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PDBsum entry 1fz8
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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1fz8

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
511 a.a. *
388 a.a. *
167 a.a. *
Ligands
2BM ×10
Metals
_FE ×4
_CA ×3
Waters ×1069
* Residue conservation analysis
PDB id:
1fz8
Name: Oxidoreductase
Title: Methane monooxygenase hydroxylase, form ii cocrystallized with dibromomethane
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:
2.10Å     R-factor:   0.201     R-free:   0.250
Authors: D.A.Whittington,A.C.Rosenzweig,C.A.Frederick,S.J.Lippard
Key ref:
D.A.Whittington et al. (2001). Xenon and halogenated alkanes track putative substrate binding cavities in the soluble methane monooxygenase hydroxylase. Biochemistry, 40, 3476-3482. PubMed id: 11297413 DOI: 10.1021/bi0022487
Date:
03-Oct-00     Release date:   27-Apr-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.
167 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/bi0022487 Biochemistry 40:3476-3482 (2001)
PubMed id: 11297413  
 
 
Xenon and halogenated alkanes track putative substrate binding cavities in the soluble methane monooxygenase hydroxylase.
D.A.Whittington, A.C.Rosenzweig, C.A.Frederick, S.J.Lippard.
 
  ABSTRACT  
 
To investigate the role of protein cavities in facilitating movement of the substrates, methane and dioxygen, in the soluble methane monooxygenase hydroxylase (MMOH), we determined the X-ray structures of MMOH from Methylococcus capsulatus (Bath) cocrystallized with dibromomethane or iodoethane, or by using crystals pressurized with xenon gas. The halogenated alkanes bind in two cavities within the alpha-subunit that extend from one surface of the protein to the buried dinuclear iron active site. Two additional binding sites were located in the beta-subunit. Pressurization of two crystal forms of MMOH with xenon resulted in the identification of six binding sites located exclusively in the alpha-subunit. These results indicate that hydrophobic species bind preferentially in preexisting cavities in MMOH and support the hypothesis that such cavities may play a functional role in sequestering and enhancing the availability of the physiological substrates for reaction at the active site.
 

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
20485834 S.Friedle, E.Reisner, and S.J.Lippard (2010).
Current challenges of modeling diiron enzyme active sites for dioxygen activation by biomimetic synthetic complexes.
  Chem Soc Rev, 39, 2768-2779.  
18410129 L.Chen, A.Y.Lyubimov, L.Brammer, A.Vrielink, and N.S.Sampson (2008).
The binding and release of oxygen and hydrogen peroxide are directed by a hydrophobic tunnel in cholesterol oxidase.
  Biochemistry, 47, 5368-5377.
PDB code: 3cnj
17409383 B.J.Johnson, J.Cohen, R.W.Welford, A.R.Pearson, K.Schulten, J.P.Klinman, and C.M.Wilmot (2007).
Exploring molecular oxygen pathways in Hansenula polymorpha copper-containing amine oxidase.
  J Biol Chem, 282, 17767-17776.
PDB codes: 2oov 2oqe
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.  
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
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.  
15234986 D.Dantsker, U.Samuni, Y.Ouellet, B.A.Wittenberg, J.B.Wittenberg, M.Milani, M.Bolognesi, M.Guertin, and J.M.Friedman (2004).
Viscosity-dependent relaxation significantly modulates the kinetics of CO recombination in the truncated hemoglobin TrHbN from Mycobacterium tuberculosis.
  J Biol Chem, 279, 38844-38853.  
15596727 I.Moudrakovski, D.V.Soldatov, J.A.Ripmeester, D.N.Sears, and C.J.Jameson (2004).
Xe NMR lineshapes in channels of peptide molecular crystals.
  Proc Natl Acad Sci U S A, 101, 17924-17929.  
14766537 L.P.Wackett, A.G.Dodge, and L.B.Ellis (2004).
Microbial genomics and the periodic table.
  Appl Environ Microbiol, 70, 647-655.  
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
15057940 W.Radding, and G.N.Phillips (2004).
Kinetic proofreading by the cavity system of myoglobin: protection from poisoning.
  Bioessays, 26, 422-433.  
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.  
12736253 U.Samuni, D.Dantsker, A.Ray, J.B.Wittenberg, B.A.Wittenberg, S.Dewilde, L.Moens, Y.Ouellet, M.Guertin, and J.M.Friedman (2003).
Kinetic modulation in carbonmonoxy derivatives of truncated hemoglobins: the role of distal heme pocket residues and extended apolar tunnel.
  J Biol Chem, 278, 27241-27250.  
12039005 C.M.Wilmot, and A.R.Pearson (2002).
Cryocrystallography of metalloprotein reaction intermediates.
  Curr Opin Chem Biol, 6, 202-207.  
12413539 D.A.Kopp, and S.J.Lippard (2002).
Soluble methane monooxygenase: activation of dioxygen and methane.
  Curr Opin Chem Biol, 6, 568-576.  
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.  
12039004 M.J.Ryle, and R.P.Hausinger (2002).
Non-heme iron oxygenases.
  Curr Opin Chem Biol, 6, 193-201.  
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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