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PDBsum entry 1fup

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1fup
Jmol
Contents
Protein chains
455 a.a. *
Ligands
MLT ×2
PMA ×2
Waters ×347
* Residue conservation analysis
PDB id:
1fup
Name: Lyase
Title: Fumarase with bound pyromellitic acid
Structure: FumarasE C. Chain: a, b. Synonym: fumc. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.30Å     R-factor:   0.185     R-free:   0.234
Authors: T.Weaver,L.Banaszak
Key ref:
T.Weaver and L.Banaszak (1996). Crystallographic studies of the catalytic and a second site in fumarase C from Escherichia coli. Biochemistry, 35, 13955-13965. PubMed id: 8909293 DOI: 10.1021/bi9614702
Date:
29-Aug-96     Release date:   12-Mar-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05042  (FUMC_ECOLI) -  Fumarate hydratase class II
Seq:
Struc:
467 a.a.
455 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.2  - Fumarate hydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Citric acid cycle
      Reaction: (S)-malate = fumarate + H2O
(S)-malate
Bound ligand (Het Group name = MLT)
corresponds exactly
= fumarate
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi9614702 Biochemistry 35:13955-13965 (1996)
PubMed id: 8909293  
 
 
Crystallographic studies of the catalytic and a second site in fumarase C from Escherichia coli.
T.Weaver, L.Banaszak.
 
  ABSTRACT  
 
Fumarase C catalyzes the stereospecific interconversion of fumarate to L-malate as part of the metabolic citric acid or Kreb's cycle. The recent three-dimensional structure of fumarase C from Escherichia coli has identified a binding site for anions which is generated by side chains from three of the four subunits within the tetramer (Weaver et al., 1995). These same side chains are found in the three most highly conserved regions within the class II fumarase superfamily. The site was initially characterized by crystallographic studies through the binding of a heavy atom derivative, tungstate. A number of additional crystallographic structures using fumarase crystals with bound inhibitors and poor substrates have now been studied. The new structures have both confirmed the originally proposed active site, site A, and led to the discovery of a novel second binding site that is structurally nearby, site B. Site A utilizes a combination of residues, including H188, T187, K324, N326, T100, N141, S139, and S140, to form direct hydrogen bonds to each of the inhibitors. The A-site has been demonstrated by studying crystalline fumarase with the bound competitive inhibitors-citrate and 1,2,4,5-benzenetetracarboxylic acid. The crystal structure of fumarase C with beta-(trimethylsilyl)maleate, a cis substrate for fumarase, has led to the discovery of the second site or B-site. Sites A and B have different properties in terms of their three-dimensional structures. Site B, for example, is formed by atoms from only one of the subunits within the tetramer and mainly by atoms from a pi-helix between residues H129 through N135. The crystal structures show that the two locations are separated by approximately 12 A. A highly coordinated buried water molecule is also found at the active or A-site. The high-resolution crystal structures describe both sites, and atoms near the A-site are used to propose a likely enzyme/substrate complex.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21243161 J.Jin, and U.Hanefeld (2011).
The selective addition of water to C=C bonds; enzymes are the best chemists.
  Chem Commun (Camb), 47, 2502-2510.  
  19936305 C.W.Huang, Y.H.Chen, Y.H.Chen, Y.C.Tsai, and H.J.Lee (2009).
The interaction of Glu294 at the subunit interface is important for the activity and stability of goose delta-crystallin.
  Mol Vis, 15, 2358-2363.  
19490103 V.Puthan Veetil, H.Raj, W.J.Quax, D.B.Janssen, and G.J.Poelarends (2009).
Site-directed mutagenesis, kinetic and inhibition studies of aspartate ammonia lyase from Bacillus sp. YM55-1.
  FEBS J, 276, 2994-3007.  
17245573 W.Lin, M.Chan, L.L.Goh, and T.S.Sim (2007).
Molecular basis for thermal properties of Streptomyces thermovulgaris fumarase C hinge at hydrophilic amino acids R163, E170 and S347.
  Appl Microbiol Biotechnol, 75, 329-335.  
16597677 M.Pithukpakorn, M.H.Wei, O.Toure, P.J.Steinbach, G.M.Glenn, B.Zbar, W.M.Linehan, and J.R.Toro (2006).
Fumarate hydratase enzyme activity in lymphoblastoid cells and fibroblasts of individuals in families with hereditary leiomyomatosis and renal cell cancer.
  J Med Genet, 43, 755-762.  
16717409 T.Genda, S.Watabe, and H.Ozaki (2006).
Purification and characterization of fumarase from Corynebacterium glutamicum.
  Biosci Biotechnol Biochem, 70, 1102-1109.  
15803386 L.L.Goh, T.Barkham, and T.S.Sim (2005).
Molecular cloning and functional characterization of fumarases C in Neisseria species.
  Antonie Van Leeuwenhoek, 87, 205-213.  
16204892 T.Weaver (2005).
Structure of free fumarase C from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 61, 1395-1401.
PDB code: 1yfe
14990798 I.A.Rose, and T.M.Weaver (2004).
The role of the allosteric B site in the fumarase reaction.
  Proc Natl Acad Sci U S A, 101, 3393-3397.  
15118093 J.A.Bittker, B.V.Le, J.M.Liu, and D.R.Liu (2004).
Directed evolution of protein enzymes using nonhomologous random recombination.
  Proc Natl Acad Sci U S A, 101, 7011-7016.  
15502303 P.Bhaumik, M.K.Koski, U.Bergmann, and R.K.Wierenga (2004).
Structure determination and refinement at 2.44 A resolution of argininosuccinate lyase from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 60, 1964-1970.
PDB code: 1tj7
11698398 L.M.Sampaleanu, B.Yu, and P.L.Howell (2002).
Mutational analysis of duck delta 2 crystallin and the structure of an inactive mutant with bound substrate provide insight into the enzymatic mechanism of argininosuccinate lyase.
  J Biol Chem, 277, 4166-4175.
PDB code: 1k7w
11294638 A.R.Horswill, and J.C.Escalante-Semerena (2001).
In vitro conversion of propionate to pyruvate by Salmonella enterica enzymes: 2-methylcitrate dehydratase (PrpD) and aconitase Enzymes catalyze the conversion of 2-methylcitrate to 2-methylisocitrate.
  Biochemistry, 40, 4703-4713.  
11258884 L.M.Sampaleanu, F.Vallée, C.Slingsby, and P.L.Howell (2001).
Structural studies of duck delta 1 and delta 2 crystallin suggest conformational changes occur during catalysis.
  Biochemistry, 40, 2732-2742.
PDB codes: 1hy0 1hy1 1i0a
11076513 K.H.Lee, D.R.Benson, and K.Kuczera (2000).
Transitions from alpha to pi helix observed in molecular dynamics simulations of synthetic peptides.
  Biochemistry, 39, 13737-13747.  
  10739264 T.M.Weaver (2000).
The pi-helix translates structure into function.
  Protein Sci, 9, 201-206.  
10029537 A.R.Chakraborty, A.Davidson, and P.L.Howell (1999).
Mutational analysis of amino acid residues involved in argininosuccinate lyase activity in duck delta II crystallin.
  Biochemistry, 38, 2435-2443.  
10029536 F.Vallée, M.A.Turner, P.L.Lindley, and P.L.Howell (1999).
Crystal structure of an inactive duck delta II crystallin mutant with bound argininosuccinate.
  Biochemistry, 38, 2425-2434.
PDB code: 1dcn
  10091655 L.M.Sampaleanu, A.R.Davidson, C.Graham, G.J.Wistow, and P.L.Howell (1999).
Domain exchange experiments in duck delta-crystallins: functional and evolutionary implications.
  Protein Sci, 8, 529-537.  
10091606 S.M.Pitson, G.L.Mendz, S.Srinivasan, and S.L.Hazell (1999).
The tricarboxylic acid cycle of Helicobacter pylori.
  Eur J Biochem, 260, 258-267.  
9890879 T.T.Lee, C.Worby, Z.Q.Bao, J.E.Dixon, and R.F.Colman (1999).
His68 and His141 are critical contributors to the intersubunit catalytic site of adenylosuccinate lyase of Bacillus subtilis.
  Biochemistry, 38, 22-32.  
9922130 I.A.Rose (1998).
How fumarase recycles after the malate --> fumarate reaction. Insights into the reaction mechanism.
  Biochemistry, 37, 17651-17658.  
9822627 S.Beeckmans, and E.Van Driessche (1998).
Pig heart fumarase contains two distinct substrate-binding sites differing in affinity.
  J Biol Chem, 273, 31661-31669.  
10076800 T.Neufeld, M.Eisenstein, K.A.Muszkat, and G.Fleminger (1998).
A citrate-binding site in calmodulin.
  J Mol Recognit, 11, 20-24.  
9792664 Y.Nobe, S.Kawaguchi, H.Ura, T.Nakai, K.Hirotsu, R.Kato, and S.Kuramitsu (1998).
The novel substrate recognition mechanism utilized by aspartate aminotransferase of the extreme thermophile Thermus thermophilus HB8.
  J Biol Chem, 273, 29554-29564.  
9315875 I.A.Rose (1997).
Restructuring the active site of fumarase for the fumarate to malate reaction.
  Biochemistry, 36, 12346-12354.  
9369472 M.Abu-Abed, M.A.Turner, F.Vallée, A.Simpson, C.Slingsby, and P.L.Howell (1997).
Structural comparison of the enzymatically active and inactive forms of delta crystallin and the role of histidine 91.
  Biochemistry, 36, 14012-14022.
PDB code: 1auw
  9098893 T.Weaver, M.Lees, and L.Banaszak (1997).
Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site.
  Protein Sci, 6, 834-842.
PDB codes: 1fur 2fus
9230045 W.Shi, J.Dunbar, M.M.Jayasekera, R.E.Viola, and G.K.Farber (1997).
The structure of L-aspartate ammonia-lyase from Escherichia coli.
  Biochemistry, 36, 9136-9144.
PDB code: 1jsw
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.