PDBsum entry 1ex2

Structural genomics

PDB id: 1ex2

Contents

Protein chains

185 a.a. *

Ligands

GLC-FRU

PO4 ×3

Waters ×306

* Residue conservation analysis

PDB id:

1ex2

Name:

Structural genomics

Title:

Crystal structure of bacillus subtilis maf protein

Structure:

Protein maf. Chain: a, b. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.85Å R-factor: 0.195 R-free: 0.223

Authors:

G.Minasov,M.Teplova,G.C.Stewart,E.V.Koonin,W.F.Anderson,M.Egli, Midwest Center For Structural Genomics (Mcsg)

Key ref:

G.Minasov et al. (2000). Functional implications from crystal structures of the conserved Bacillus subtilis protein Maf with and without dUTP. Proc Natl Acad Sci U S A, 97, 6328-6333. PubMed id: 10841541 DOI: 10.1073/pnas.97.12.6328

Date:

28-Apr-00 Release date: 14-Jun-00

Protein chains

Q02169  (MAF_BACSU) -  dTTP/UTP pyrophosphatase from Bacillus subtilis (strain 168)

Seq: 189 a.a.

Struc: 185 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.9 - nucleotide diphosphatase.
• Reaction:
  1. a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-phosphate + diphosphate + H⁺
  2. a 2'-deoxyribonucleoside 5'-triphosphate + H2O = a 2'-deoxyribonucleoside 5'-phosphate + diphosphate + H⁺

ribonucleoside 5'-triphosphate + H2O = ribonucleoside 5'-phosphate + diphosphate (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + H(+)

2'-deoxyribonucleoside 5'-triphosphate + H2O = 2'-deoxyribonucleoside 5'-phosphate + diphosphate (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1073/pnas.97.12.6328

Proc Natl Acad Sci U S A 97:6328-6333 (2000)

PubMed id: 10841541

Functional implications from crystal structures of the conserved Bacillus subtilis protein Maf with and without dUTP.

G.Minasov, M.Teplova, G.C.Stewart, E.V.Koonin, W.F.Anderson, M.Egli.

ABSTRACT

Three-dimensional structures of functionally uncharacterized proteins may furnish insight into their functions. The potential benefits of three-dimensional structural information regarding such proteins are particularly obvious when the corresponding genes are conserved during evolution, implying an important function, and no functional classification can be inferred from their sequences. The Bacillus subtilis Maf protein is representative of a family of proteins that has homologs in many of the completely sequenced genomes from archaea, prokaryotes, and eukaryotes, but whose function is unknown. As an aid in exploring function, we determined the crystal structure of this protein at a resolution of 1.85 A. The structure, in combination with multiple sequence alignment, reveals a putative active site. Phosphate ions present at this site and structural similarities between a portion of Maf and the anticodon-binding domains of several tRNA synthetases suggest that Maf may be a nucleic acid-binding protein. The crystal structure of a Maf-nucleoside triphosphate complex provides support for this hypothesis and hints at di- or oligonucleotides with either 5'- or 3'-terminal phosphate groups as ligands or substrates of Maf. A further clue comes from the observation that the structure of the Maf monomer bears similarity to that of the recently reported Methanococcus jannaschii Mj0226 protein. Just as for Maf, the structure of this predicted NTPase was determined as part of a structural genomics pilot project. The structural relation between Maf and Mj0226 was not apparent from sequence analysis approaches. These results emphasize the potential of structural genomics to reveal new unexpected connections between protein families previously considered unrelated.

Selected figure(s)

Figure 1.
Fig. 1. (A) Final (2 F[o] F[c]) electron density at 1.85 Å resolution [1 level, drawn with TURBO FRODO (37)], depicting the phosphate ion bound at the Maf putative active site. Atoms of selected side chains are colored yellow, blue, and red for carbon, nitrogen, and oxygen, respectively, and oxygen atoms of water molecules are shown as small red spheres. (B) Overall structure of the Maf protein drawn with the program RIBBONS (38). The helices and strands are colored cyan and green, respectively, and are numbered. Loop regions are colored orange, N and C termini are labeled, and a yellow dot indicates the location of the disulfide bridge.

Figure 3.
Fig. 3. (A) Arrangement of conserved residues on the 3D surface of Maf. Green, yellow, and cyan patches indicate the locations of amino acids that are conserved in 18 or more, in 17 or 16 of 19, and in 15 of 19 analyzed proteins, respectively (see Fig. 2). All other residues are white. (B) Electrostatic surface potential of Maf calculated with the program GRASP (39). Blue and red patches indicate regions of positive and negative charge, respectively. The views in A and B are similar to that in Fig. 1B.

Figures were selected by an automated process.