5D5P

HcgB from Methanococcus maripaludis

Summary for 5D5P

• Entry DOI: 10.2210/pdb5d5p/pdb
• Related: 3BRC 3WB0 3WB1 3WB2
• Descriptor: HcgB (2 entities in total)
• Functional Keywords: guanylyltransferase, transferase
• Biological source: Methanococcus maripaludis (strain S2 / LL)
• Total number of polymer chains: 4
• Total formula weight: 73128.19

Authors

Fujishiro, T.,Ermler, U.,Shima, S. (deposition date: 2015-08-11, release date: 2016-10-26, Last modification date: 2024-01-10)

Primary citation

Bai, L.,Fujishiro, T.,Huang, G.,Koch, J.,Takabayashi, A.,Yokono, M.,Tanaka, A.,Xu, T.,Hu, X.,Ermler, U.,Shima, S.
Towards artificial methanogenesis: biosynthesis of the [Fe]-hydrogenase cofactor and characterization of the semi-synthetic hydrogenase.
Faraday Discuss., 198:37-58, 2017

PubMed Abstract: The greenhouse gas and energy carrier methane is produced on Earth mainly by methanogenic archaea. In the hydrogenotrophic methanogenic pathway the reduction of one CO to one methane molecule requires four molecules of H containing eight electrons. Four of the electrons from two H are supplied for reduction of an electron carrier F, which is catalyzed by F-reducing [NiFe]-hydrogenase under nickel-sufficient conditions. The same reaction is catalysed under nickel-limiting conditions by [Fe]-hydrogenase coupled with a reaction catalyzed by F-dependent methylene tetrahydromethanopterin dehydrogenase. [Fe]-hydrogenase contains an iron-guanylylpyridinol (FeGP) cofactor for H activation at the active site. Fe of FeGP is coordinated to a pyridinol-nitrogen, an acyl-carbon, two CO and a cysteine-thiolate. We report here on comparative genomic analyses of biosynthetic genes of the FeGP cofactor, which are primarily located in a hmd-co-occurring (hcg) gene cluster. One of the gene products is HcgB which transfers the guanosine monophosphate (GMP) moiety from guanosine triphosphate (GTP) to a pyridinol precursor. Crystal structure analysis of HcgB from Methanococcus maripaludis and its complex with 6-carboxymethyl-3,5-dimethyl-4-hydroxy-2-pyridinol confirmed the physiological guanylyltransferase reaction. Furthermore, we tested the properties of semi-synthetic [Fe]-hydrogenases using the [Fe]-hydrogenase apoenzyme from several methanogenic archaea and a mimic of the FeGP cofactor. On the basis of the enzymatic reactions involved in the methanogenic pathway, we came up with an idea how the methanogenic pathway could be simplified to develop an artificial methanogenesis system.

PubMed: 28294213
DOI: 10.1039/c6fd00209a

Experimental method

X-RAY DIFFRACTION (1.7 Å)