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PDBsum entry 1fz5
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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
1fz5

 

 

 

 

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Contents
Protein chains
511 a.a. *
388 a.a. *
166 a.a. *
Metals
_CA ×2
FE2 ×2
Waters ×524
* Residue conservation analysis
PDB id:
1fz5
Name: Oxidoreductase
Title: Methane monooxygenase hydroxylase, form ii crystallized anaerobically from reduced enzyme
Structure: Methane monooxygenase component a, alpha chain. Chain: a, b. Synonym: hydroxylase alpha subunit. Methane monooxygenase component a, beta chain. Chain: c, d. Synonym: hydroxylase beta subunit, methane monooxygenase a beta chain. Methane monooxygenase component a, gamma chain. Chain: e, f.
Source: Methylococcus capsulatus. Organism_taxid: 414. Organism_taxid: 414
Biol. unit: Hexamer (from PQS)
Resolution:
2.40Å     R-factor:   0.218     R-free:   0.253
Authors: D.A.Whittington,S.J.Lippard
Key ref: D.A.Whittington and S.J.Lippard (2001). Crystal structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath) demonstrating geometrical variability at the dinuclear iron active site. J Am Chem Soc, 123, 827-838. PubMed id: 11456616 DOI: 10.1021/ja003240n
Date:
03-Oct-00     Release date:   28-Feb-01    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P22869  (MEMA_METCA) -  Methane monooxygenase component A alpha chain from Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)
Seq:
Struc: 		 
Seq:
Struc: 		527 a.a.
511 a.a.*
Protein chains
Pfam   ArchSchema ?
P18798  (MEMB_METCA) -  Methane monooxygenase component A beta chain from Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)
Seq:
Struc: 		389 a.a.
388 a.a.
Protein chains
Pfam   ArchSchema ?
P11987  (MEMG_METCA) -  Methane monooxygenase component A gamma chain from Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)
Seq:
Struc: 		170 a.a.
166 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F: E.C.1.14.13.25  - methane monooxygenase (soluble).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. methane + NADH + O2 + H+ = methanol + NAD+ + H2O
2. methane + NADPH + O2 + H+ = methanol + NADP+ + H2O
methane
 + NADH
 + O2
 + H(+)
 = methanol
 + NAD(+)
 + H2O
methane
 + NADPH
 + O2
 + H(+)
 = methanol
 + NADP(+)
 + H2O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1021/ja003240n J Am Chem Soc 123:827-838 (2001)
PubMed id: 11456616  
 
 
Crystal structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath) demonstrating geometrical variability at the dinuclear iron active site.
D.A.Whittington, S.J.Lippard.
 
  ABSTRACT  
 
The oxidation of methane to methanol is performed at carboxylate-bridged dinuclear iron centers in the soluble methane monooxygenase hydroxylase (MMOH). Previous structural studies of MMOH, and the related R2 subunit of ribonucleotide reductase, have demonstrated the occurrence of carboxylate shifts involving glutamate residues that ligate the catalytic iron atoms. These shifts are thought to have important mechanistic implications. Recent kinetic and theoretical studies have also emphasized the importance of hydrogen bonding and pH effects at the active site. We report here crystal structures of MMOH from Methylococcus capsulatus (Bath) in the diiron(II), diiron(III), and mixed-valent Fe(II)Fe(III) oxidation states, and at pH values of 6.2, 7.0, and 8.5. These structures were investigated in an effort to delineate the range of possible motions at the MMOH active site and to identify hydrogen-bonding interactions that may be important in understanding catalysis by the enzyme. Our results present the first view of the diiron center in the mixed-valent state, and they indicate an increased lability for ferrous ions in the enzyme. Alternate conformations of Asn214 near the active site according to redox state and a distortion in one of the alpha-helices adjacent to the metal center in the diiron(II) state have also been identified. These changes alter the surface of the protein in the vicinity of the catalytic core and may have implications for small-molecule accessibility to the active site and for protein component interactions in the methane monooxygenase system. Collectively, these results help to explain previous spectroscopic observations and provide new insight into catalysis by the enzyme.
 

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
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.  
19921958 C.E.Tinberg, and S.J.Lippard (2009).
Revisiting the mechanism of dioxygen activation in soluble methane monooxygenase from M. capsulatus (Bath): evidence for a multi-step, proton-dependent reaction pathway.
  Biochemistry, 48, 12145-12158.  
19780121 I.Siewert, and C.Limberg (2009).
Low-molecular-weight analogues of the soluble methane monooxygenase (sMMO): from the structural mimicking of resting states and intermediates to functional models.
  Chemistry, 15, 10316-10328.  
19610611 J.R.Frisch, V.V.Vu, M.Martinho, E.Münck, and L.Que (2009).
Characterization of two distinct adducts in the reaction of a nonheme diiron(II) complex with O2.
  Inorg Chem, 48, 8325-8336.  
18576633 J.K.Schwartz, X.S.Liu, T.Tosha, E.C.Theil, and E.I.Solomon (2008).
Spectroscopic definition of the ferroxidase site in M ferritin: comparison of binuclear substrate vs cofactor active sites.
  J Am Chem Soc, 130, 9441-9450.  
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.  
17326634 D.Rinaldo, D.M.Philipp, S.J.Lippard, and R.A.Friesner (2007).
Intermediates in dioxygen activation by methane monooxygenase: a QM/MM study.
  J Am Chem Soc, 129, 3135-3147.  
17463003 J.E.Guy, E.Whittle, D.Kumaran, Y.Lindqvist, and J.Shanklin (2007).
The crystal structure of the ivy Delta4-16:0-ACP desaturase reveals structural details of the oxidized active site and potential determinants of regioselectivity.
  J Biol Chem, 282, 19863-19871.
PDB code: 2uw1
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.  
16411721 E.C.Carson, and S.J.Lippard (2006).
Synthesis, characterization, and preliminary oxygenation studies of benzyl- and ethyl-substituted pyridine ligands of carboxylate-rich diiron(II) complexes.
  Inorg Chem, 45, 828-836.  
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.  
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.  
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
17012379 P.M.Brown, T.T.Caradoc-Davies, J.M.Dickson, G.J.Cooper, K.M.Loomes, and E.N.Baker (2006).
Crystal structure of a substrate complex of myo-inositol oxygenase, a di-iron oxygenase with a key role in inositol metabolism.
  Proc Natl Acad Sci U S A, 103, 15032-15037.
PDB code: 2huo
16813407 S.Yoon, and S.J.Lippard (2006).
Mechanistic studies of the oxidative N-dealkylation of a substrate tethered to carboxylate-bridged diiron(II) complexes, [Fe2(mu-O2CAr(Tol))2(O2CAr(Tol))2(N,N-Bn2en)2].
  Inorg Chem, 45, 5438-5446.  
16332086 J.L.Blazyk, G.T.Gassner, and S.J.Lippard (2005).
Intermolecular electron-transfer reactions in soluble methane monooxygenase: a role for hysteresis in protein function.
  J Am Chem Soc, 127, 17364-17376.  
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.  
15796706 R.A.Friesner, and V.Guallar (2005).
Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis.
  Annu Rev Phys Chem, 56, 389-427.  
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
15383840 N.Ward, Ã.˜.Larsen, J.Sakwa, L.Bruseth, H.Khouri, A.S.Durkin, G.Dimitrov, L.Jiang, D.Scanlan, K.H.Kang, M.Lewis, K.E.Nelson, B.Methé, M.Wu, J.F.Heidelberg, I.T.Paulsen, D.Fouts, J.Ravel, H.Tettelin, Q.Ren, T.Read, R.T.DeBoy, R.Seshadri, S.L.Salzberg, H.B.Jensen, N.K.Birkeland, W.C.Nelson, R.J.Dodson, S.H.Grindhaug, I.Holt, I.Eidhammer, I.Jonasen, S.Vanaken, T.Utterback, T.V.Feldblyum, C.M.Fraser, J.R.Lillehaug, and J.A.Eisen (2004).
Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).
  PLoS Biol, 2, e303.  
15385566 W.C.Kao, Y.R.Chen, E.C.Yi, H.Lee, Q.Tian, K.M.Wu, S.F.Tsai, S.S.Yu, Y.J.Chen, R.Aebersold, and S.I.Chan (2004).
Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath).
  J Biol Chem, 279, 51554-51560.  
12847518 A.Glasfeld, E.Guedon, J.D.Helmann, and R.G.Brennan (2003).
Structure of the manganese-bound manganese transport regulator of Bacillus subtilis.
  Nat Struct Biol, 10, 652-657.
PDB codes: 1on1 1on2
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.  
12704186 M.Moche, J.Shanklin, A.Ghoshal, and Y.Lindqvist (2003).
Azide and acetate complexes plus two iron-depleted crystal structures of the di-iron enzyme delta9 stearoyl-acyl carrier protein desaturase. Implications for oxygen activation and catalytic intermediates.
  J Biol Chem, 278, 25072-25080.
PDB codes: 1oq4 1oq7 1oq9 1oqb
12655072 O.Maglio, F.Nastri, V.Pavone, A.Lombardi, and W.F.DeGrado (2003).
Preorganization of molecular binding sites in designed diiron proteins.
  Proc Natl Acad Sci U S A, 100, 3772-3777.
PDB code: 1nvo
12413539 D.A.Kopp, and S.J.Lippard (2002).
Soluble methane monooxygenase: activation of dioxygen and methane.
  Curr Opin Chem Biol, 6, 568-576.  
12087093 K.R.Strand, S.Karlsen, and K.K.Andersson (2002).
Cobalt substitution of mouse R2 ribonucleotide reductase as a model for the reactive diferrous state Spectroscopic and structural evidence for a ferromagnetically coupled dinuclear cobalt cluster.
  J Biol Chem, 277, 34229-34238.
PDB codes: 1h0n 1h0o
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.  
12039004 M.J.Ryle, and R.P.Hausinger (2002).
Non-heme iron oxygenases.
  Curr Opin Chem Biol, 6, 193-201.  
11709550 M.Merkx, and S.J.Lippard (2002).
Why OrfY? Characterization of MMOD, a long overlooked component of the soluble methane monooxygenase from Methylococcus capsulatus (Bath).
  J Biol Chem, 277, 5858-5865.  
12039010 V.Guallar, B.F.Gherman, S.J.Lippard, and R.A.Friesner (2002).
Quantum chemical studies of methane monooxygenase: comparision with P450.
  Curr Opin Chem Biol, 6, 236-242.  
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.  
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.

 

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