• Prosthetic group features
• Ribonucleotide reductase reaction
• Methane monooxygenase reaction
• RNR R2­type proteins in enzyme databases
• RNR R2­type proteins in motif databases
• RNR R2­type proteins in alignment databases
• RNR R2­type proteins in 3­D databases
• References

Ribonucleotide reductase R2­type proteins (Class I diiron-carboxylate proteins) include [1, 2]:

• Ribonucleotide reductase R2 (RNR R2) (EC 1.17.4.1)
• Methane monooxygenase hydroxylase (MMOH) (EC 1.14.13.25)
• Alkane hydroxylase (EC 1.14.15.3)
• Alkene monooxygenase epoxygenase (EC 1.14.13.-)
• Phenol hydroxylase (EC 1.14.13.7)
• Stearoyl­acyl carrier protein ⁹­desaturase (EC 1.14.99.6)
• Toluene­2 monooxygenase
• Toluene­4 monooxygenase
• Xylene monooxygenase

• For each iron, a ligand sphere composed of a single His nitrogen, several carboxylate oxygens and oxo or hydroxo bridge(s)
• Flexible ligand coordinations which undergo rearrangements upon reduction: loss of an oxygen bridge and carboxylate ligand shifts
• Accessible coordination sites for exogenous ligands on each iron
• Relatively symmetric ligand environment of the binuclear site

Ribonucleotide reductase (RNR) catalyses the reduction (deoxygenation) of the ribose ring to yield 2'­deoxyribose in nucleotides (1).

	+	/ \--SH / \--SH /			+	/ \--S / | \--S /	+	HOH	(1)
ribonucleotide		dithiol		2'­deoxyribonucleotide		disulphide

The enzyme from Escherichia coli is an ₂ß₂ tetramer in which the subunits (R1) contain the substrate­binding site and the ß subunits (R2) contain the diiron centre. This centre catalyses the oxidation of a neighboring Tyr­122 resulting in generation of a catalytically essential tyrosyl radical. The RNR R2 iron site is buried in a four­­helix bundle [

The free coordination sites at which O₂ can be expected to interact, as well as the hydroxyl group of Tyr­122, are exposed to a hydrophobic pocket which surrounds the diiron site [1]. Apart from oxidised and reduced forms, the diferryl (Fe^IVFe^IV) and mixed valent (Fe^IIFe^III) and (Fe^IIIFe^IV) states possibly are generated during the RNR reaction cycle [3].

The soluble methane monooxygenase (MMO) enzyme system from methanotrophic bacteria catalyses the oxidation of methane to methanol (2) [4]:

CH4 + NADH + H+ + O2 CH3OH + NAD+ + H2O

(2)

MMO consists of three components: the hydroxylase (MMOH), the iron-sulphur flavoprotein reductase (MMOR), and the coupling protein B (MMOB), which binds no cofactors and has a regulatory role. The multisubunit (₂ß₂₂) MMOH component contains two diiron centres, which are coordinated to the subunits [

In the resting state of the MMOH component, the diiron centre is in the diferric form MMOH_ox. During the catalytic cycle, the centre is reduced to the diferrous form MMOH_red by two electrons which are transferred to MMOH from NADH through MMOR. The diferrous state then reacts with O₂ in the presence of MMOB to form several transient intermediates sequentially: diferrous compound O (O₂ adduct), diferric compound P (peroxide adduct), and diferryl compound Q. Compound Q reacts with substrate RH to form two more intermediates: a hypothetical mixed valent (Fe^IIIFe^IV) compound R (radical substrate adduct) and diferric enzyme­product complex, compound T (terminal adduct). The decay of compound T yields product ROH and regenerates state MMOH_ox [2]. The structures of compounds O to T are not known in detail.

Stearoyl­acyl carrier protein ⁹­desaturase is structurally similar to RNR R2 and MMO. Toluene hydroxylase, phenol hydroxylase and alkene monooxygenase epoxygenase show significant sequence similarity to MMO [1]. A dimanganese catalase structure also appears to be related to these proteins [7].

RNR R2­type proteins in enzyme databases

ENZYME	LIGAND	BRENDA	UMBBD	Official name	Alternative name(s)
1.14.13.7	1.14.13.7	1.14.13.7	e0208	Phenol 2­monooxygenase	Phenol hydroxylase
1.14.13.25	1.14.13.25	1.14.13.25	e0007	Methane monooxygenase	Methane hydroxylase
1.14.99.6	1.14.99.6	1.14.99.6	-	Acyl­(acyl­carrier protein) desaturase	Stearoyl­ACP desaturase; stearoyl­acyl protein 9­desaturase
1.17.4.1	1.17.4.1	1.17.4.1	-	Ribonucleoside­diphosphate reductase	Ribonucleotide reductase
1.14.13.-	1.14.13.-	1.14.13.-	e0039	Alkene monooxygenase	Alkene epoxidase

RNR R2­type proteins in motif databases

PRINTS ID	PRINTS AC	PROSITE/BLOCKS ID	PROSITE AC	BLOCKS AC
-	-	FATTY_ACID_DESATUR_2	PS00574	BL00574
-	-	RIBORED_SMALL	PS00368	BL00368

RNR R2­type proteins in alignment databases

Protein (Super)Family	Pfam	LPFC 3­D alignment
00203; acyl­(acyl­carrier protein) desaturase	PF00487; FA_desaturase	-
00210; ribonucleoside­diphosphate reductase small chain	PF00268; ribonuc_red	-
06760; methane monooxygenase component A chain	-	-
07290; methane monooxygenase component A ß chain	-	-
09348; phenol 2­monooxygenase	-	-
09723; phenol 2­monooxygenase	-	-

PDB	scop	BSM	RELI Base	Header	¹
1afr	1afr	1afr	1afr	9­Stearoyl­acyl carrier protein desaturase; castor bean (Ricinus communis)	-
1av8	-	1av8	-	Protein R2 of ribonucleotide reductase; Escherichia coli	-
1mhy	1mhy	1mhy	1mhy	Methane monooxygenase hydrolase (diferric); Methylosinus trichosporium	-
1mhz	1mhz	1mhz	1mhz	Methane monooxygenase hydrolase (diferric); Methylosinus trichosporium	-
1mmo	1mmo	1mmo	1mmo	Methane monooxygenase hydrolase (diferric) (complex with acetate); Methylococcus capsulatus	MMS94177
1mty	1mty	1mty	1mty	Methane monooxygenase hydrolase (diferric); Methylococcus capsulatus	MMS94177
1mrr*	1mrr*	1mrr*	1mrr*	Protein R2 of ribonucleotide reductase (Mn2+ substituted for Fe2+) (complex with Hg2+); Escherichia coli	MMS91110*
1pfr	1pfr	1pfr	1pfr	Protein R2 of ribonucleotide reductase (diferric) (complex with Hg2+); Escherichia coli	-
1rib	1rib	1rib	1rib	Protein R2 of ribonucleotide reductase; Escherichia coli	-
1rnr	1rnr	1rnr	1rnr	Protein R2 of ribonucleotide reductase (F208Y mutant, then converted to dihydroxy phenylalanine) (diferric) (complex with Hg2+); Escherichia coli	-
1xik	1xik	1xik	1xik	Protein R2 of ribonucleotide reductase (diferrous) (complex with Hg2+); Escherichia coli	-
1xsm	1xsm	1xsm	1xsm	Protein R2 of ribonucleotide reductase (diferric); mouse	-
2av8	-	2av8	-	Protein R2 of ribonucleotide reductase (Y122F mutant); Escherichia coli	-
2r2f	-	2r2f	-	Protein R2 of ribonucleotide reductase (oxidised); Salmonella typhimurium	-

¹ Macromolecular Structures abstract. Full text is available to BioMedNet Members

References

1. Nordlund, P. and Eklund, H. (1995) Di­iron-carboxylate proteins. Curr. Opin. Struct. Biol. 5, 758-766.
2. Wallar, B.J. and Lipscomb, J.D. (1996) Dioxygen activation by enzymes containing binuclear non­heme iron clusters. Chem. Rev. 96, 2625-2657.
3. Logan, D.T., Su, X.­D., Åberg, A., Regnström, K., Hajdu, J., Eklund, H. and Nordlund, P. (1996) Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site. Structure 4, 1053-1064.
4. Lipscomb, J.D. (1994) Biochemistry of the soluble methane monooxygenase. Annu. Rev. Biochem. 48, 371-399.
5. Rosenzweig, A.C., Nordlund, P., Takahara, P.M., Frederick, C.A. and Lippard, S.J. (1995) Geometry of the soluble methane monooxygenase catalytic diiron center in two oxidation states. Chemistry & Biology 2, 409-418.
6. Siegbahn, P.E.M. and Crabtree, R.H. (1997) Mechanism of C-H activation by diiron methane monooxygenases: Quantum chemical studies. J. Am. Chem. Soc. 119, 3103-3113.
7. Barynin, V.V., Vagin, A.A., Melik­Adamyan, W.R., Grebenko, A.I., Khangulov, S.V., Popov, A.N., Adrianova, M.E. and Vainshtein, B.K. (1986) Three­dimensional structure of the T­catalase with a 3 Å resolution. Dokl. Akad. Nauk SSSR 288, 877-880.

Bibliography on structural studies of ribonucleotide reductase R2­type proteins

Reviews on ribonucleotide reductase R2­type proteins