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PDBsum entry 1b0m

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Hydrolase PDB id
1b0m
Jmol
Contents
Protein chain
753 a.a. *
Ligands
FLC
SF4
Waters ×341
* Residue conservation analysis
PDB id:
1b0m
Name: Hydrolase
Title: Aconitase r644q:fluorocitrate complex
Structure: Protein (aconitase). Chain: a. Engineered: yes. Mutation: yes. Other_details: [4fe-4s] bound by cys 358, cys 421, cys 424
Source: Sus scrofa. Pig. Organism_taxid: 9823. Strain: bl21 de3. Organ: heart. Organelle: mitochondria. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.50Å     R-factor:   0.193    
Authors: S.J.Lloyd,H.Lauble,G.S.Prasad,C.D.Stout
Key ref:
S.J.Lloyd et al. (1999). The mechanism of aconitase: 1.8 A resolution crystal structure of the S642a:citrate complex. Protein Sci, 8, 2655-2662. PubMed id: 10631981 DOI: 10.1110/ps.8.12.2655
Date:
11-Nov-98     Release date:   18-Nov-98    
Supersedes: 1atq
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P16276  (ACON_PIG) -  Aconitate hydratase, mitochondrial
Seq:
Struc:
 
Seq:
Struc:
781 a.a.
753 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.3  - Aconitate hydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Aconitate Hydratase
      Reaction: Citrate = isocitrate
Citrate
Bound ligand (Het Group name = FLC)
corresponds exactly
= isocitrate
      Cofactor: Iron-sulfur
Iron-sulfur
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     lyase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1110/ps.8.12.2655 Protein Sci 8:2655-2662 (1999)
PubMed id: 10631981  
 
 
The mechanism of aconitase: 1.8 A resolution crystal structure of the S642a:citrate complex.
S.J.Lloyd, H.Lauble, G.S.Prasad, C.D.Stout.
 
  ABSTRACT  
 
The crystal structure of the S642A mutant of mitochondrial aconitase (mAc) with citrate bound has been determined at 1.8 A resolution and 100 K to capture this binding mode of substrates to the native enzyme. The 2.0 A resolution, 100 K crystal structure of the S642A mutant with isocitrate binding provides a control, showing that the Ser --> Ala replacement does not alter the binding of substrates in the active site. The aconitase mechanism requires that the intermediate product, cis-aconitate, flip over by 180 degrees about the C alpha-C beta double bond. Only one of these two alternative modes of binding, that of the isocitrate mode, has been previously visualized. Now, however, the structure revealing the citrate mode of binding provides direct support for the proposed enzyme mechanism.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Model for the mechanism of the reaction catalyzed by aconitase. Only one of the four states depicted corresponds to a previously determined crystal structure, that of the isocitrate complex. In this paper direct structural evidence for the existence of the citrate complex is presented, and the isocitrate complex is independently confirmed. The intermediate product, cis-aconitate, is proposed to bind in two ways related by 1808 rotation about Ca--Cb double bond. The asterisk denotes the proton that is stereospe- cifically abstracted from citrate and replaced in isocitrate. Hydrogen atoms on the H 2O molecule bound to the unique Fe ~Fe4! of the @4Fe-4S# cluster are also depicted. Atoms are shaded: white, Fe; light gray, S; dark gray, O; black, C and H. This figure is reprinted from Lauble et al. ~1994!.
Figure 3.
Fig. 3. The conformation of citrate bound to the S642A mutant of aconi- tase. The citrate hydroxyl and one Cb-carboxyl oxygen are coordinated to Fe4 of the @4Fe-4S# cluster ~Fe-O distances 2.59 and 2.37 , respectively; black dotted lines!. There are 13 hydrogen bonds between citrate and the enzyme ~gray dotted lines, 2.6--3.0 !. Hydrogen bonds between the side chains of Gln72 and the Cg-carboxyl group, Ser166 and the Ca-carboxyl group, and His101 and the hydroxyl group, are not shown for clarity.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (1999, 8, 2655-2662) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  16511074 J.Dupuy, C.Darnault, X.Brazzolotto, L.C.Kühn, J.M.Moulis, A.Volbeda, and J.C.Fontecilla-Camps (2005).
Crystallization and preliminary X-ray diffraction data for the aconitase form of human iron-regulatory protein 1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 482-485.  
14568143 K.S.Makarova, and E.V.Koonin (2003).
Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis.
  FEMS Microbiol Lett, 227, 17-23.  
11329290 H.Cai, J.Strouse, D.Dumlao, M.E.Jung, and S.Clarke (2001).
Distinct reactions catalyzed by bacterial and yeast trans-aconitate methyltransferases.
  Biochemistry, 40, 2210-2219.  
11248696 H.Uhrigshardt, M.Walden, H.John, and S.Anemüller (2001).
Purification and characterization of the first archaeal aconitase from the thermoacidophilic Sulfolobus acidocaldarius.
  Eur J Biochem, 268, 1760-1771.  
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.