spacer
spacer
Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1z69
Jmol
Contents
Protein chains
327 a.a. *
Ligands
F42 ×4
1PG
Metals
_CL ×2
Waters ×239
* Residue conservation analysis
PDB id:
1z69
Name: Oxidoreductase
Title: Crystal structure of methylenetetrahydromethanopterin reductase (mer) in complex with coenzyme f420
Structure: Coenzyme f420-dependent n(5),n(10)- methylenetetrahydromethanopterin reductase. Chain: a, b, c, d. Synonym: cog2141. Methylene-h(4)mpt reductase. Ec: 1.5.99.11
Source: Methanosarcina barkeri. Organism_taxid: 2208. Strain: fusaro (dsmz 804)
Biol. unit: Tetramer (from PQS)
Resolution:
2.61Å     R-factor:   0.185     R-free:   0.222
Authors: S.W.Aufhammer,E.Warkentin,U.Ermler,C.H.Hagemeier,R.K.Thauer, S.Shima
Key ref:
S.W.Aufhammer et al. (2005). 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. PubMed id: 15937276 DOI: 10.1110/ps.041289805
Date:
22-Mar-05     Release date:   21-Jun-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

 Enzyme reactions 
   Enzyme class: E.C.1.5.99.11  - 5,10-methylenetetrahydromethanopterin reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Methane Biosynthesis
      Reaction: 5-methyltetrahydromethanopterin + coenzyme F420 = 5,10- methylenetetrahydromethanopterin + reduced coenzyme F420
5-methyltetrahydromethanopterin
 +
coenzyme F420
Bound ligand (Het Group name = F42)
corresponds exactly 		= 5,10- methylenetetrahydromethanopterin
 + reduced coenzyme F420
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen     2 terms  

 

 
    reference    
 
 
DOI no: 10.1110/ps.041289805 Protein Sci 14:1840-1849 (2005)
PubMed id: 15937276  
 
 
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.
S.W.Aufhammer, E.Warkentin, U.Ermler, C.H.Hagemeier, R.K.Thauer, S.Shima.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (A) F[420]-dependent methylenetetrahydromethanopterin reductase (Mer) catalyzes the reversible reduction of N5, N10-methylenetetrahydromethanopterin (Methylene-H[4]MPT) to N5-methyltetrahydromethanopterin (Methyl-H[4]MPT) with the concomitant oxidation ofF[420]H[2] toF[420]. The enzyme is Si-face specificwith respect to the C^5 atom of F[420]. (B) F[420] is a deazaflavin derivative and tetrahydromethanopterin (H[4]MPT) a tetrahydrofolate analog. (R') in H[4]MPT consists of an aminophenyl, a 1-deoxyribose, a ribose, a phosphate and a 2-hydroxyglutarate group. This figure was produced with ChemWindow (Bio-Rad Laboratories). 		Figure 6.
Figure 6. Superposition of the C^ chains of bMer (red) and Adf (blue) within the F[420] binding regions. The nonprolyl cis-peptide bonds (indicated by an arrow), formed by Gly61 and Val62 in bMer and by Cys72 and Ile73 in Adf are shown as ball-and-stick representations. This figure was created using Molscript (Kraulis 1991) and Raster 3D (Bacon and Anderson 1988).
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2005, 14, 1840-1849) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21209917 G.Bashiri, A.M.Rehan, D.R.Greenwood, J.M.Dickson, and E.N.Baker (2010).
Metabolic engineering of cofactor F420 production in Mycobacterium smegmatis.
  PLoS One, 5, e15803.  
19490118 S.T.Philominathan, O.Matsushita, R.Gensure, and J.Sakon (2009).
Ca2+-induced linker transformation leads to a compact and rigid collagen-binding domain of Clostridium histolyticum collagenase.
  FEBS J, 276, 3589-3601.  
16540542 K.D.Loh, P.Gyaneshwar, E.Markenscoff Papadimitriou, R.Fong, K.S.Kim, R.Parales, Z.Zhou, W.Inwood, and S.Kustu (2006).
A previously undescribed pathway for pyrimidine catabolism.
  Proc Natl Acad Sci U S A, 103, 5114-5119.  
16218963 H.Seedorf, J.Kahnt, A.J.Pierik, and R.K.Thauer (2005).
Si-face stereospecificity at C5 of coenzyme F420 for F420H2 oxidase from methanogenic Archaea as determined by mass spectrometry.
  FEBS J, 272, 5337-5342.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.