2NTM

Crystal structure of PurO from Methanothermobacter thermoautotrophicus

Summary for 2NTM

• Entry DOI: 10.2210/pdb2ntm/pdb
• Related: 2NTK 2NTL
• Descriptor: IMP cyclohydrolase (2 entities in total)
• Functional Keywords: alpha-beta-beta-alpha ntn hydrolase fold, hydrolase
• Biological source: Methanothermobacter thermautotrophicus
• Total number of polymer chains: 4
• Total formula weight: 96123.15

Authors

Kang, Y.N.,Tran, A.,White, R.H.,Ealick, S.E. (deposition date: 2006-11-07, release date: 2007-04-24, Last modification date: 2023-08-30)

Primary citation

Kang, Y.N.,Tran, A.,White, R.H.,Ealick, S.E.
A novel function for the N-terminal nucleophile hydrolase fold demonstrated by the structure of an archaeal inosine monophosphate cyclohydrolase.
Biochemistry, 46:5050-5062, 2007

PubMed Abstract: Inosine 5'-monophosphate (IMP) cyclohydrolase catalyzes the cyclization of 5-formaminoimidazole-4-carboxamide ribonucleotide (FAICAR) to IMP in the final step of de novo purine biosynthesis. Two major types of this enzyme have been discovered to date: PurH in Bacteria and Eukarya and PurO in Archaea. The structure of the MTH1020 gene product from Methanothermobacter thermoautotrophicus was previously solved without functional annotation but shows high amino acid sequence similarity to other PurOs. We determined the crystal structure of the MTH1020 gene product in complex with either IMP or 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) at 2.0 and 2.6 A resolution, respectively. On the basis of the sequence analysis, ligand-bound structures, and biochemical data, MTH1020 is confirmed as an archaeal IMP cyclohydrolase, thus designated as MthPurO. MthPurO has a four-layered alphabeta betaalpha core structure, showing an N-terminal nucleophile (NTN) hydrolase fold. The active site is located at the deep pocket between two central beta-sheets and contains residues strictly conserved within PurOs. Comparisons of the two types of IMP cyclohydrolase, PurO and PurH, revealed that there are no similarities in sequence, structure, or the active site architecture, suggesting that they are evolutionarily not related to each other. The MjR31K mutant of PurO from Methanocaldococcus jannaschii showed 76% decreased activity and the MjE102Q mutation completely abolished enzymatic activity, suggesting that these highly conserved residues play critical roles in catalysis. Interestingly, green fluorescent protein (GFP), which has no structural homology to either PurO or PurH but catalyzes a similar intramolecular cyclohydrolase reaction required for chromophore maturation, utilizes Arg96 and Glu222 in a mechanism analogous to that of PurO.

PubMed: 17407260
DOI: 10.1021/bi061637j

Experimental method

X-RAY DIFFRACTION (2.6 Å)