PDBsum entry: 1mkz

Biosynthetic protein

PDB id: 1mkz

Contents

Protein chains

170 a.a. *

Ligands

SO4 ×7

ACY ×3

Waters ×235

* Residue conservation analysis

PDB id:

1mkz

Name:

Biosynthetic protein

Title:

Crystal structure of moab protein at 1.6 a resolution.

Structure:

Molybdenum cofactor biosynthesis protein b. Chain: a, b. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: moab. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Hexamer (from PQS)

Resolution:

1.60Å R-factor: 0.185 R-free: 0.219

Authors:

R.Sanishvili,T.Skarina,A.Joachimiak,A.Edwards,A.Savchenko, Midwest Center For Structural Genomics (Mcsg)

Key ref:

R.Sanishvili et al. (2004). The crystal structure of Escherichia coli MoaB suggests a probable role in molybdenum cofactor synthesis. J Biol Chem, 279, 42139-42146. PubMed id: 15269205 DOI: 10.1074/jbc.M407694200

Date:

29-Aug-02 Release date: 22-Apr-03

Protein chains

P0AEZ9  (MOAB_ECOLI) -  Molybdenum cofactor biosynthesis protein B

Seq: 170 a.a.

Struc: 170 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Biological process: Mo-molybdopterin cofactor biosynthetic process (1 term)
• Biochemical function: nucleotide binding (2 terms)

DOI no: 10.1074/jbc.M407694200

J Biol Chem 279:42139-42146 (2004)

PubMed id: 15269205

The crystal structure of Escherichia coli MoaB suggests a probable role in molybdenum cofactor synthesis.

R.Sanishvili, S.Beasley, T.Skarina, D.Glesne, A.Joachimiak, A.Edwards, A.Savchenko.

ABSTRACT

The crystal structure of Escherichia coli MoaB was determined by multiwavelength anomalous diffraction phasing and refined at 1.6-A resolution. The molecule displayed a modified Rossman fold. MoaB is assembled into a hexamer composed of two trimers. The monomers have high structural similarity with two proteins, MogA and MoeA, from the molybdenum cofactor synthesis pathway in E. coli, as well as with domains of mammalian gephyrin and plant Cnx1, which are also involved in molybdopterin synthesis. Structural comparison between these proteins and the amino acid conservation patterns revealed a putative active site in MoaB. The structural analysis of this site allowed to advance several hypothesis that can be tested in further studies.

Selected figure(s)

Figure 2.
FIG. 2. Oligomerization of MoaB. A, view of a trimer along the crystallographic 3-fold axis. Six strands of the sheet (yellow), along with and 3[10] helices (pink), are labeled in one monomer. The 3[10] helix (perpendicular to the plane of the paper) of one monomer forms rich hydrophobic interactions in the cleft created by helices 4, 5, and the loop between 5 and 6 (labeled L56) of the other. B, electrostatic representation of the surface of MoaB hexamer. Red and blue correspond to the negatively and positively charged areas, respectively, whereas white represents neutral regions. The hexamer can be approximated as a cylinder 62-Å high with a radius of 35 Å. Longitudinal and equatorial grooves are also visible intersecting at the central hole created between the four monomers. Bound sulfate ions are represented with red (oxygens) and yellow (sulfur) spheres. Two sulfate ions, which could mimic the phosphate groups in the binding site, are labeled Pho1 and Pho2. The binding of remaining sulfates is probably opportunistic. Fig. 2B was prepared with GRASP (42).

Figure 7.
FIG. 7. Modeled GTP in the binding site of MoaB. The surface of the protein containing the binding site is color-coded with red oxygens, blue nitrogens, and gray carbons. Experimentally observed sulfate ions (orange S and red O atoms) are shown with their corresponding 2F[o] - F[c] electron densities contoured at a 1 level (green mesh). Water molecules are shown as cyan spheres. Sulfates are labeled Pho1 and Pho2 because they likely are phosphate groups in vivo. Associated with Pho1, electron density has an additional feature, which cannot be explained with the sulfate ion and which extends toward Pho2. It is likely the remnant of a phosphate-containing compound from the physiological complex. Arg21 and Arg22 are also labeled. The guanidinium group of the Arg22 side chain is not entirely visible in our structure but is added in this figure to show its proximal position and to avoid the creation of an apparent extended surface depression that could lead to erroneous interpretations. The ridge, separating two deeper cavities on either side of Pho1, is formed by two conserved motifs, Gly77-Gly78-Thr79-Gly80 and Pro137-Gly138-Ser139. Modeled GTP is shown with stick model color coded as yellow carbons, blue nitrogens, red oxygens, and magenta phosphors. The locations of the Glu52 and Asp85 carboxyl groups are indicated with labels, and the location of Ser110 is shown with an arrow.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 42139-42146) copyright 2004.

Figures were selected by an automated process.