MATalpha2 are homeodomain proteins that bind DNA cooperatively to repress transcription of cell type specific genes. The DNA affinity and specificity of MATa1 in the absence of MATalpha2, however, is very low. MATa1 is converted to a higher affinity DNA-binding protein by its interaction with the C-terminal tail of MATalpha2. To understand why MATa1 binds DNA weakly by itself, and how the MATalpha2 tail affects the affinity of MATa1 for DNA, we determined the crystal structure of a maltose-binding protein (MBP)-a1 chimera whose DNA binding behavior is similar to MATa1. The overall MATa1 conformation in the MBP-a1 structure, which was determined in the absence of alpha2 and DNA, is similar to that in the a1/alpha2/DNA structure. The sole difference is in the C-terminal portion of the DNA recognition helix of MATa1, which is flexible in the present structure. However, these residues are not in a location likely to be affected by binding of the MATalpha2 tail. The results argue against conformational changes in a1 induced by the tail of MATalpha2, suggesting instead that the MATalpha2 tail energetically couples the DNA binding of MATalpha2 and MATa1.

Selected figure(s)

Figure 1.
Figure 1. Overview of the crystal structure of the a1/ 2/DNA ternary complex. The a1 homeodomain is shown in red, 2 in blue, and the DNA in silver. The three helices of a1 and the tail of 2 have been noted. The 2 tail folds into a short amphipathic helix and packs against the groove formed by Helix 1 and 2 of a1.

Figure 2.
Figure 2. Overview of the MBP-a1 chimeric protein structure. The MBP moiety is shown in cyan; the five-residue polyalanine linker and the a1 homeodomain are shown in magenta. Note the short alanine linker that adopts a turn conformation to avoid steric clashes between a1 and MBP molecule. The 2 tail binding site on the a1 homeodomain is not in contact with MBP.

The above figures are reprinted by permission from the Protein Society: Protein Sci (2003, 12, 306-312) copyright 2003.

Figures were selected by the author.