ISDA

Deposition Date 1999-07-09

Release Date 1999-11-26

Last Version Date 2024-02-14

Entry Detail

PDB ID:

1QD9

Keywords:

GENE REGULATION

Title:

Bacillus subtilis YABJ

Biological Source:

Source Organism:

Bacillus subtilis (Taxon ID: 1423)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.70 Å

R-Value Free:

0.19

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 65

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PURINE REGULATORY PROTEIN YABJ
Gene (Uniprot):ridA
Chain IDs:A, B, C
Chain Length:124
Number of Molecules:3
Biological Source:Bacillus subtilis

UniProt ID:P37552 Pfam ID:PF01042 EC:3.5.99.10

Ligand Molecules

ACY

EMC

Primary Citation

Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family.

Sinha, S, Rappu, P, Lange, S.C, Mantsala, P, Zalkin, H, Smith, J.L.Show

Proc.Natl.Acad.Sci.USA 96 13074 13079 (1999)

PMID: 10557275 DOI: 10.1073/pnas.96.23.13074

Abstact

The yabJ gene in Bacillus subtilis is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The molecular mechanism of YabJ is unknown. YabJ is a member of a large, widely distributed family of proteins of unknown biochemical function. The 1.7-A crystal structure of YabJ reveals a trimeric organization with extensive buried hydrophobic surface and an internal water-filled cavity. The most important finding in the structure is a deep, narrow cleft between subunits lined with nine side chains that are invariant among the 25 most similar homologs. This conserved site is proposed to be a binding or catalytic site for a ligand or substrate that is common to YabJ and other members of the YER057c/YjgF/UK114 family of proteins.

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Primary Citation of related structures