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PDBsum entry 1bjp

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
1bjp
Jmol
Contents
Protein chains
62 a.a. *
58 a.a. *
Ligands
OXP ×5
Waters ×78
* Residue conservation analysis
PDB id:
1bjp
Name: Isomerase
Title: Crystal structure of 4-oxalocrotonate tautomerase inactivate oxo-3-pentynoate at 2.4 angstroms resolution
Structure: 4-oxalocrotonate tautomerase. Chain: a, b, c, d, e. Synonym: 4-oxalocrotonate isomerase. Engineered: yes
Source: Pseudomonas putida. Organism_taxid: 303. Strain: mt-2. Atcc: atcc 33015. Collection: atcc 33015. Gene: xylh. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
Resolution:
2.40Å     R-factor:   0.206     R-free:   0.244
Authors: A.B.Taylor,R.M.Czerwinski,W.H.Johnson Junior,C.P.Whitman,M.L
Key ref:
A.B.Taylor et al. (1998). Crystal structure of 4-oxalocrotonate tautomerase inactivated by 2-oxo-3-pentynoate at 2.4 A resolution: analysis and implications for the mechanism of inactivation and catalysis. Biochemistry, 37, 14692-14700. PubMed id: 9778344 DOI: 10.1021/bi981607j
Date:
26-Jun-98     Release date:   02-Dec-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q01468  (4OT1_PSEPU) -  2-hydroxymuconate tautomerase
Seq:
Struc:
63 a.a.
62 a.a.
Protein chains
Pfam   ArchSchema ?
Q01468  (4OT1_PSEPU) -  2-hydroxymuconate tautomerase
Seq:
Struc:
63 a.a.
58 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, E: E.C.5.3.2.6  - 2-hydroxymuconate tautomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (3E)-2-oxohex-3-enedioate
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cellular aromatic compound metabolic process   4 terms 
  Biochemical function     isomerase activity     1 term  

 

 
DOI no: 10.1021/bi981607j Biochemistry 37:14692-14700 (1998)
PubMed id: 9778344  
 
 
Crystal structure of 4-oxalocrotonate tautomerase inactivated by 2-oxo-3-pentynoate at 2.4 A resolution: analysis and implications for the mechanism of inactivation and catalysis.
A.B.Taylor, R.M.Czerwinski, W.H.Johnson, C.P.Whitman, M.L.Hackert.
 
  ABSTRACT  
 
The crystal structure of 4-oxalocrotonate tautomerase (4-OT) inactivated by the active site-directed irreversible inhibitor 2-oxo-3-pentynoate (2-OP) has been determined to 2.4 A resolution. The structure of the enzyme covalently modified at Pro-1 by the resulting 2-oxo-3-pentenoate adduct is nearly superimposable on that of the free enzyme and confirms that the active site is located in a hydrophobic region surrounding Pro-1. Both structures can be described as a trimer of dimers where each dimer consists of a four-stranded beta-sheet with two antiparallel alpha-helices on one side. Examination of the structure also reveals noncovalent interactions between the adduct and two residues in the active site. The epsilon and eta nitrogens of the guanidinium side chain of Arg-39" from a neighboring dimer interact respectively with the C-2 carbonyl oxygen and one C-1 carboxylate oxygen of the adduct while the side chain of Arg-61' from the same dimer as the modified Pro-1 interacts with the C-1 carboxylate group in a bidentate fashion. An additional interaction to the 2-oxo group of the adduct is provided by one of the two ordered water molecules within the active site region. These interactions coupled with the observation that 2-oxo-3-butynoate is a more potent irreversible inhibitor of 4-oxalocrotonate tautomerase than is 2-OP suggest that Arg-39" and the ordered water molecule polarize the carbonyl group of 2-OP which facilitates a Michael reaction between Pro-1 and the acetylene compound. On the basis of the crystal structure, a mechanism for the enzyme-catalyzed reaction is proposed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21219457 J.Nogales, A.Canales, J.Jiménez-Barbero, B.Serra, J.M.Pingarrón, J.L.García, and E.Díaz (2011).
Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida.
  Mol Microbiol, 79, 359-374.  
19199636 J.J.Ruiz-Pernía, M.Garcia-Viloca, S.Bhattacharyya, J.Gao, D.G.Truhlar, and I.Tuñón (2009).
Critical role of substrate conformational change in the proton transfer process catalyzed by 4-oxalocrotonate tautomerase.
  J Am Chem Soc, 131, 2687-2698.  
19437047 P.E.Siegbahn, and F.Himo (2009).
Recent developments of the quantum chemical cluster approach for modeling enzyme reactions.
  J Biol Inorg Chem, 14, 643-651.  
18695941 G.J.Poelarends, V.P.Veetil, and C.P.Whitman (2008).
The chemical versatility of the beta-alpha-beta fold: catalytic promiscuity and divergent evolution in the tautomerase superfamily.
  Cell Mol Life Sci, 65, 3606-3618.  
17902707 S.C.Wang, W.H.Johnson, R.M.Czerwinski, S.L.Stamps, and C.P.Whitman (2007).
Kinetic and stereochemical analysis of YwhB, a 4-oxalocrotonate tautomerase homologue in Bacillus subtilis: mechanistic implications for the YwhB- and 4-oxalocrotonate tautomerase-catalyzed reactions.
  Biochemistry, 46, 11919-11929.  
16784221 G.J.Poelarends, J.J.Almrud, H.Serrano, J.E.Darty, W.H.Johnson, M.L.Hackert, and C.P.Whitman (2006).
Evolution of enzymatic activity in the tautomerase superfamily: mechanistic and structural consequences of the L8R mutation in 4-oxalocrotonate tautomerase.
  Biochemistry, 45, 7700-7708.
PDB code: 2fm7
15048836 D.Kihara, and J.Skolnick (2004).
Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q.
  Proteins, 55, 464-473.  
14701869 R.M.de Jong, W.Brugman, G.J.Poelarends, C.P.Whitman, and B.W.Dijkstra (2004).
The X-ray structure of trans-3-chloroacrylic acid dehalogenase reveals a novel hydration mechanism in the tautomerase superfamily.
  J Biol Chem, 279, 11546-11552.
PDB code: 1s0y
12084071 E.Machado Benelli, M.Buck, I.Polikarpov, E.Maltempi de Souza, L.M.Cruz, and F.O.Pedrosa (2002).
Herbaspirillum seropedicae signal transduction protein PII is structurally similar to the enteric GlnK.
  Eur J Biochem, 269, 3296-3303.
PDB code: 1hwu
12382291 T.A.Soares, R.D.Lins, T.P.Straatsma, and J.M.Briggs (2002).
Internal dynamics and ionization states of the macrophage migration inhibitory factor: comparison between wild-type and mutant forms.
  Biopolymers, 65, 313-323.  
11729263 E.Díaz, A.Ferrández, M.A.Prieto, and J.L.García (2001).
Biodegradation of aromatic compounds by Escherichia coli.
  Microbiol Mol Biol Rev, 65, 523.  
11418568 G.J.Poelarends, R.Saunier, and D.B.Janssen (2001).
trans-3-Chloroacrylic acid dehalogenase from Pseudomonas pavonaceae 170 shares structural and mechanistic similarities with 4-oxalocrotonate tautomerase.
  J Bacteriol, 183, 4269-4277.  
11284706 P.Silinski, M.J.Allingham, and M.C.Fitzgerald (2001).
Guanidine-induced equilibrium unfolding of a homo-hexameric enzyme 4-oxalocrotonate tautomerase (4-OT).
  Biochemistry, 40, 4493-4502.  
11329265 R.M.Czerwinski, T.K.Harris, M.A.Massiah, A.S.Mildvan, and C.P.Whitman (2001).
The structural basis for the perturbed pKa of the catalytic base in 4-oxalocrotonate tautomerase: kinetic and structural effects of mutations of Phe-50.
  Biochemistry, 40, 1984-1995.  
10933783 S.L.Stamps, A.B.Taylor, S.C.Wang, M.L.Hackert, and C.P.Whitman (2000).
Mechanism of the phenylpyruvate tautomerase activity of macrophage migration inhibitory factor: properties of the P1G, P1A, Y95F, and N97A mutants.
  Biochemistry, 39, 9671-9678.
PDB code: 1mff
10867710 T.Soares, D.Goodsell, R.Ferreira, A.J.Olson, and J.M.Briggs (2000).
Ionization state and molecular docking studies for the macrophage migration inhibitory factor: the role of lysine 32 in the catalytic mechanism.
  J Mol Recognit, 13, 146-156.  
10360941 A.B.Taylor, W.H.Johnson, R.M.Czerwinski, H.S.Li, M.L.Hackert, and C.P.Whitman (1999).
Crystal structure of macrophage migration inhibitory factor complexed with (E)-2-fluoro-p-hydroxycinnamate at 1.8 A resolution: implications for enzymatic catalysis and inhibition.
  Biochemistry, 38, 7444-7452.
PDB code: 1mfi
10231533 G.Gadda, L.J.Dangott, W.H.Johnson, C.P.Whitman, and P.F.Fitzpatrick (1999).
Characterization of 2-oxo-3-pentynoate as an active-site-directed inactivator of flavoprotein oxidases: identification of active-site peptides in tryptophan 2-monooxygenase.
  Biochemistry, 38, 5822-5828.  
10353846 J.B.Lubetsky, M.Swope, C.Dealwis, P.Blake, and E.Lolis (1999).
Pro-1 of macrophage migration inhibitory factor functions as a catalytic base in the phenylpyruvate tautomerase activity.
  Biochemistry, 38, 7346-7354.
PDB codes: 1ca7 1cgq 1p1g
10397792 T.A.Soares, D.S.Goodsell, J.M.Briggs, R.Ferreira, and A.J.Olson (1999).
Docking of 4-oxalocrotonate tautomerase substrates: implications for the catalytic mechanism.
  Biopolymers, 50, 319-328.  
10625471 W.H.Johnson, R.M.Czerwinski, S.L.Stamps, and C.P.Whitman (1999).
A kinetic and stereochemical investigation of the role of lysine-32 in the phenylpyruvate tautomerase activity catalyzed by macrophage migration inhibitory factor.
  Biochemistry, 38, 16024-16033.  
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.