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PDBsum entry 2bbk

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protein Protein-protein interface(s) links
Electron transport PDB id
2bbk
Jmol
Contents
Protein chains
355 a.a. *
125 a.a. *
Waters ×556
* Residue conservation analysis
PDB id:
2bbk
Name: Electron transport
Title: Crystal structure of the quinoprotein methylamine dehydrogenase from paracoccus denitrificans at 1.75 angstroms
Structure: Methylamine dehydrogenase (heavy subunit). Chain: h, j. Engineered: yes. Methylamine dehydrogenase (light subunit). Chain: l, m. Engineered: yes
Source: Paracoccus denitrificans. Organism_taxid: 266. Organism_taxid: 266
Biol. unit: Tetramer (from PQS)
Resolution:
1.75Å     R-factor:   0.167    
Authors: L.Chen,F.S.Mathews
Key ref:
L.Chen et al. (1998). Refined crystal structure of methylamine dehydrogenase from Paracoccus denitrificans at 1.75 A resolution. J Mol Biol, 276, 131-149. PubMed id: 9514722 DOI: 10.1006/jmbi.1997.1511
Date:
17-Dec-93     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P29894  (DHMH_PARDE) -  Methylamine dehydrogenase heavy chain
Seq:
Struc:
417 a.a.
355 a.a.*
Protein chains
Pfam   ArchSchema ?
P22619  (DHML_PARDE) -  Methylamine dehydrogenase light chain
Seq:
Struc:
188 a.a.
125 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains H, L, J, M: E.C.1.4.9.1  - Methylamine dehydrogenase (amicyanin).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Methylamine + H2O + amicyanin = formaldehyde + ammonia + reduced amicyanin
Methylamine
+ H(2)O
+ amicyanin
= formaldehyde
+ ammonia
+ reduced amicyanin
      Cofactor: Tryptophan tryptophylquinone
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   2 terms 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     methylamine dehydrogenase (amicyanin) activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.1997.1511 J Mol Biol 276:131-149 (1998)
PubMed id: 9514722  
 
 
Refined crystal structure of methylamine dehydrogenase from Paracoccus denitrificans at 1.75 A resolution.
L.Chen, M.Doi, R.C.Durley, A.Y.Chistoserdov, M.E.Lidstrom, V.L.Davidson, F.S.Mathews.
 
  ABSTRACT  
 
The three-dimensional structure of the quinoprotein methylamine dehydrogenase from Paracoccus denitrificans has been refined at 1.75 A resolution utilizing the DNA-based protein sequence. The final model incorporates 8034 atoms per molecule, including 552 molecules of solvent, and gives an R-factor of 0.163. The molecule is an H2L2 hetero-tetramer containing a non-crystallographic 2-fold axis of symmetry. The 373-residue H subunit is folded into seven repeats of a four-stranded antiparallel beta-sheet motif, arranged in a propeller-like pattern about a pseudo-7-fold rotational axis of symmetry. Each L subunit contains 131 residues folded in a tight structure composed of five beta-strands in two sheets and crosslinked by six disulfide bonds. In addition there is an intrasubunit covalent linkage between two tryptophan side-chains that form the unique redox center, tryptophan tryptophylquinone (TTQ). The active site contains the O-6 carbonyl of TTQ, the side-chains of Asp32L Asp76L, Tyr119L and Thr122L, and two solvent molecules. A potential "gate" (Phe55H) separates the closed active-site cavity from a channel containing a group of highly ordered water molecules to bulk solvent. Phe55H and Tyr119L, and a number of neighboring oxygen atoms, may also provide a binding site for monovalent cations that are known to affect the reactivity and spectral properties of TTQ as well as the oxidative half reaction. The overall reaction has been dissected into a number of discrete steps that may require participation by several individual amino acid residues in the active site acting as general acids and bases.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. C^a stick representation of the H[2]L[2] subunit of PD-MADH. The H subunits are shown in gold and the L subunits in green. The TTQ moiety is shown in violet. This diagram was prepared using the molecular graphics program TURBO-FRODO [Roussel and Cambillau 1991].
Figure 13.
Figure 13. The overall reaction mechanism of MADH. Reaction steps that have been proposed for the oxidative and reductive half-reactions of MADH with methylamine and amicyanin are presented. Only the quinone portion of TTQ is shown. B[1] to B[12] represent active-site residues that function as general acids or bases in the reaction mechanism. This mechanism does not require 12 such residues because it is possible that a single residue may participate in multiple steps. The details of the reaction mechanism are described in the text.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 276, 131-149) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20936199 V.L.Davidson (2011).
Generation of protein-derived redox cofactors by posttranslational modification.
  Mol Biosyst, 7, 29-37.  
20223975 J.M.Bollinger, and M.L.Matthews (2010).
Biochemistry. Remote enzyme microsurgery.
  Science, 327, 1337-1338.  
20223990 L.M.Jensen, R.Sanishvili, V.L.Davidson, and C.M.Wilmot (2010).
In crystallo posttranslational modification within a MauG/pre-methylamine dehydrogenase complex.
  Science, 327, 1392-1394.
PDB codes: 3l4m 3l4o
19196017 S.Lee, S.Shin, X.Li, and V.L.Davidson (2009).
Kinetic mechanism for the initial steps in MauG-dependent tryptophan tryptophylquinone biosynthesis.
  Biochemistry, 48, 2442-2447.  
19788236 S.Shin, S.Lee, and V.L.Davidson (2009).
Suicide inactivation of MauG during reaction with O(2) or H(2)O(2) in the absence of its natural protein substrate.
  Biochemistry, 48, 10106-10112.  
18331637 K.Manikandan, D.Pal, S.Ramakumar, N.E.Brener, S.S.Iyengar, and G.Seetharaman (2008).
Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments.
  Genome Biol, 9, R52.  
18562294 X.Li, R.Fu, S.Lee, C.Krebs, V.L.Davidson, and A.Liu (2008).
A catalytic di-heme bis-Fe(IV) intermediate, alternative to an Fe(IV)=O porphyrin radical.
  Proc Natl Acad Sci U S A, 105, 8597-8600.  
18043650 J.D.Neufeld, H.Schäfer, M.J.Cox, R.Boden, I.R.McDonald, and J.C.Murrell (2007).
Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism.
  ISME J, 1, 480-491.  
16984182 A.R.Pearson, S.Marimanikkuppam, X.Li, V.L.Davidson, and C.M.Wilmot (2006).
Isotope labeling studies reveal the order of oxygen incorporation into the tryptophan tryptophylquinone cofactor of methylamine dehydrogenase.
  J Am Chem Soc, 128, 12416-12417.  
17005560 A.Roujeinikova, N.S.Scrutton, and D.Leys (2006).
Atomic level insight into the oxidative half-reaction of aromatic amine dehydrogenase.
  J Biol Chem, 281, 40264-40272.
PDB codes: 2hxc 2iup 2iuq 2iur 2iuv
16546999 K.Ono, T.Okajima, M.Tani, S.Kuroda, D.Sun, V.L.Davidson, and K.Tanizawa (2006).
Involvement of a putative [Fe-S]-cluster-binding protein in the biogenesis of quinohemoprotein amine dehydrogenase.
  J Biol Chem, 281, 13672-13684.  
16873126 S.Nuñez, G.Tresadern, I.H.Hillier, and N.A.Burton (2006).
An analysis of reaction pathways for proton tunnelling in methylamine dehydrogenase.
  Philos Trans R Soc Lond B Biol Sci, 361, 1387-1398.  
15778956 D.Segal, and M.Eisenstein (2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.
  Proteins, 59, 580-591.  
15581887 I.I.Serysheva, S.L.Hamilton, W.Chiu, and S.J.Ludtke (2005).
Structure of Ca2+ release channel at 14 A resolution.
  J Mol Biol, 345, 427-431.  
15734739 L.H.Jones, A.R.Pearson, Y.Tang, C.M.Wilmot, and V.L.Davidson (2005).
Active site aspartate residues are critical for tryptophan tryptophylquinone biogenesis in methylamine dehydrogenase.
  J Biol Chem, 280, 17392-17396.  
15696544 M.D.Swain, and D.E.Benson (2005).
Geometric preferences of crosslinked protein-derived cofactors reveal a high propensity for near-sequence pairs.
  Proteins, 59, 64-71.  
15162493 A.Berchanski, B.Shapira, and M.Eisenstein (2004).
Hydrophobic complementarity in protein-protein docking.
  Proteins, 56, 130-142.  
15465820 T.Uchida, T.Mogi, H.Nakamura, and T.Kitagawa (2004).
Role of Tyr-288 at the dioxygen reduction site of cytochrome bo studied by stable isotope labeling and resonance raman spectroscopy.
  J Biol Chem, 279, 53613-53620.  
12672814 M.M.Whittaker, and J.W.Whittaker (2003).
Cu(I)-dependent biogenesis of the galactose oxidase redox cofactor.
  J Biol Chem, 278, 22090-22101.  
12906826 R.Thoma, B.Löffler, M.Stihle, W.Huber, A.Ruf, and M.Hennig (2003).
Structural basis of proline-specific exopeptidase activity as observed in human dipeptidyl peptidase-IV.
  Structure, 11, 947-959.
PDB codes: 1nu6 1nu8
12925784 S.Datta, T.Ikeda, K.Kano, and F.S.Mathews (2003).
Structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from Paracoccus denitrificans at 1.7 A resolution.
  Acta Crystallogr D Biol Crystallogr, 59, 1551-1556.
PDB code: 1pby
12437349 D.Sun, Z.W.Chen, F.S.Mathews, and V.L.Davidson (2002).
Mutation of alphaPhe55 of methylamine dehydrogenase alters the reorganization energy and electronic coupling for its electron transfer reaction with amicyanin.
  Biochemistry, 41, 13926-13933.
PDB codes: 1mg2 1mg3
12377130 H.Jing, J.Takagi, J.H.Liu, S.Lindgren, R.G.Zhang, A.Joachimiak, J.H.Wang, and T.A.Springer (2002).
Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related to metazoan cell surface proteins.
  Structure, 10, 1453-1464.
PDB code: 1l0q
11733518 Y.Wang, D.Sun, and V.L.Davidson (2002).
Use of indirect site-directed mutagenesis to alter the substrate specificity of methylamine dehydrogenase.
  J Biol Chem, 277, 4119-4122.  
11591147 D.Sun, and V.L.Davidson (2001).
Re-engineering monovalent cation binding sites of methylamine dehydrogenase: effects on spectral properties and gated electron transfer.
  Biochemistry, 40, 12285-12291.  
11168384 K.Takagi, K.Yamamoto, K.Kano, and T.Ikeda (2001).
New pathway of amine oxidation respiratory chain of Paracoccus denitrificans IFO 12442.
  Eur J Biochem, 268, 470-476.  
11717396 S.Datta, Y.Mori, K.Takagi, K.Kawaguchi, Z.W.Chen, T.Okajima, S.Kuroda, T.Ikeda, K.Kano, K.Tanizawa, and F.S.Mathews (2001).
Structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking.
  Proc Natl Acad Sci U S A, 98, 14268-14273.
PDB code: 1jju
11698678 S.J.Firbank, M.S.Rogers, C.M.Wilmot, D.M.Dooley, M.A.Halcrow, P.F.Knowles, M.J.McPherson, and S.E.Phillips (2001).
Crystal structure of the precursor of galactose oxidase: an unusual self-processing enzyme.
  Proc Natl Acad Sci U S A, 98, 12932-12937.
PDB code: 1k3i
10903941 N.M.Okeley, and W.A.van der Donk (2000).
Novel cofactors via post-translational modifications of enzyme active sites.
  Chem Biol, 7, R159-R171.  
10673426 S.Carr, C.N.Penfold, V.Bamford, R.James, and A.M.Hemmings (2000).
The structure of TolB, an essential component of the tol-dependent translocation system, and its protein-protein interaction with the translocation domain of colicin E9.
  Structure, 8, 57-66.
PDB code: 1c5k
10985763 Z.Zhu, D.Sun, and V.L.Davidson (2000).
Conversion of methylamine dehydrogenase to a long-chain amine dehydrogenase by mutagenesis of a single residue.
  Biochemistry, 39, 11184-11186.  
10913294 Z.Zhu, L.H.Jones, M.E.Graichen, and V.L.Davidson (2000).
Molecular basis for complex formation between methylamine dehydrogenase and amicyanin revealed by inverse mutagenesis of an interprotein salt bridge.
  Biochemistry, 39, 8830-8836.  
10506161 Y.L.Hyun, Z.Zhu, and V.L.Davidson (1999).
Gated and ungated electron transfer reactions from aromatic amine dehydrogenase to azurin.
  J Biol Chem, 274, 29081-29086.  
9748238 G.Labesse, D.Ferrari, Z.W.Chen, G.L.Rossi, V.Kuusk, W.S.McIntire, and F.S.Mathews (1998).
Crystallographic and spectroscopic studies of native, aminoquinol, and monovalent cation-bound forms of methylamine dehydrogenase from Methylobacterium extorquens AM1.
  J Biol Chem, 273, 25703-25712.  
9603931 Z.Zhu, and V.L.Davidson (1998).
Redox properties of tryptophan tryptophylquinone enzymes. Correlation with structure and reactivity.
  J Biol Chem, 273, 14254-14260.  
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.