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PDBsum entry 1mhy

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
1mhy
Jmol
Contents
Protein chains
383 a.a. *
510 a.a. *
167 a.a. *
Metals
_FE ×2
Waters ×2199
* Residue conservation analysis
PDB id:
1mhy
Name: Oxidoreductase
Title: Methane monooxygenase hydroxylase
Structure: Methane monooxygenase hydroxylase. Chain: b. Methane monooxygenase hydroxylase. Chain: d. Methane monooxygenase hydroxylase. Chain: g. Ec: 1.14.13.25
Source: Methylosinus trichosporium. Organism_taxid: 426. Organism_taxid: 426
Biol. unit: Dimer (from PDB file)
Resolution:
2.00Å     R-factor:   0.137    
Authors: N.Elango,R.Radhakrishnan,W.A.Froland,B.J.Waller,C.A.Earhart, J.D.Lipscomb,D.H.Ohlendorf
Key ref:
N.Elango et al. (1997). Crystal structure of the hydroxylase component of methane monooxygenase from Methylosinus trichosporium OB3b. Protein Sci, 6, 556-568. PubMed id: 9070438 DOI: 10.1002/pro.5560060305
Date:
21-Oct-96     Release date:   15-May-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P27354  (MEMB_METTR) -  Methane monooxygenase component A beta chain
Seq:
Struc:
394 a.a.
383 a.a.*
Protein chain
Pfam   ArchSchema ?
P27353  (MEMA_METTR) -  Methane monooxygenase component A alpha chain
Seq:
Struc:
 
Seq:
Struc:
526 a.a.
510 a.a.*
Protein chain
Pfam   ArchSchema ?
P27355  (MEMG_METTR) -  Methane monooxygenase component A gamma chain
Seq:
Struc:
169 a.a.
167 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 30 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains B, D, G: E.C.1.14.13.25  - Methane monooxygenase (soluble).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Methane + NAD(P)H + O2 = methanol + NAD(P)(+) + H(2)O
Methane
+ NAD(P)H
+ O(2)
= methanol
+ NAD(P)(+)
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1002/pro.5560060305 Protein Sci 6:556-568 (1997)
PubMed id: 9070438  
 
 
Crystal structure of the hydroxylase component of methane monooxygenase from Methylosinus trichosporium OB3b.
N.Elango, R.Radhakrishnan, W.A.Froland, B.J.Wallar, C.A.Earhart, J.D.Lipscomb, D.H.Ohlendorf.
 
  ABSTRACT  
 
Methane monooxygenase (MMO), found in aerobic methanotrophic bacteria, catalyzes the O2-dependent conversion of methane to methanol. The soluble form of the enzyme (sMMO) consists of three components: a reductase, a regulatory "B" component (MMOB), and a hydroxylase component (MMOH), which contains a hydroxo-bridged dinuclear iron cluster. Two genera of methanotrophs, termed Type X and Type II, which differ markedly in cellular and metabolic characteristics, are known to produce the sMMO. The structure of MMOH from the Type X methanotroph Methylococcus capsulatus Bath (MMO Bath) has been reported recently. Two different structures were found for the essential diiron cluster, depending upon the temperature at which the diffraction data were collected. In order to extend the structural studies to the Type II methanotrophs and to determine whether one of the two known MMOH structures is generally applicable to the MMOH family, we have determined the crystal structure of the MMOH from Type II Methylosinus trichosporium OB3b (MMO OB3b) in two crystal forms to 2.0 A resolution, respectively, both determined at 18 degrees C. The crystal forms differ in that MMOB was present during crystallization of the second form. Both crystal forms, however, yielded very similar results for the structure of the MMOH. Most of the major structural features of the MMOH Bath were also maintained with high fidelity. The two irons of the active site cluster of MMOH OB3b are bridged by two OH (or one OH and one H2O), as well as both carboxylate oxygens of Glu alpha 144. This bis-mu-hydroxo-bridged "diamond core" structure, with a short Fe-Fe distance of 2.99 A, is unique for the resting state of proteins containing analogous diiron clusters, and is very similar to the structure reported for the cluster from flash frozen (-160 degrees C) crystals of MMOH Bath, suggesting a common active site structure for the soluble MMOHs. The high-resolution structure of MMOH OB3b indicates 26 consecutive amino acid sequence differences in the beta chain when compared to the previously reported sequence inferred from the cloned gene. Fifteen additional sequence differences distributed randomly over the three chains were also observed, including D alpha 209E, a ligand of one of the irons.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. (Facing page) Selectd sections of 2F0 - F, electrondensitymap ofthe finalmoel ofMMOH OB3bcontouredat la. A: ortionofthe active site andtheadjacenthydrophobiccavityoccupied by ourwater molecules. B: Residues p363-p368 f OH OB3b.apartofthe26 consecutiveequencecorrectionsfound in this region. C: A closeup iew ofthe 2F0 - F, shown in lightgray,contouredat la) and F, - , electron density(shown in ark,contouredat50) at 209 Glu. Side-chainatoms Cy,C6,Ocl.062 forresidue a209 ereomittedfromtherefinementand fromthemapcalculation.
Figure 6.
Fig. 6. Geometry of the diiron center. : center in MMOH OB3b. R: Superposition of diiron center f one of the monomers of MMOH Bath at 4°C (Rosenzweig et al.. 1993) (shown in gray)onto thatofMMOH OB3b at 18°C (shown in black).
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1997, 6, 556-568) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23395959 S.J.Lee, M.S.McCormick, S.J.Lippard, and U.S.Cho (2013).
Control of substrate access to the active site in methane monooxygenase.
  Nature, 494, 380-384.
PDB code: 4gam
19421508 G.D.Pirngruber, L.Frunz, and M.Lüchinger (2009).
The characterisation and catalytic properties of biomimetic metal-peptide complexes immobilised on mesoporous silica.
  Phys Chem Chem Phys, 11, 2928-2938.  
19623405 W.G.Han, and L.Noodleman (2009).
DFT calculations of comparative energetics and ENDOR/Mössbauer properties for two protonation states of the iron dimer cluster of ribonucleotide reductase intermediate X.
  Dalton Trans, (), 6045-6057.  
17910062 K.H.Kaminska, U.Baraniak, M.Boniecki, K.Nowaczyk, A.Czerwoniec, and J.M.Bujnicki (2008).
Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA.
  Proteins, 70, 1.  
18383583 K.Y.Ng, L.C.Tu, Y.S.Wang, S.I.Chan, and S.S.Yu (2008).
Probing the hydrophobic pocket of the active site in the particulate methane monooxygenase (pMMO) from Methylococcus capsulatus (Bath) by variable stereoselective alkane hydroxylation and olefin epoxidation.
  Chembiochem, 9, 1116-1123.  
18627173 N.Mitić, J.K.Schwartz, B.J.Brazeau, J.D.Lipscomb, and E.I.Solomon (2008).
CD and MCD studies of the effects of component B variant binding on the biferrous active site of methane monooxygenase.
  Biochemistry, 47, 8386-8397.  
19915653 S.Friedle, J.J.Kodanko, K.L.Fornace, and S.J.Lippard (2008).
9-Triptycenecarboxylate-Bridged Diiron(II) Complexes: Capture of the Paddlewheel Geometric Isomer.
  J Mol Struct, 890, 317-327.  
  19262682 W.G.Han, and L.Noodleman (2008).
Structural Model Studies for the High-Valent Intermediate Q of Methane Monooxygenase from Broken-Symmetry Density Functional Calculations.
  Inorganica Chim Acta, 361, 973-986.  
17704278 E.Borodina, T.Nichol, M.G.Dumont, T.J.Smith, and J.C.Murrell (2007).
Mutagenesis of the "leucine gate" to explore the basis of catalytic versatility in soluble methane monooxygenase.
  Appl Environ Microbiol, 73, 6460-6467.  
17213640 H.Shaofeng, L.Shuben, X.Jiayin, N.Jianzhong, X.Chungu, T.Haidong, and T.Wei (2007).
Purification and biochemical characterization of soluble methane monooxygenase hydroxylase from Methylosinus trichosporium IMV 3011.
  Biosci Biotechnol Biochem, 71, 122-129.  
17353953 J.Bhattacharyya, S.Das, and S.Mukhopadhyay (2007).
Mechanistic studies on oxidation of L-ascorbic acid by an oxo-bridged diiron complex in aqueous acidic media.
  Dalton Trans, (), 1214-1220.  
18052283 M.Martinho, D.W.Choi, A.A.Dispirito, W.E.Antholine, J.D.Semrau, and E.Münck (2007).
Mössbauer studies of the membrane-associated methane monooxygenase from Methylococcus capsulatus bath: evidence for a Diiron center.
  J Am Chem Soc, 129, 15783-15785.  
17602477 N.Mitić, M.D.Clay, L.Saleh, J.M.Bollinger, and E.I.Solomon (2007).
Spectroscopic and electronic structure studies of intermediate X in ribonucleotide reductase R2 and two variants: a description of the FeIV-oxo bond in the FeIII-O-FeIV dimer.
  J Am Chem Soc, 129, 9049-9065.  
17158667 S.R.Kane, A.Y.Chakicherla, P.S.Chain, R.Schmidt, M.W.Shin, T.C.Legler, K.M.Scow, F.W.Larimer, S.M.Lucas, P.M.Richardson, and K.R.Hristova (2007).
Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1.
  J Bacteriol, 189, 1931-1945.  
17082857 D.S.Nesterov, V.N.Kokozay, V.V.Dyakonenko, O.V.Shishkin, J.Jezierska, A.Ozarowski, A.M.Kirillov, M.N.Kopylovich, and A.J.Pombeiro (2006).
An unprecedented heterotrimetallic Fe/Cu/Co core for mild and highly efficient catalytic oxidation of cycloalkanes by hydrogen peroxide.
  Chem Commun (Camb), (), 4605-4607.  
16411722 E.C.Carson, and S.J.Lippard (2006).
Dioxygen-initiated oxidation of heteroatomic substrates incorporated into ancillary pyridine ligands of carboxylate-rich diiron(II) complexes.
  Inorg Chem, 45, 837-848.  
16830148 L.Noodleman, and W.G.Han (2006).
Structure, redox, pKa, spin. A golden tetrad for understanding metalloenzyme energetics and reaction pathways.
  J Biol Inorg Chem, 11, 674-694.  
17176061 M.H.Sazinsky, P.W.Dunten, M.S.McCormick, A.DiDonato, and S.J.Lippard (2006).
X-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, Pseudomonas sp. OX1 phenol hydroxylase.
  Biochemistry, 45, 15392-15404.
PDB codes: 2inn 2inp
17117860 M.S.McCormick, M.H.Sazinsky, K.L.Condon, and S.J.Lippard (2006).
X-ray crystal structures of manganese(II)-reconstituted and native toluene/o-xylene monooxygenase hydroxylase reveal rotamer shifts in conserved residues and an enhanced view of the protein interior.
  J Am Chem Soc, 128, 15108-15110.
PDB codes: 2inc 2ind
16786546 W.G.Han, T.Liu, T.Lovell, and L.Noodleman (2006).
DFT calculations of 57Fe Mössbauer isomer shifts and quadrupole splittings for iron complexes in polar dielectric media: applications to methane monooxygenase and ribonucleotide reductase.
  J Comput Chem, 27, 1292-1306.  
15812019 C.K.Chan Kwo Chion, S.E.Askew, and D.J.Leak (2005).
Cloning, expression, and site-directed mutagenesis of the propene monooxygenase genes from Mycobacterium sp. strain M156.
  Appl Environ Microbiol, 71, 1909-1914.  
15929999 D.H.Dyer, K.S.Lyle, I.Rayment, and B.G.Fox (2005).
X-ray structure of putative acyl-ACP desaturase DesA2 from Mycobacterium tuberculosis H37Rv.
  Protein Sci, 14, 1508-1517.
PDB code: 1za0
15696279 G.Vardar, and T.K.Wood (2005).
Protein engineering of toluene-o-xylene monooxygenase from Pseudomonas stutzeri OX1 for enhanced chlorinated ethene degradation and o-xylene oxidation.
  Appl Microbiol Biotechnol, 68, 510-517.  
16147517 H.Dalton (2005).
The Leeuwenhoek Lecture 2000 the natural and unnatural history of methane-oxidizing bacteria.
  Philos Trans R Soc Lond B Biol Sci, 360, 1207-1222.  
15858269 J.Benach, W.C.Edstrom, I.Lee, K.Das, B.Cooper, R.Xiao, J.Liu, B.Rost, T.B.Acton, G.T.Montelione, and J.F.Hunt (2005).
The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism.
  Acta Crystallogr D Biol Crystallogr, 61, 589-598.
PDB code: 1rtw
15184119 G.Vardar, and T.K.Wood (2004).
Protein engineering of toluene-o-xylene monooxygenase from Pseudomonas stutzeri OX1 for synthesizing 4-methylresorcinol, methylhydroquinone, and pyrogallol.
  Appl Environ Microbiol, 70, 3253-3262.  
15349166 J.Bhattacharyya, K.Dutta, and S.Mukhopadhyay (2004).
Mechanistic studies on oxidation of hydrazine by a mu-oxo diiron(III,III) complex in aqueous acidic media-proton coupled electron transfer.
  Dalton Trans, (), 2910-2917.  
12595730 A.M.Orville, J.M.Studts, G.T.Lountos, K.H.Mitchell, and B.G.Fox (2003).
Crystallization and preliminary analysis of native and N-terminal truncated isoforms of toluene-4-monooxygenase catalytic effector protein.
  Acta Crystallogr D Biol Crystallogr, 59, 572-575.  
14550940 J.G.Leahy, P.J.Batchelor, and S.M.Morcomb (2003).
Evolution of the soluble diiron monooxygenases.
  FEMS Microbiol Rev, 27, 449-479.  
12631270 M.M.Whittaker, V.V.Barynin, T.Igarashi, and J.W.Whittaker (2003).
Outer sphere mutagenesis of Lactobacillus plantarum manganese catalase disrupts the cluster core. Mechanistic implications.
  Eur J Biochem, 270, 1102-1116.
PDB code: 1o9i
12752444 S.Divari, F.Valetti, P.Caposio, E.Pessione, M.Cavaletto, E.Griva, G.Gribaudo, G.Gilardi, and C.Giunta (2003).
The oxygenase component of phenol hydroxylase from Acinetobacter radioresistens S13.
  Eur J Biochem, 270, 2244-2253.  
14645271 T.Kotani, T.Yamamoto, H.Yurimoto, Y.Sakai, and N.Kato (2003).
Propane monooxygenase and NAD+-dependent secondary alcohol dehydrogenase in propane metabolism by Gordonia sp. strain TY-5.
  J Bacteriol, 185, 7120-7128.  
11751810 K.A.Canada, S.Iwashita, H.Shim, and T.K.Wood (2002).
Directed evolution of toluene ortho-monooxygenase for enhanced 1-naphthol synthesis and chlorinated ethene degradation.
  J Bacteriol, 184, 344-349.  
11863457 K.H.Mitchell, J.M.Studts, and B.G.Fox (2002).
Combined participation of hydroxylase active site residues and effector protein binding in a para to ortho modulation of toluene 4-monooxygenase regiospecificity.
  Biochemistry, 41, 3176-3188.  
12491240 L.Que, and W.B.Tolman (2002).
Bis(mu-oxo)dimetal "diamond" cores in copper and iron complexes relevant to biocatalysis.
  Angew Chem Int Ed Engl, 41, 1114-1137.  
12406713 T.J.Smith, S.E.Slade, N.P.Burton, J.C.Murrell, and H.Dalton (2002).
Improved system for protein engineering of the hydroxylase component of soluble methane monooxygenase.
  Appl Environ Microbiol, 68, 5265-5273.  
11329291 B.J.Wallar, and J.D.Lipscomb (2001).
Methane monooxygenase component B mutants alter the kinetics of steps throughout the catalytic cycle.
  Biochemistry, 40, 2220-2233.  
11297413 D.A.Whittington, A.C.Rosenzweig, C.A.Frederick, and S.J.Lippard (2001).
Xenon and halogenated alkanes track putative substrate binding cavities in the soluble methane monooxygenase hydroxylase.
  Biochemistry, 40, 3476-3482.
PDB codes: 1fz8 1fz9 1fzh 1fzi
11500872 M.Merkx, D.A.Kopp, M.H.Sazinsky, J.L.Blazyk, J.Müller, and S.J.Lippard (2001).
Dioxygen Activation and Methane Hydroxylation by Soluble Methane Monooxygenase: A Tale of Two Irons and Three Proteins A list of abbreviations can be found in Section 7.
  Angew Chem Int Ed Engl, 40, 2782-2807.  
11352719 S.A.Ensign (2001).
Microbial metabolism of aliphatic alkenes.
  Biochemistry, 40, 5845-5853.  
11063587 B.J.Brazeau, and J.D.Lipscomb (2000).
Kinetics and activation thermodynamics of methane monooxygenase compound Q formation and reaction with substrates.
  Biochemistry, 39, 13503-13515.  
10759840 D.E.Coufal, J.L.Blazyk, D.A.Whittington, W.W.Wu, A.C.Rosenzweig, and S.J.Lippard (2000).
Sequencing and analysis of the Mmethylococcus capsulatus (Bath) solublemethane monooxygenase genes.
  Eur J Biochem, 267, 2174-2185.  
10651645 J.D.Pikus, K.H.Mitchell, J.M.Studts, K.McClay, R.J.Steffan, and B.G.Fox (2000).
Threonine 201 in the diiron enzyme toluene 4-monooxygenase is not required for catalysis.
  Biochemistry, 39, 791-799.  
10956041 K.S.Lyle, P.Möenne-Loccoz, J.Ai, J.Sanders-Loehr, T.M.Loehr, and B.G.Fox (2000).
Resonance Raman studies of the stoichiometric catalytic turnover of a substrate-stearoyl-acyl carrier protein delta(9) desaturase complex.
  Biochemistry, 39, 10507-10513.  
11031286 M.E.Wall, S.C.Gallagher, and J.Trewhella (2000).
Large-scale shape changes in proteins and macromolecular complexes.
  Annu Rev Phys Chem, 51, 355-380.  
10194335 R.Davydov, A.M.Valentine, S.Komar-Panicucci, B.M.Hoffman, and S.J.Lippard (1999).
An EPR study of the dinuclear iron site in the soluble methane monooxygenase from Methylococcus capsulatus (Bath) reduced by one electron at 77 K: the effects of component interactions and the binding of small molecules to the diiron(III) center.
  Biochemistry, 38, 4188-4197.  
10194363 S.K.Lee, and J.D.Lipscomb (1999).
Oxygen activation catalyzed by methane monooxygenase hydroxylase component: proton delivery during the O-O bond cleavage steps.
  Biochemistry, 38, 4423-4432.  
10231531 S.L.Chang, B.J.Wallar, J.D.Lipscomb, and K.H.Mayo (1999).
Solution structure of component B from methane monooxygenase derived through heteronuclear NMR and molecular modeling.
  Biochemistry, 38, 5799-5812.
PDB code: 2mob
10095780 T.J.Smith, J.S.Lloyd, S.C.Gallagher, W.L.Fosdike, J.C.Murrell, and H.Dalton (1999).
Heterologous expression of alkene monooxygenase from Rhodococcus rhodochrous B-276.
  Eur J Biochem, 260, 446-452.  
  10583965 T.Shigematsu, S.Hanada, M.Eguchi, Y.Kamagata, T.Kanagawa, and R.Kurane (1999).
Soluble methane monooxygenase gene clusters from trichloroethylene-degrading Methylomonas sp. strains and detection of methanotrophs during in situ bioremediation.
  Appl Environ Microbiol, 65, 5198-5206.  
10320346 Y.Jin, and J.D.Lipscomb (1999).
Probing the mechanism of C-H activation: oxidation of methylcubane by soluble methane monooxygenase from Methylosinus trichosporium OB3b.
  Biochemistry, 38, 6178-6186.  
9665690 A.S.Pereira, W.Small, C.Krebs, P.Tavares, D.E.Edmondson, E.C.Theil, and B.H.Huynh (1998).
Direct spectroscopic and kinetic evidence for the involvement of a peroxodiferric intermediate during the ferroxidase reaction in fast ferritin mineralization.
  Biochemistry, 37, 9871-9876.  
9778341 J.A.Broadwater, J.Ai, T.M.Loehr, J.Sanders-Loehr, and B.G.Fox (1998).
Peroxodiferric intermediate of stearoyl-acyl carrier protein delta 9 desaturase: oxidase reactivity during single turnover and implications for the mechanism of desaturation.
  Biochemistry, 37, 14664-14671.  
9454605 S.E.Parkin, S.Chen, B.A.Ley, L.Mangravite, D.E.Edmondson, B.H.Huynh, and J.M.Bollinger (1998).
Electron injection through a specific pathway determines the outcome of oxygen activation at the diiron cluster in the F208Y mutant of Escherichia coli ribonucleotide reductase protein R2.
  Biochemistry, 37, 1124-1130.  
9280437 J.D.Pikus, J.M.Studts, K.McClay, R.J.Steffan, and B.G.Fox (1997).
Changes in the regiospecificity of aromatic hydroxylation produced by active site engineering in the diiron enzyme toluene 4-monooxygenase.
  Biochemistry, 36, 9283-9289.  
9136884 Y.Liu, J.C.Nesheim, K.E.Paulsen, M.T.Stankovich, and J.D.Lipscomb (1997).
Roles of the methane monooxygenase reductase component in the regulation of catalysis.
  Biochemistry, 36, 5223-5233.  
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 code is shown on the right.