1Z69

Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420

Summary for 1Z69

• Entry DOI: 10.2210/pdb1z69/pdb
• Related: 1EZW 1F07
• Descriptor: Coenzyme F420-dependent N(5),N(10)-methylenetetrahydromethanopterin reductase, COENZYME F420, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: (alpha, beta)8 barrel, oxidoreductase
• Biological source: Methanosarcina barkeri
• Total number of polymer chains: 4
• Total formula weight: 141425.33

Authors

Aufhammer, S.W.,Warkentin, E.,Ermler, U.,Hagemeier, C.H.,Thauer, R.K.,Shima, S. (deposition date: 2005-03-22, release date: 2005-06-21, Last modification date: 2023-08-23)

Primary citation

Aufhammer, S.W.,Warkentin, E.,Ermler, U.,Hagemeier, C.H.,Thauer, R.K.,Shima, S.
Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420: Architecture of the F420/FMN binding site of enzymes within the nonprolyl cis-peptide containing bacterial luciferase family
Protein Sci., 14:1840-1849, 2005

PubMed Abstract: Methylenetetratetrahydromethanopterin reductase (Mer) is involved in CO(2) reduction to methane in methanogenic archaea and catalyses the reversible reduction of methylenetetrahydromethanopterin (methylene-H(4)MPT) to methyl-H(4)MPT with coenzyme F(420)H(2), which is a reduced 5'-deazaflavin. Mer was recently established as a TIM barrel structure containing a nonprolyl cis-peptide bond but the binding site of the substrates remained elusive. We report here on the crystal structure of Mer in complex with F(420) at 2.6 A resolution. The isoalloxazine ring is present in a pronounced butterfly conformation, being induced from the Re-face of F(420) by a bulge that contains the non-prolyl cis-peptide bond. The bindingmode of F(420) is very similar to that in F(420)-dependent alcohol dehydrogenase Adf despite the low sequence identity of 21%. Moreover, binding of F(420) to the apoenzyme was only associated with minor conformational changes of the polypeptide chain. These findings allowed us to build an improved model of FMN into its binding site in bacterial luciferase, which belongs to the same structural family as Mer and Adf and also contains a nonprolyl cis-peptide bond in an equivalent position.

PubMed: 15937276
DOI: 10.1110/ps.041289805

Experimental method

X-RAY DIFFRACTION (2.61 Å)