PDBsum entry 1jax

Structural genomics

PDB id

1jax

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Contents

			Protein chains

					212 a.a. *

			Metals

					_MG


					_NA ×2

			Waters ×270

* Residue conservation analysis

PDB id:

1jax

Links

Name:

Structural genomics

Title:

Structure of coenzyme f420h2:nadp+ oxidoreductase (fno)

Structure:

Conserved hypothetical protein. Chain: a, b. Engineered: yes

Source:

Archaeoglobus fulgidus. Organism_taxid: 2234. Gene: af0892. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å

R-factor:

0.185

R-free:

0.221

Authors:

E.Warkentin,B.Mamat,R.Thauer,U.Ermler,S.Shima

Key ref:

E.Warkentin et al. (2001). Structures of F420H2:NADP+ oxidoreductase with and without its substrates bound. EMBO J, 20, 6561-6569. PubMed id: 11726492 DOI: 10.1093/emboj/20.23.6561

Date:

01-Jun-01

Release date:

21-Dec-01

PROCHECK

	Headers

	References

Protein chains

O29370 (FNO_ARCFU) - F420-dependent NADP reductase from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)

Seq: Struc:					212 a.a. 212 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.1.5.1.40 - 8-hydroxy-5-deazaflavin:Nadph oxidoreductase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

reduced coenzyme F420-(gamma-L-Glu)(n) + NADP⁺ = oxidized coenzyme F420-(gamma-L-Glu)(n) + NADPH + 2 H⁺

reduced coenzyme F420-(gamma-L-Glu)(n)	+	NADP(+)	=	oxidized coenzyme F420-(gamma-L-Glu)(n)	+	NADPH	+	2 × H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1093/emboj/20.23.6561	EMBO J 20:6561-6569 (2001)
PubMed id: 11726492

Structures of F420H2:NADP+ oxidoreductase with and without its substrates bound.
E.Warkentin, B.Mamat, M.Sordel-Klippert, M.Wicke, R.K.Thauer, M.Iwata, S.Iwata, U.Ermler, S.Shima.

ABSTRACT

Cofactor F420 is a 5'-deazaflavin derivative first discovered in methanogenic archaea but later found also to be present in some bacteria. As a coenzyme, it is involved in hydride transfer reactions and as a prosthetic group in the DNA photolyase reaction. We report here for the first time on the crystal structure of an F420-dependent oxidoreductase bound with F420. The structure of F420H2:NADP+ oxidoreductase resolved to 1.65 A contains two domains: an N-terminal domain characteristic of a dinucleotide-binding Rossmann fold and a smaller C-terminal domain. The nicotinamide and the deazaflavin part of the two coenzymes are bound in the cleft between the domains such that the Si-faces of both face each other at a distance of 3.1 A, which is optimal for hydride transfer. Comparison of the structures bound with and without substrates reveals that of the two substrates NADP has to bind first, the binding being associated with an induced fit.

Selected figure(s)



	Figure 1. Figure 1 Reaction catalysed by F[420]H[2]:NADP+ oxidoreductase. The Re-faces of the cofactors are shown. The amide group of NADP is shown in the trans conformation.		Figure 4. Figure 4 Stereo diagram of the active site of Fno. The nicotinamide ring of NADP+ and the deazaflavin ring of F[420] are embedded face on face in the hydrophobic pocket.

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21464839

A.Sharma, P.P.Chaudhary, S.K.Sirohi, and J.Saxena (2011).
Structure modeling and inhibitor prediction ofNADP oxidoreductase enzyme from Methanobrevibacter smithii.

Bioinformation, 6, 15-19.

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.

18495927

A.K.Sendamarai, R.S.Ohgami, M.D.Fleming, and C.M.Lawrence (2008).
Structure of the membrane proximal oxidoreductase domain of human Steap3, the dominant ferrireductase of the erythroid transferrin cycle.

Proc Natl Acad Sci U S A, 105, 7410-7415.

PDB codes:

2vns 2vq3

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

17669425

B.Nocek, E.Evdokimova, M.Proudfoot, M.Kudritska, L.L.Grochowski, R.H.White, A.Savchenko, A.F.Yakunin, A.Edwards, and A.Joachimiak (2007).
Structure of an amide bond forming F(420):gamma-glutamyl ligase from Archaeoglobus fulgidus -- a member of a new family of non-ribosomal peptide synthases.

J Mol Biol, 372, 456-469.

PDB codes:

2g9i 2phn

17480207

H.Seedorf, C.H.Hagemeier, S.Shima, R.K.Thauer, E.Warkentin, and U.Ermler (2007).
Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic Archaea catalyzing the reduction of O2 to H2O.

FEBS J, 274, 1588-1599.

PDB codes:

2ohh 2ohi 2ohj

15897894

C.G.Korkmaz, K.S.Korkmaz, P.Kurys, C.Elbi, L.Wang, T.I.Klokk, C.Hammarstrom, G.Troen, A.Svindland, G.L.Hager, and F.Saatcioglu (2005).
Molecular cloning and characterization of STAMP2, an androgen-regulated six transmembrane protein that is overexpressed in prostate cancer.

Oncogene, 24, 4934-4945.

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.

16227996

R.S.Ohgami, D.R.Campagna, E.L.Greer, B.Antiochos, A.McDonald, J.Chen, J.J.Sharp, Y.Fujiwara, J.E.Barker, and M.D.Fleming (2005).
Identification of a ferrireductase required for efficient transferrin-dependent iron uptake in erythroid cells.

Nat Genet, 37, 1264-1269.

16322583

R.Tyagi, S.Duquerroy, J.Navaza, L.W.Guddat, and R.G.Duggleby (2005).
The crystal structure of a bacterial class II ketol-acid reductoisomerase: domain conservation and evolution.

Protein Sci, 14, 3089-3100.

PDB code:

1yrl

15557260

S.Sakasegawa, C.H.Hagemeier, R.K.Thauer, L.O.Essen, and S.Shima (2004).
Structural and functional analysis of the gpsA gene product of Archaeoglobus fulgidus: a glycerol-3-phosphate dehydrogenase with an unusual NADP+ preference.

Protein Sci, 13, 3161-3171.

PDB code:

1txg

12925803

C.H.Hagemeier, S.Shima, E.Warkentin, R.K.Thauer, and U.Ermler (2003).
Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase from Methanopyrus kandleri: the selenomethionine-labelled and non-labelled enzyme crystallized in two different forms.

Acta Crystallogr D Biol Crystallogr, 59, 1653-1655.

12192068

C.A.Bottoms, P.E.Smith, and J.J.Tanner (2002).
A structurally conserved water molecule in Rossmann dinucleotide-binding domains.

Protein Sci, 11, 2125-2137.

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.