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

 

 

 

 

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Contents
Protein chains
510 a.a. *
388 a.a. *
166 a.a. *
Ligands
BHL ×10
BBU
BBX
3BR ×2
Metals
_FE ×4
_CA
Waters ×1116
* Residue conservation analysis
PDB id:
1xvb
Name: Oxidoreductase
Title: Soluble methane monooxygenase hydroxylase: 6-bromohexanol soaked structure
Structure: Methane monooxygenase component a alpha chain. Chain: a, b. Synonym: methane hydroxylase. Methane monooxygenase component a beta chain. Chain: c, d. Synonym: methane hydroxylase. Methane monooxygenase component a gamma chain. Chain: e, f. Synonym: methane hydroxylase.
Source: Methylococcus capsulatus. Organism_taxid: 414. Organism_taxid: 414
Biol. unit: Hexamer (from PQS)
Resolution:
1.80Å     R-factor:   0.219     R-free:   0.251
Authors: M.H.Sazinsky,S.J.Lippard
Key ref: M.H.Sazinsky and S.J.Lippard (2005). Product bound structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): protein motion in the alpha-subunit. J Am Chem Soc, 127, 5814-5825. PubMed id: 15839679 DOI: 10.1021/ja044099b
Date:
27-Oct-04     Release date:   03-May-05    
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.
510 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/ja044099b J Am Chem Soc 127:5814-5825 (2005)
PubMed id: 15839679  
 
 
Product bound structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): protein motion in the alpha-subunit.
M.H.Sazinsky, S.J.Lippard.
 
  ABSTRACT  
 
The soluble methane monooxygenase hydroxylase (MMOH) alpha-subunit contains a series of cavities that delineate the route of substrate entrance to and product egress from the buried carboxylate-bridged diiron center. The presence of discrete cavities is a major structural difference between MMOH, which can hydroxylate methane, and toluene/o-xylene monooxygenase hydroxylase (ToMOH), which cannot. To understand better the functions of the cavities and to investigate how an enzyme designed for methane hydroxylation can also accommodate larger substrates such as octane, methylcubane, and trans-1-methyl-2-phenylcyclopropane, MMOH crystals were soaked with an assortment of different alcohols and their X-ray structures were solved to 1.8-2.4 A resolution. The product analogues localize to cavities 1-3 and delineate a path of product exit and/or substrate entrance from the active site to the surface of the protein. The binding of the alcohols to a position bridging the two iron atoms in cavity 1 extends and validates previous crystallographic, spectroscopic, and computational work indicating this site to be where substrates are hydroxylated and products form. The presence of these alcohols induces perturbations in the amino acid side-chain gates linking pairs of cavities, allowing for the formation of a channel similar to one observed in ToMOH. Upon binding of 6-bromohexan-1-ol, the pi helix formed by residues 202-211 in helix E of the alpha-subunit is extended through residue 216, changing the orientations of several amino acid residues in the active site cavity. This remarkable secondary structure rearrangement in the four-helix bundle has several mechanistic implications for substrate accommodation and the function of the effector protein, MMOB.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20688982 A.K.Boal, J.A.Cotruvo, J.Stubbe, and A.C.Rosenzweig (2010).
Structural basis for activation of class Ib ribonucleotide reductase.
  Science, 329, 1526-1530.
PDB codes: 3n37 3n38 3n39 3n3a 3n3b
20827723 K.Lasker, A.Sali, and H.J.Wolfson (2010).
Determining macromolecular assembly structures by molecular docking and fitting into an electron density map.
  Proteins, 78, 3205-3211.  
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.  
19033467 L.J.Bailey, J.G.McCoy, G.N.Phillips, and B.G.Fox (2008).
Structural consequences of effector protein complex formation in a diiron hydroxylase.
  Proc Natl Acad Sci U S A, 105, 19194-19198.
PDB codes: 3dhg 3dhh 3dhi
17967027 L.J.Murray, S.G.Naik, D.O.Ortillo, R.García-Serres, J.K.Lee, B.H.Huynh, and S.J.Lippard (2007).
Characterization of the arene-oxidizing intermediate in ToMOH as a diiron(III) species.
  J Am Chem Soc, 129, 14500-14510.  
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
16605252 P.Sobrado, K.S.Lyle, S.P.Kaul, M.M.Turco, I.Arabshahi, A.Marwah, and B.G.Fox (2006).
Identification of the binding region of the [2Fe-2S] ferredoxin in stearoyl-acyl carrier protein desaturase: insight into the catalytic complex and mechanism of action.
  Biochemistry, 45, 4848-4858.  
16116657 G.Vardar, Y.Tao, J.Lee, and T.K.Wood (2005).
Alanine 101 and alanine 110 of the alpha subunit of Pseudomonas stutzeri OX1 toluene-o-xylene monooxygenase influence the regiospecific oxidation of aromatics.
  Biotechnol Bioeng, 92, 652-658.  
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 codes are shown on the right.

 

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