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PDBsum entry 1rhc
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Oxidoreductase PDB id
1rhc

 

 

 

 

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Contents
Protein chain
330 a.a. *
Ligands
F42-ACN
Metals
_CL ×2
__K
Waters ×146
* Residue conservation analysis
PDB id:
1rhc
Name: Oxidoreductase
Title: F420-dependent secondary alcohol dehydrogenase in complex with an f420-acetone adduct
Structure: F420-dependent alcohol dehydrogenase. Chain: a. Ec: 1.1.99.-
Source: Methanoculleus thermophilus. Organism_taxid: 2200
Biol. unit: Dimer (from PDB file)
Resolution:
1.80Å     R-factor:   0.158     R-free:   0.188
Authors: S.W.Aufhammer,E.Warkentin,H.Berk,S.Shima,R.K.Thauer,U.Ermler
Key ref:
S.W.Aufhammer et al. (2004). Coenzyme binding in F420-dependent secondary alcohol dehydrogenase, a member of the bacterial luciferase family. Structure, 12, 361-370. PubMed id: 15016352 DOI: 10.1016/j.str.2004.02.010
Date:
14-Nov-03     Release date:   30-Mar-04    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
O93734  (O93734_9EURY) -  F420-dependent alcohol dehydrogenase (Fragment) from Methanoculleus thermophilus
Seq:
Struc: 		330 a.a.
330 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.99.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/j.str.2004.02.010 Structure 12:361-370 (2004)
PubMed id: 15016352  
 
 
Coenzyme binding in F420-dependent secondary alcohol dehydrogenase, a member of the bacterial luciferase family.
S.W.Aufhammer, E.Warkentin, H.Berk, S.Shima, R.K.Thauer, U.Ermler.
 
  ABSTRACT  
 
F(420)-dependent secondary alcohol dehydrogenase (Adf) from methanogenic archaea is a member of the growing bacterial luciferase family which are all TIM barrel enzymes, most of which with an unusual nonprolyl cis peptide bond. We report here on the crystal structure of Adf from Methanoculleus thermophilicus at 1.8 A resolution in complex with a F(420)-acetone adduct. The knowledge of the F(420) binding mode in Adf provides the molecular basis for modeling F(420) and FMN into the other enzymes of the family. A nonprolyl cis peptide bond was identified as an essential part of a bulge that serves as backstop at the Re-face of F(420) to keep it in a bent conformation. The acetone moiety of the F(420)-acetone adduct is positioned at the Si-face of F(420) deeply buried inside the protein. Isopropanol can be reliably modeled and a hydrogen transfer mechanism postulated. His39 and Glu108 can be identified as key players for binding of the acetone or isopropanol oxygens and for catalysis.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. The Nonprolyl cis Peptide Bond in AdfThe nonprolyl cis peptide bond between Cys72 and Ile73 is an essential constituent of a bulge that is directed toward the F[420] binding site, causing a bent conformation of the deazaisoalloxazine ring. The well-conserved Asp38, which would partly interfere with a straight course of strand b3, is strongly linked to the polypeptide chain and stabilizes the bulge. These favorable interactions might compensate for the energy lost when forming the nonprolyl cis peptide bond.
 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 361-370) copyright 2004.  
  Figure was 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.  
19495416 I.Anderson, L.E.Ulrich, B.Lupa, D.Susanti, I.Porat, S.D.Hooper, A.Lykidis, M.Sieprawska-Lupa, L.Dharmarajan, E.Goltsman, A.Lapidus, E.Saunders, C.Han, M.Land, S.Lucas, B.Mukhopadhyay, W.B.Whitman, C.Woese, J.Bristow, and N.Kyrpides (2009).
Genomic characterization of methanomicrobiales reveals three classes of methanogens.
  PLoS One, 4, e5797.  
18252724 F.Forouhar, M.Abashidze, H.Xu, L.L.Grochowski, J.Seetharaman, M.Hussain, A.Kuzin, Y.Chen, W.Zhou, R.Xiao, T.B.Acton, G.T.Montelione, A.Galinier, R.H.White, and L.Tong (2008).
Molecular insights into the biosynthesis of the F420 coenzyme.
  J Biol Chem, 283, 11832-11840.
PDB codes: 3c3d 3c3e 3cgw
18434308 G.Bashiri, C.J.Squire, N.J.Moreland, and E.N.Baker (2008).
Crystal structures of F420-dependent glucose-6-phosphate dehydrogenase FGD1 involved in the activation of the anti-tuberculosis drug candidate PA-824 reveal the basis of coenzyme and substrate binding.
  J Biol Chem, 283, 17531-17541.
PDB codes: 3b4y 3c8n
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.  
15937276 S.W.Aufhammer, E.Warkentin, U.Ermler, C.H.Hagemeier, R.K.Thauer, and S.Shima (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.
PDB code: 1z69
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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