5AVM

Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, PurM, from Thermus thermophilus

Summary for 5AVM

• Entry DOI: 10.2210/pdb5avm/pdb
• Descriptor: Phosphoribosylformylglycinamidine cyclo-ligase, SULFATE ION (3 entities in total)
• Functional Keywords: purine biosynthesis, atp binding, structural genomics, riken structural genomics/proteomics initiative, rsgi, ligase
• Biological source: Thermus thermophilus HB8
• Total number of polymer chains: 8
• Total formula weight: 285166.45

Authors

Kanagawa, M.,Baba, S.,Watanabe, Y.,Nakagawa, N.,Ebihara, A.,Sampei, G.,Kawai, G.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2015-06-23, release date: 2015-11-25, Last modification date: 2023-11-08)

Primary citation

Kanagawa, M.,Baba, S.,Watanabe, Y.,Nakagawa, N.,Ebihara, A.,Kuramitsu, S.,Yokoyama, S.,Sampei, G.,Kawai, G.
Crystal structures and ligand binding of PurM proteins from Thermus thermophilus and Geobacillus kaustophilus
J.Biochem., 159:313-321, 2016

PubMed Abstract: Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, also known as PurM, from Thermus thermophilus (Tt) and Geobacillus kaustophilus (Gk) were determined. For TtPurM, the maximum resolution was 2.2 Å and the space group was P21212 with four dimers in an asymmetric unit. For GkPurM, the maximum resolution was 2.2 Å and the space group was P21212 with one monomer in asymmetric unit. The biological unit is dimer for both TtPurM and GkPurM and the dimer structures were similar to previously determined structures of PurM in general. For TtPurM, ∼50 residues at the amino terminal were disordered in the crystal structure whereas, for GkPurM, the corresponding region covered the ATP-binding site forming an α helix in part, suggesting that the N-terminal region of PurM changes its conformation upon binding of ligands. FGAM binding site was predicted by the docking simulation followed by the MD simulation based on the SO4 (2-) binding site found in the crystal structure of TtPurM.

PubMed: 26515187
DOI: 10.1093/jb/mvv107

Experimental method

X-RAY DIFFRACTION (2.2 Å)