3AV3

Crystal structure of glycinamide ribonucleotide transformylase 1 from Geobacillus kaustophilus

Summary for 3AV3

• Entry DOI: 10.2210/pdb3av3/pdb
• Descriptor: Phosphoribosylglycinamide formyltransferase, MAGNESIUM ION (3 entities in total)
• Functional Keywords: structural genomics, riken structural genomics/proteomics initiative, rsgi, rossmann fold, transformylase, folate binding, transferase
• Biological source: Geobacillus kaustophilus
• Total number of polymer chains: 1
• Total formula weight: 23517.72

Authors

Kanagawa, M.,Baba, S.,Nakagawa, N.,Ebihara, A.,Kuramitsu, S.,Yokoyama, S.,Sampei, G.,Kawai, G.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2011-02-18, release date: 2012-03-07, Last modification date: 2024-10-23)

Primary citation

Sampei, G.,Kanagawa, M.,Baba, S.,Shimasaki, T.,Taka, H.,Mitsui, S.,Fujiwara, S.,Yanagida, Y.,Kusano, M.,Suzuki, S.,Terao, K.,Kawai, H.,Fukai, Y.,Nakagawa, N.,Ebihara, A.,Kuramitsu, S.,Yokoyama, S.,Kawai, G.
Structures and reaction mechanisms of the two related enzymes, PurN and PurU.
J.Biochem., 154:569-579, 2013

PubMed Abstract: The crystal structures of glycinamide ribonucleotide transformylases (PurNs) from Aquifex aeolicus (Aa), Geobacillus kaustophilus (Gk) and Symbiobacterium toebii (St), and of formyltetrahydrofolate hydrolase (PurU) from Thermus thermophilus (Tt) were determined. The monomer structures of the determined PurN and PurU were very similar to the known structure of PurN, but oligomeric states were different; AaPurN and StPurN formed dimers, GkPurN formed monomer and PurU formed tetramer in the crystals. PurU had a regulatory ACT domain in its N-terminal side. So far several structures of PurUs have been determined, yet, the mechanisms of the catalysis and the regulation of PurU have not been elucidated. We, therefore, modelled ligand-bound structures of PurN and PurU, and performed molecular dynamics simulations to elucidate the reaction mechanisms. The evolutionary relationship of the two enzymes is discussed based on the comparisons of the structures and the catalytic mechanisms.

PubMed: 24108189
DOI: 10.1093/jb/mvt090

Experimental method

X-RAY DIFFRACTION (1.7 Å)