PDBsum entry 3epm

Biosynthetic protein

PDB id: 3epm

Contents

Protein chains

515 a.a. *

Ligands

HMH

SO4

Metals

_ZN ×2

Waters ×133

* Residue conservation analysis

PDB id:

3epm

Name:

Biosynthetic protein

Title:

Crystal structure of caulobacter crescentus thic

Structure:

Thiamine biosynthesis protein thic. Chain: a, b. Engineered: yes

Source:

Caulobacter crescentus. Organism_taxid: 155892. Gene: thic. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.79Å R-factor: 0.185 R-free: 0.244

Authors:

S.Li,A.Chatterjee,Y.Zhang,T.L.Grove,M.Lee,C.Krebs,S.J.Booker, T.P.Begley,S.E.Ealick

Key ref:

A.Chatterjee et al. (2008). Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily. Nat Chem Biol, 4, 758-765. PubMed id: 18953358 DOI: 10.1038/nchembio.121

Date:

29-Sep-08 Release date: 28-Oct-08

Protein chains

Q9A6Q5  (THIC_CAUVC) -  Phosphomethylpyrimidine synthase from Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)

Seq: 612 a.a.

Struc: 515 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.99.17 - phosphomethylpyrimidine synthase.
• Reaction: 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + CO + 5'-deoxyadenosine + formate + L-methionine + 3 H⁺

5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + CO (Bound ligand (Het Group name = HMH) matches with 55.56% similarity) + 5'-deoxyadenosine + formate + L-methionine + 3 × H(+)

• Cofactor: Iron-sulfur

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

reference

DOI no: 10.1038/nchembio.121

Nat Chem Biol 4:758-765 (2008)

PubMed id: 18953358

Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily.

A.Chatterjee, Y.Li, Y.Zhang, T.L.Grove, M.Lee, C.Krebs, S.J.Booker, T.P.Begley, S.E.Ealick.

ABSTRACT

4-Amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase catalyzes a complex rearrangement of 5-aminoimidazole ribonucleotide (AIR) to form HMP-P, the pyrimidine moiety of thiamine phosphate. We determined the three-dimensional structures of HMP-P synthase and its complexes with the product HMP-P and a substrate analog imidazole ribotide. The structure of HMP-P synthase reveals a homodimer in which each protomer comprises three domains: an N-terminal domain with a novel fold, a central (betaalpha)(8) barrel and a disordered C-terminal domain that contains a conserved CX(2)CX(4)C motif, which is suggestive of a [4Fe-4S] cluster. Biochemical studies have confirmed that HMP-P synthase is iron sulfur cluster-dependent, that it is a new member of the radical SAM superfamily and that HMP-P and 5'-deoxyadenosine are products of the reaction. Mössbauer and EPR spectroscopy confirm the presence of one [4Fe-4S] cluster. Structural comparisons reveal that HMP-P synthase is homologous to a group of adenosylcobalamin radical enzymes. This similarity supports an evolutionary relationship between these two superfamilies.

Selected figure(s)

Figure 1.
(a) Overall bacterial pathway. AIR (12) is converted to HMP-P (15) by HMP-P synthase (ThiC), which is phosphorylated by ThiD to give HMP pyrophosphate (3). The thiazole moiety (2) is biosynthesized from DXP (6), cysteine (8) and dehydroglycine (34). The dehydroglycine is generated from glycine (ThiO) in B. subtilis and from tyrosine (ThiH) in E. coli. The pyrimidine and thiazole are coupled by ThiE to give thiamine phosphate (4), and ThiL catalyzes the final phosphorylation. (b) Conversion of AIR to the thiamine pyrimidine in bacteria and plants. The color coding indicates the source of nonhydrogen atoms in HMP-P as demonstrated by labeling studies. (c) Biosynthesis of thiamine pyrimidine in fungi. In fungi the pyrimidine moiety is derived from histidine (13) and pyridoxal 5'-phosphate (14) using a single enzyme, THI5p. The color coding indicates the source of nonhydrogen atoms. (d) The HMP-P synthase reactions. When iron-sulfur cluster–loaded HMP-P synthase is reduced with dithionite, it reduces SAM (16) to generate methionine (28) and the 5'-deoxyadenosyl (5-dAdo) radical (17), which is required by HMP-P synthase to convert AIR to HMP-P.

Figure 4.
(a) The HMP-P synthase homodimer. The protomer consists of three domains. The N-terminal domains are colored in shades of blue, the ( )[8] core domains are colored in shades of green and the C-terminal domains are colored in shades of red. HMP-P is shown as a ball-and-stick model. The final 66 amino acids are disordered; however, the final ordered residues, which immediately precede a conserved CX[2]CX[4]C motif, extend into the active site of the adjacent protomer. The C-terminal tail is anchored to the adjacent protomer by a three-helix bundle motif located at the beginning of the C-terminal domain. (b) Stereoview of the HMP-P synthase active site with modeled SAM and the [4Fe-4S] cluster. The atoms are color coded by atom type (green = C, blue = N, red = O, yellow = S and orange = Fe). The substrate analog IMR 22 from the crystal structure is shown. Residues Cys561, Cys564 and Cys569, SAM and the [4Fe-4S] cluster were modeled using biotin synthase as a guide. Hydrogen bonds are indicated by dotted lines. (c) Superposition of the ( )[8] domains from HMP-P synthase and biotin synthase (PDB ID 1R3O). HMP-P synthase is shown in blue, and biotin synthase is shown in silver. The [4Fe-4S] cluster and SAM from biotin synthase are shown as ball-and-stick models.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nat Chem Biol (2008, 4, 758-765) copyright 2008.

Figures were selected by an automated process.