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PDBsum entry 1fc4

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1fc4
Jmol
Contents
Protein chains
401 a.a. *
Ligands
AKB-PLP ×2
Waters ×1103
* Residue conservation analysis
PDB id:
1fc4
Name: Transferase
Title: 2-amino-3-ketobutyrate coa ligase
Structure: 2-amino-3-ketobutyrate conenzyme a ligase. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.151     R-free:   0.212
Authors: A.Schmidt,A.Matte,Y.Li,J.Sivaraman,R.Larocque,J.D.Schrag,C.S V.Sauve,M.Cygler,Montreal-Kingston Bacterial Structural Gen Initiative (Bsgi)
Key ref:
A.Schmidt et al. (2001). Three-dimensional structure of 2-amino-3-ketobutyrate CoA ligase from Escherichia coli complexed with a PLP-substrate intermediate: inferred reaction mechanism. Biochemistry, 40, 5151-5160. PubMed id: 11318637
Date:
17-Jul-00     Release date:   02-May-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AB77  (KBL_ECOLI) -  2-amino-3-ketobutyrate coenzyme A ligase
Seq:
Struc:
398 a.a.
401 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
Biochemistry 40:5151-5160 (2001)
PubMed id: 11318637  
 
 
Three-dimensional structure of 2-amino-3-ketobutyrate CoA ligase from Escherichia coli complexed with a PLP-substrate intermediate: inferred reaction mechanism.
A.Schmidt, J.Sivaraman, Y.Li, R.Larocque, J.A.Barbosa, C.Smith, A.Matte, J.D.Schrag, M.Cygler.
 
  ABSTRACT  
 
2-Amino-3-ketobutyrate CoA ligase (KBL, EC 2.3.1.29) is a pyridoxal phosphate (PLP) dependent enzyme, which catalyzes the second reaction step on the main metabolic degradation pathway for threonine. It acts in concert with threonine dehydrogenase and converts 2-amino-3-ketobutyrate, the product of threonine dehydrogenation by the latter enzyme, with the participation of cofactor CoA, to glycine and acetyl-CoA. The enzyme has been well conserved during evolution, with 54% amino acid sequence identity between the Escherichia coli and human enzymes. We present the three-dimensional structure of E. coli KBL determined at 2.0 A resolution. KBL belongs to the alpha family of PLP-dependent enzymes, for which the prototypic member is aspartate aminotransferase. Its closest structural homologue is E. coli 8-amino-7-oxononanoate synthase. Like many other members of the alpha family, the functional form of KBL is a dimer, and one such dimer is found in the asymmetric unit in the crystal. There are two active sites per dimer, located at the dimer interface. Both monomers contribute side chains to each active/substrate binding site. Electron density maps indicated the presence in the crystal of the Schiff base intermediate of 2-amino-3-ketobutyrate and PLP, an external aldimine, which remained bound to KBL throughout the protein purification procedure. The observed interactions between the aldimine and the side chains in the substrate binding site explain the specificity for the substrate and provide the basis for a detailed proposal of the reaction mechanism of KBL. A putative binding site of the CoA cofactor was assigned, and implications for the cooperation with threonine dehydrogenase were considered.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20445930 J.Lowther, B.A.Yard, K.A.Johnson, L.G.Carter, V.T.Bhat, M.C.Raman, D.J.Clarke, B.Ramakers, S.A.McMahon, J.H.Naismith, and D.J.Campopiano (2010).
Inhibition of the PLP-dependent enzyme serine palmitoyltransferase by cycloserine: evidence for a novel decarboxylative mechanism of inactivation.
  Mol Biosyst, 6, 1682-1693.
PDB code: 2xbn
20578000 M.C.Raman, K.A.Johnson, D.J.Clarke, J.H.Naismith, and D.J.Campopiano (2010).
The serine palmitoyltransferase from Sphingomonas wittichii RW1: An interesting link to an unusual acyl carrier protein.
  Biopolymers, 93, 811-822.
PDB code: 2x8u
19376777 M.C.Raman, K.A.Johnson, B.A.Yard, J.Lowther, L.G.Carter, J.H.Naismith, and D.J.Campopiano (2009).
The External Aldimine Form of Serine Palmitoyltransferase: STRUCTURAL, KINETIC, AND SPECTROSCOPIC ANALYSIS OF THE WILD-TYPE ENZYME AND HSAN1 MUTANT MIMICS.
  J Biol Chem, 284, 17328-17339.
PDB codes: 2w8j 2w8t 2w8u 2w8v 2w8w
19562746 T.Lendrihas, J.Zhang, G.A.Hunter, and G.C.Ferreira (2009).
Arg-85 and Thr-430 in murine 5-aminolevulinate synthase coordinate acyl-CoA-binding and contribute to substrate specificity.
  Protein Sci, 18, 1847-1859.  
19346561 Y.Shiraiwa, H.Ikushiro, and H.Hayashi (2009).
Multifunctional role of his159in the catalytic reaction of serine palmitoyltransferase.
  J Biol Chem, 284, 15487-15495.  
18167344 H.Ikushiro, S.Fujii, Y.Shiraiwa, and H.Hayashi (2008).
Acceleration of the substrate Calpha deprotonation by an analogue of the second substrate palmitoyl-CoA in Serine Palmitoyltransferase.
  J Biol Chem, 283, 7542-7553.  
18221517 J.R.Manning, E.R.Jefferson, and G.J.Barton (2008).
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction.
  BMC Bioinformatics, 9, 51.  
18411263 T.Spirig, A.Tiaden, P.Kiefer, C.Buchrieser, J.A.Vorholt, and H.Hilbi (2008).
The Legionella autoinducer synthase LqsA produces an alpha-hydroxyketone signaling molecule.
  J Biol Chem, 283, 18113-18123.  
17485466 G.A.Hunter, J.Zhang, and G.C.Ferreira (2007).
Transient kinetic studies support refinements to the chemical and kinetic mechanisms of aminolevulinate synthase.
  J Biol Chem, 282, 23025-23035.  
17557831 H.Ikushiro, M.M.Islam, H.Tojo, and H.Hayashi (2007).
Molecular characterization of membrane-associated soluble serine palmitoyltransferases from Sphingobacterium multivorum and Bdellovibrio stolpii.
  J Bacteriol, 189, 5749-5761.  
17469798 T.D.Turbeville, J.Zhang, G.A.Hunter, and G.C.Ferreira (2007).
Histidine 282 in 5-aminolevulinate synthase affects substrate binding and catalysis.
  Biochemistry, 46, 5972-5981.  
17146529 Q.Bashir, N.Rashid, and M.Akhtar (2006).
Mechanism and substrate stereochemistry of 2-amino-3-oxobutyrate CoA ligase: implications for 5-aminolevulinate synthase and related enzymes.
  Chem Commun (Camb), (), 5065-5067.  
16769720 V.M.Bhor, S.Dev, G.R.Vasanthakumar, P.Kumar, S.Sinha, and A.Surolia (2006).
Broad substrate stereospecificity of the Mycobacterium tuberculosis 7-keto-8-aminopelargonic acid synthase: Spectroscopic and kinetic studies.
  J Biol Chem, 281, 25076-25088.  
16121195 I.Astner, J.O.Schulze, J.van den Heuvel, D.Jahn, W.D.Schubert, and D.W.Heinz (2005).
Crystal structure of 5-aminolevulinate synthase, the first enzyme of heme biosynthesis, and its link to XLSA in humans.
  EMBO J, 24, 3166-3177.
PDB codes: 2bwn 2bwo 2bwp
15840827 J.Zhang, A.V.Cheltsov, and G.C.Ferreira (2005).
Conversion of 5-aminolevulinate synthase into a more active enzyme by linking the two subunits: spectroscopic and kinetic properties.
  Protein Sci, 14, 1190-1200.  
12837772 A.Matte, J.Sivaraman, I.Ekiel, K.Gehring, Z.Jia, and M.Cygler (2003).
Contribution of structural genomics to understanding the biology of Escherichia coli.
  J Bacteriol, 185, 3994-4002.  
12097150 A.J.Edgar (2002).
Molecular cloning and tissue distribution of mammalian L-threonine 3-dehydrogenases.
  BMC Biochem, 3, 19.  
12191993 J.Zhang, and G.C.Ferreira (2002).
Transient state kinetic investigation of 5-aminolevulinate synthase reaction mechanism.
  J Biol Chem, 277, 44660-44669.  
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.