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PDBsum entry 1fur

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protein ligands Protein-protein interface(s) links
Hydrolyase PDB id
1fur
Jmol
Contents
Protein chains
456 a.a. *
Ligands
MLT ×2
Waters ×1206
* Residue conservation analysis
PDB id:
1fur
Name: Hydrolyase
Title: Fumarase mutant h188n with bound substrate l-malate at putat activator site
Structure: FumarasE C. Chain: a, b. Synonym: fumc. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: jm105. Cell_line: 293. Cellular_location: cytoplasm. Gene: fumc. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: site-directed mutant of fumarasE C was gener
Biol. unit: Tetramer (from PDB file)
Resolution:
1.95Å     R-factor:   0.170     R-free:   0.209
Authors: T.M.Weaver,M.Lees,L.J.Banaszak
Key ref:
T.Weaver et al. (1997). Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site. Protein Sci, 6, 834-842. PubMed id: 9098893 DOI: 10.1002/pro.5560060410
Date:
09-Jan-97     Release date:   23-Jul-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05042  (FUMC_ECOLI) -  Fumarate hydratase class II
Seq:
Struc:
467 a.a.
456 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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: 10.1002/pro.5560060410 Protein Sci 6:834-842 (1997)
PubMed id: 9098893  
 
 
Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site.
T.Weaver, M.Lees, L.Banaszak.
 
  ABSTRACT  
 
Two mutant forms of fumarase C from E. coli have been made using PCR and recombinant DNA. The recombinant form of the protein included a histidine arm on the C-terminal facilitating purification. Based on earlier studies, two different carboxylic acid binding sites, labeled A- and B-, were observed in crystal structures of the wild type and inhibited forms of the enzyme. A histidine at each of the sites was mutated to an asparagine. H188N at the A-site resulted in a large decrease in specific activity, while the H129N mutation at the B-site had essentially no effect. From the results, we conclude that the A-site is indeed the active site, and a dual role for H188 as a potential catalytic base is proposed. Crystal structures of the two mutant proteins produced some unexpected results. Both mutations reduced the affinity for the carboxylic acids at their respective sites. The H129N mutant should be particularly useful in future kinetic studies because it sterically blocks the B-site with the carboxyamide of asparagine assuming the position of the ligand's carboxylate. In the H188N mutation at the active site, the new asparagine side chain still interacts with an active site water that appears to have moved slightly as a result of the mutation.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. B-site in native, H 129N. and H I88N fumarases. The stereodrawing summarizes the crystallographlc results atthe B-site in threeforms of fumarase. The ball and representationareshaded such thatcarbon are lightest. nitrogen atoms areshaded medium. and oxgen atoms are black. Unlike Figure 3 below, all of he atoms belong tothe suhunit. A: The toppanel contains representation of the crystal structureatthe B-site nthe H129N mutant. R: middle panelrepresentsthe B-site in thecrystal structure of the H 188Nmtant. C: The ottompanelillustratesthestructure in the wild-type enzyme.
Figure 3.
ig. 3. he A-site or active site in native, HIXXN. and H129N fumarases. The stereodrawing summarizes the crystallographic results t the A-site or site in three crystalline forms of fumarase. The balland stick representation are shaded s in Figure 2. Sidechains identified by the one-letteramino acid code followed by a sequence number and the letters a through d." The small letters following the sequence number are used to identify one of the four identical subunits in the fumarase tetramer. Dotted lines describe hydrogen bonds and the single black all near the center of panel is a solvent molecule described more fully in the accompanying text. : Theatoms near the A-site in the crystal structure f the HIXXN mutant are shown. R: Atoms near the A-site in the crystal structure of the 129N mutant are shown. C: The bottom panel illustrates the structure at active site in the wild-type enzyme.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1997, 6, 834-842) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19949549 E.Kirches (2009).
Mitochondrial and nuclear genes of mitochondrial components in cancer.
  Curr Genomics, 10, 281-293.  
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.  
18366737 J.P.Bayley, V.Launonen, and I.P.Tomlinson (2008).
The FH mutation database: an online database of fumarate hydratase mutations involved in the MCUL (HLRCC) tumor syndrome and congenital fumarase deficiency.
  BMC Med Genet, 9, 20.  
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.  
  16237213 N.A.Alam, S.Olpin, A.Rowan, D.Kelsell, I.M.Leigh, I.P.Tomlinson, and T.Weaver (2005).
Missense mutations in fumarate hydratase in multiple cutaneous and uterine leiomyomatosis and renal cell cancer.
  J Mol Diagn, 7, 437-443.  
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.  
11865300 I.P.Tomlinson, N.A.Alam, A.J.Rowan, E.Barclay, E.E.Jaeger, D.Kelsell, I.Leigh, P.Gorman, H.Lamlum, S.Rahman, R.R.Roylance, S.Olpin, S.Bevan, K.Barker, N.Hearle, R.S.Houlston, M.Kiuru, R.Lehtonen, A.Karhu, S.Vilkki, P.Laiho, C.Eklund, O.Vierimaa, K.Aittomäki, M.Hietala, P.Sistonen, A.Paetau, R.Salovaara, R.Herva, V.Launonen, and L.A.Aaltonen (2002).
Germline mutations in FH predispose to dominantly inherited uterine fibroids, skin leiomyomata and papillary renal cell cancer.
  Nat Genet, 30, 406-410.  
12021453 M.Estévez, J.Skarda, J.Spencer, L.Banaszak, and T.M.Weaver (2002).
X-ray crystallographic and kinetic correlation of a clinically observed human fumarase mutation.
  Protein Sci, 11, 1552-1557.
PDB code: 1kq7
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
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
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.  
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
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.