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Monooxygenase PDB id
1mty
Jmol
Contents
Protein chains
512 a.a. *
384 a.a. *
162 a.a. *
Metals
_FE ×4
Waters ×4464
* Residue conservation analysis
PDB id:
1mty
Name: Monooxygenase
Title: Methane monooxygenase hydroxylase from methylococcus capsulatus (bath)
Structure: Methane monooxygenase hydroxylase. Chain: d, e. Methane monooxygenase hydroxylase. Chain: b, c. Methane monooxygenase hydroxylase. Chain: g, h. Ec: 1.14.13.25
Source: Methylococcus capsulatus str. Bath. Organism_taxid: 243233. Strain: bath. Cellular_location: cytoplasm. Cellular_location: cytoplasm
Biol. unit: Dimer (from PDB file)
Resolution:
1.70Å     R-factor:   0.183    
Authors: A.C.Rosenzweig,P.Nordlund,S.J.Lippard,C.A.Frederick
Key ref: A.C.Rosenzweig et al. (1997). Crystal structures of the methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): implications for substrate gating and component interactions. Proteins, 29, 141-152. PubMed id: 9329079 DOI: 10.1002/(SICI)1097-0134(199710)29:2<141::AID-PROT2>3.3.CO;2-W
Date:
10-Jul-96     Release date:   21-Apr-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P22869  (MEMA_METCA) -  Methane monooxygenase component A alpha chain
Seq:
Struc: 		 
Seq:
Struc: 		527 a.a.
512 a.a.*
Protein chains
Pfam   ArchSchema ?
P18798  (MEMB_METCA) -  Methane monooxygenase component A beta chain
Seq:
Struc: 		389 a.a.
384 a.a.
Protein chains
Pfam   ArchSchema ?
P11987  (MEMG_METCA) -  Methane monooxygenase component A gamma chain
Seq:
Struc: 		170 a.a.
162 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains D, E, B, C, G, H: 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   4 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1002/(SICI)1097-0134(199710)29:2<141::AID-PROT2>3.3.CO;2-W Proteins 29:141-152 (1997)
PubMed id: 9329079  
 
 
Crystal structures of the methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): implications for substrate gating and component interactions.
A.C.Rosenzweig, H.Brandstetter, D.A.Whittington, P.Nordlund, S.J.Lippard, C.A.Frederick.
 
  ABSTRACT  
 
The crystal structure of the nonheme iron-containing hydroxylase component of methane monooxygenase hydroxylase (MMOH) from Methylococcus capsulatus (Bath) has been solved in two crystal forms, one of which was refined to 1.7 A resolution. The enzyme is composed of two copies each of three subunits (alpha 2 beta 2 gamma 2), and all three subunits are almost completely alpha-helical, with the exception of two beta hairpin structures in the alpha subunit. The active site of each alpha subunit contains one dinuclear iron center, housed in a four-helix bundle. The two iron atoms are octahedrally coordinated by 2 histidine and 4 glutamic acid residues as well as by a bridging hydroxide ion, a terminal water molecule, and at 4 degrees C, a bridging acetate ion, which is replaced at -160 degrees C with a bridging water molecule. Comparison of the results for two crystal forms demonstrates overall conservation and relative orientation of the domain structures. The most prominent structural differences identified between the two crystal forms is in an altered side chain conformation for Leu 110 at the active site cavity. We suggest that this residue serves as one component of a hydrophobic gate controlling access of substrates to and products from the active site. The leucine gate may be responsible for the effect of the B protein component on the reactivity of the reduced hydroxylase with dioxygen. A potential reductase binding site has been assigned based on an analysis of crystal packing in the two forms and corroborated by inhibition studies with a synthetic peptide corresponding to the proposed docking position.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19090676 C.B.Bell, J.R.Calhoun, E.Bobyr, P.P.Wei, B.Hedman, K.O.Hodgson, W.F.Degrado, and E.I.Solomon (2009).
Spectroscopic definition of the biferrous and biferric sites in de novo designed four-helix bundle DFsc peptides: implications for O2 reactivity of binuclear non-heme iron enzymes.
  Biochemistry, 48, 59-73.  
19074607 E.Notomista, V.Cafaro, G.Bozza, and A.Di Donato (2009).
Molecular determinants of the regioselectivity of toluene/o-xylene monooxygenase from Pseudomonas sp. strain OX1.
  Appl Environ Microbiol, 75, 823-836.  
19383682 R.B.Cooley, B.L.Dubbels, L.A.Sayavedra-Soto, P.J.Bottomley, and D.J.Arp (2009).
Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly 'Pseudomonas butanovora'.
  Microbiology, 155, 2086-2096.  
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.  
18192418 R.Feingersch, J.Shainsky, T.K.Wood, and A.Fishman (2008).
Protein engineering of toluene monooxygenases for synthesis of chiral sulfoxides.
  Appl Environ Microbiol, 74, 1555-1566.  
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.  
18044971 L.J.Murray, R.García-Serres, M.S.McCormick, R.Davydov, S.G.Naik, S.H.Kim, B.M.Hoffman, B.H.Huynh, and S.J.Lippard (2007).
Dioxygen activation at non-heme diiron centers: oxidation of a proximal residue in the I100W variant of toluene/o-xylene monooxygenase hydroxylase.
  Biochemistry, 46, 14795-14809.
PDB code: 2rdb
16788204 K.H.Halsey, L.A.Sayavedra-Soto, P.J.Bottomley, and D.J.Arp (2006).
Site-directed amino acid substitutions in the hydroxylase alpha subunit of butane monooxygenase from Pseudomonas butanovora: Implications for substrates knocking at the gate.
  J Bacteriol, 188, 4962-4969.  
16756297 L.J.Murray, R.García-Serres, S.Naik, B.H.Huynh, and S.J.Lippard (2006).
Dioxygen activation at non-heme diiron centers: characterization of intermediates in a mutant form of toluene/o-xylene monooxygenase hydroxylase.
  J Am Chem Soc, 128, 7458-7459.  
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
15498762 A.Fishman, Y.Tao, L.Rui, and T.K.Wood (2005).
Controlling the regiospecific oxidation of aromatics via active site engineering of toluene para-monooxygenase of Ralstonia pickettii PKO1.
  J Biol Chem, 280, 506-514.  
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.  
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.  
15700297 J.R.Calhoun, F.Nastri, O.Maglio, V.Pavone, A.Lombardi, and W.F.DeGrado (2005).
Artificial diiron proteins: from structure to function.
  Biopolymers, 80, 264-278.  
15653774 Y.Zhang, and J.Skolnick (2005).
The protein structure prediction problem could be solved using the current PDB library.
  Proc Natl Acad Sci U S A, 102, 1029-1034.  
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.  
15322079 K.R.Strand, S.Karlsen, M.Kolberg, A.K.Røhr, C.H.Görbitz, and K.K.Andersson (2004).
Crystal structural studies of changes in the native dinuclear iron center of ribonucleotide reductase protein R2 from mouse.
  J Biol Chem, 279, 46794-46801.
PDB codes: 1w68 1w69
15184118 L.Rui, Y.M.Kwon, A.Fishman, K.F.Reardon, and T.K.Wood (2004).
Saturation mutagenesis of toluene ortho-monooxygenase of Burkholderia cepacia G4 for Enhanced 1-naphthol synthesis and chloroform degradation.
  Appl Environ Microbiol, 70, 3246-3252.  
15096510 M.H.Sazinsky, J.Bard, A.Di Donato, and S.J.Lippard (2004).
Crystal structure of the toluene/o-xylene monooxygenase hydroxylase from Pseudomonas stutzeri OX1. Insight into the substrate specificity, substrate channeling, and active site tuning of multicomponent monooxygenases.
  J Biol Chem, 279, 30600-30610.
PDB codes: 1t0q 1t0r 1t0s
15087448 R.Schwarzenbacher, F.Stenner-Liewen, H.Liewen, H.Robinson, H.Yuan, E.Bossy-Wetzel, J.C.Reed, and R.C.Liddington (2004).
Structure of the Chlamydia protein CADD reveals a redox enzyme that modulates host cell apoptosis.
  J Biol Chem, 279, 29320-29324.
PDB code: 1rcw
15211525 R.Schwarzenbacher, F.Stenner-Liewen, H.Liewen, J.C.Reed, and R.C.Liddington (2004).
Crystal structure of PqqC from Klebsiella pneumoniae at 2.1 A resolution.
  Proteins, 56, 401-403.  
15166287 X.Liu, and E.C.Theil (2004).
Ferritin reactions: direct identification of the site for the diferric peroxide reaction intermediate.
  Proc Natl Acad Sci U S A, 101, 8557-8562.  
15231803 Y.Tao, A.Fishman, W.E.Bentley, and T.K.Wood (2004).
Altering toluene 4-monooxygenase by active-site engineering for the synthesis of 3-methoxycatechol, methoxyhydroquinone, and methylhydroquinone.
  J Bacteriol, 186, 4705-4713.  
12660237 D.A.Kopp, E.A.Berg, C.E.Costello, and S.J.Lippard (2003).
Structural features of covalently cross-linked hydroxylase and reductase proteins of soluble methane monooxygenase as revealed by mass spectrometric analysis.
  J Biol Chem, 278, 20939-20945.  
12640145 K.H.Mitchell, C.E.Rogge, T.Gierahn, and B.G.Fox (2003).
Insight into the mechanism of aromatic hydroxylation by toluene 4-monooxygenase by use of specifically deuterated toluene and p-xylene.
  Proc Natl Acad Sci U S A, 100, 3784-3789.  
12727864 M.A.Carrondo (2003).
Ferritins, iron uptake and storage from the bacterioferritin viewpoint.
  EMBO J, 22, 1959-1968.  
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.  
12627224 S.Macedo, C.V.Romão, E.Mitchell, P.M.Matias, M.Y.Liu, A.V.Xavier, J.LeGall, M.Teixeira, P.Lindley, and M.A.Carrondo (2003).
The nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricans.
  Nat Struct Biol, 10, 285-290.
PDB codes: 1nf4 1nf6 1nfv
12634425 X.Liu, W.Jin, and E.C.Theil (2003).
Opening protein pores with chaotropes enhances Fe reduction and chelation of Fe from the ferritin biomineral.
  Proc Natl Acad Sci U S A, 100, 3653-3658.  
11952785 A.J.Callaghan, T.J.Smith, S.E.Slade, and H.Dalton (2002).
Residues near the N-terminus of protein B control autocatalytic proteolysis and the activity of soluble methane mono-oxygenase.
  Eur J Biochem, 269, 1835-1843.  
11959967 C.M.Barnés, E.C.Theil, and K.N.Raymond (2002).
Iron uptake in ferritin is blocked by binding of [Cr(TREN)(H(2)O)(OH)](2+), a slow dissociating model for [Fe(H(2)O)(6)](2+).
  Proc Natl Acad Sci U S A, 99, 5195-5200.  
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.  
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.  
10841536 A.Lombardi, C.M.Summa, S.Geremia, L.Randaccio, V.Pavone, and W.F.DeGrado (2000).
Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.
  Proc Natl Acad Sci U S A, 97, 6298-6305.
PDB code: 1ec5
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.  
10196150 A.M.Valentine, M.H.LeTadic-Biadatti, P.H.Toy, M.Newcomb, and S.J.Lippard (1999).
Oxidation of ultrafast radical clock substrate probes by the soluble methane monooxygenase from Methylococcus capsulatus (Bath).
  J Biol Chem, 274, 10771-10776.  
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.