Tags

Type your tag names separated by a space and hit enter

The crystal structure of d-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus in the presence of NADP(+) at 2.1 A resolution.
J Mol Biol. 2000 Mar 24; 297(2):481-500.JM

Abstract

The crystal structure of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the archaeon Methanothermus fervidus has been solved in the holo form at 2.1 A resolution by molecular replacement. Unlike bacterial and eukaryotic homologous enzymes which are strictly NAD(+)-dependent, GAPDH from this organism exhibits a dual-cofactor specificity, with a marked preference for NADP(+) over NAD(+). The present structure is the first archaeal GAPDH crystallized with NADP(+). GAPDH from M. fervidus adopts a homotetrameric quaternary structure which is topologically similar to that observed for its bacterial and eukaryotic counterparts. Within the cofactor-binding site, the positively charged side-chain of Lys33 decisively contributes to NADP(+) recognition through a tight electrostatic interaction with the adenosine 2'-phosphate group. Like other GAPDHs, GAPDH from archaeal sources binds the nicotinamide moiety of NADP(+) in a syn conformation with respect to the adjacent ribose and so belongs to the B-stereospecific class of oxidoreductases. Stabilization of the syn conformation is principally achieved through hydrogen bonding of the carboxamide group with the side-chain of Asp171, a structural feature clearly different from what is observed in all presently known GAPDHs from bacteria and eukaryotes. Within the catalytic site, the reported crystal structure definitively confirms the essential role previously assigned to Cys140 by site-directed mutagenesis studies. In conjunction with new mutation results reported in this paper, inspection of the crystal structure gives reliable evidence for the direct implication of the side-chain of His219 in the catalytic mechanism. M. fervidus grows optimally at 84 degrees C with a maximal growth temperature of 97 degrees C. The paper includes a detailed comparison of the present structure with four other homologous enzymes extracted from mesophilic as well as thermophilic organisms. Among the various phenomena related to protein thermostabilization, reinforcement of electrostatic and hydrophobic interactions as well as a more efficient molecular packing appear to be essentially promoted by the occurrence of two additional alpha-helices in the archaeal GAPDHs. The first one, named alpha4, is located in the catalytic domain and participates in the enzyme architecture at the quaternary structural level. The second one, named alphaJ, occurs at the C terminus and contributes to the molecular packing within each monomer by filling a peripherical pocket in the tetrameric assembly.

Authors+Show Affiliations

Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques - Groupe Biocristallographie - UPRESA CNRS 7036, Université Henri Poincaré, Nancy I, BP 239, Vandoeuvre-lès-Nancy, 54506, France.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

10715215

Citation

Charron, C, et al. "The Crystal Structure of D-glyceraldehyde-3-phosphate Dehydrogenase From the Hyperthermophilic Archaeon Methanothermus Fervidus in the Presence of NADP(+) at 2.1 a Resolution." Journal of Molecular Biology, vol. 297, no. 2, 2000, pp. 481-500.
Charron C, Talfournier F, Isupov MN, et al. The crystal structure of d-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus in the presence of NADP(+) at 2.1 A resolution. J Mol Biol. 2000;297(2):481-500.
Charron, C., Talfournier, F., Isupov, M. N., Littlechild, J. A., Branlant, G., Vitoux, B., & Aubry, A. (2000). The crystal structure of d-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus in the presence of NADP(+) at 2.1 A resolution. Journal of Molecular Biology, 297(2), 481-500.
Charron C, et al. The Crystal Structure of D-glyceraldehyde-3-phosphate Dehydrogenase From the Hyperthermophilic Archaeon Methanothermus Fervidus in the Presence of NADP(+) at 2.1 a Resolution. J Mol Biol. 2000 Mar 24;297(2):481-500. PubMed PMID: 10715215.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The crystal structure of d-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus in the presence of NADP(+) at 2.1 A resolution. AU - Charron,C, AU - Talfournier,F, AU - Isupov,M N, AU - Littlechild,J A, AU - Branlant,G, AU - Vitoux,B, AU - Aubry,A, PY - 2000/3/15/pubmed PY - 2000/4/15/medline PY - 2000/3/15/entrez SP - 481 EP - 500 JF - Journal of molecular biology JO - J Mol Biol VL - 297 IS - 2 N2 - The crystal structure of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the archaeon Methanothermus fervidus has been solved in the holo form at 2.1 A resolution by molecular replacement. Unlike bacterial and eukaryotic homologous enzymes which are strictly NAD(+)-dependent, GAPDH from this organism exhibits a dual-cofactor specificity, with a marked preference for NADP(+) over NAD(+). The present structure is the first archaeal GAPDH crystallized with NADP(+). GAPDH from M. fervidus adopts a homotetrameric quaternary structure which is topologically similar to that observed for its bacterial and eukaryotic counterparts. Within the cofactor-binding site, the positively charged side-chain of Lys33 decisively contributes to NADP(+) recognition through a tight electrostatic interaction with the adenosine 2'-phosphate group. Like other GAPDHs, GAPDH from archaeal sources binds the nicotinamide moiety of NADP(+) in a syn conformation with respect to the adjacent ribose and so belongs to the B-stereospecific class of oxidoreductases. Stabilization of the syn conformation is principally achieved through hydrogen bonding of the carboxamide group with the side-chain of Asp171, a structural feature clearly different from what is observed in all presently known GAPDHs from bacteria and eukaryotes. Within the catalytic site, the reported crystal structure definitively confirms the essential role previously assigned to Cys140 by site-directed mutagenesis studies. In conjunction with new mutation results reported in this paper, inspection of the crystal structure gives reliable evidence for the direct implication of the side-chain of His219 in the catalytic mechanism. M. fervidus grows optimally at 84 degrees C with a maximal growth temperature of 97 degrees C. The paper includes a detailed comparison of the present structure with four other homologous enzymes extracted from mesophilic as well as thermophilic organisms. Among the various phenomena related to protein thermostabilization, reinforcement of electrostatic and hydrophobic interactions as well as a more efficient molecular packing appear to be essentially promoted by the occurrence of two additional alpha-helices in the archaeal GAPDHs. The first one, named alpha4, is located in the catalytic domain and participates in the enzyme architecture at the quaternary structural level. The second one, named alphaJ, occurs at the C terminus and contributes to the molecular packing within each monomer by filling a peripherical pocket in the tetrameric assembly. SN - 0022-2836 UR - https://www.unboundmedicine.com/medline/citation/10715215/The_crystal_structure_of_d_glyceraldehyde_3_phosphate_dehydrogenase_from_the_hyperthermophilic_archaeon_Methanothermus_fervidus_in_the_presence_of_NADP_+__at_2_1_A_resolution_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0022-2836(00)93565-4 DB - PRIME DP - Unbound Medicine ER -