3IQF

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin

Summary for 3IQF

• Entry DOI: 10.2210/pdb3iqf/pdb
• Related: 3IQE 3IQZ
• Descriptor: F420-dependent methylenetetrahydromethanopterin dehydrogenase, 1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: binary complex of protein and substrate, methanogenesis, one-carbon metabolism, oxidoreductase
• Biological source: Methanopyrus kandleri
• Total number of polymer chains: 12
• Total formula weight: 386746.38

Authors

Ceh, K.E.,Demmer, U.,Warkentin, E.,Moll, J.,Thauer, R.K.,Shima, S.,Ermler, U. (deposition date: 2009-08-20, release date: 2009-10-06, Last modification date: 2023-11-01)

Primary citation

Ceh, K.,Demmer, U.,Warkentin, E.,Moll, J.,Thauer, R.K.,Shima, S.,Ermler, U.
Structural basis of the hydride transfer mechanism in F(420)-dependent methylenetetrahydromethanopterin dehydrogenase
Biochemistry, 48:10098-10105, 2009

PubMed Abstract: F(420)-dependent methylenetetrahydromethanopterin (methylene-H(4)MPT) dehydrogenase (Mtd) of Methanopyrus kandleri is an enzyme of the methanogenic energy metabolism that catalyzes the reversible hydride transfer between methenyl-H(4)MPT(+) and methylene-H(4)MPT using coenzyme F(420) as hydride carrier. We determined the structures of the Mtd-methylene-H(4)MPT, Mtd-methenyl-H(4)MPT(+), and the Mtd-methenyl-H(4)MPT(+)-F(420)H(2) complexes at 2.1, 2.0, and 1.8 A resolution, respectively. The pterin-imidazolidine-phenyl ring system is present in a new extended but not planar conformation which is virtually identical in methenyl-H(4)MPT(+) and methylene-H(4)MPT at the current resolution. Both substrates methenyl-H(4)MPT(+) and F(420)H(2) bind in a face to face arrangement to an active site cleft, thereby ensuring a direct hydride transfer between their C14a and C5 atoms, respectively. The polypeptide scaffold does not reveal any significant conformational change upon binding of the bulky substrates but in turn changes the conformations of the substrate rings either to avoid clashes between certain ring atoms or to adjust the rings involved in hydride transfer for providing an optimal catalytic efficiency.

PubMed: 19761261
DOI: 10.1021/bi901104d

Experimental method

X-RAY DIFFRACTION (2.1 Å)