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PDBsum entry 1igw

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1igw
Jmol
Contents
Protein chains
396 a.a. *
416 a.a. *
Ligands
PYR ×4
Metals
_HG ×21
_MG ×4
Waters ×767
* Residue conservation analysis
PDB id:
1igw
Name: Lyase
Title: Crystal structure of the isocitrate lyase from the a219c mutant of escherichia coli
Structure: Isocitrate lyase. Chain: a, b, c, d. Synonym: isocitrase, isocitratase, icl. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: acea. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.10Å     R-factor:   0.187     R-free:   0.235
Authors: K.L.Britton,I.S.B.Abeysinghe,P.J.Baker,V.Barynin,P.Diehl, S.J.Langridge,B.A.Mcfadden,S.E.Sedelnikova,T.J.Stillman, K.Weeradechapon,D.W.Rice
Key ref:
K.L.Britton et al. (2001). The structure and domain organization of Escherichia coli isocitrate lyase. Acta Crystallogr D Biol Crystallogr, 57, 1209-1218. PubMed id: 11526312 DOI: 10.1107/S0907444901008642
Date:
18-Apr-01     Release date:   05-Sep-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A9G6  (ACEA_ECOLI) -  Isocitrate lyase
Seq:
Struc:
434 a.a.
396 a.a.*
Protein chains
Pfam   ArchSchema ?
P0A9G6  (ACEA_ECOLI) -  Isocitrate lyase
Seq:
Struc:
434 a.a.
416 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.4.1.3.1  - Isocitrate lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Glyoxylate Cycle
      Reaction: Isocitrate = succinate + glyoxylate
Isocitrate
= succinate
+
glyoxylate
Bound ligand (Het Group name = PYR)
matches with 83.00% similarity
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     4 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444901008642 Acta Crystallogr D Biol Crystallogr 57:1209-1218 (2001)
PubMed id: 11526312  
 
 
The structure and domain organization of Escherichia coli isocitrate lyase.
K.L.Britton, I.S.Abeysinghe, P.J.Baker, V.Barynin, P.Diehl, S.J.Langridge, B.A.McFadden, S.E.Sedelnikova, T.J.Stillman, K.Weeradechapon, D.W.Rice.
 
  ABSTRACT  
 
Enzymes of the glyoxylate-bypass pathway are potential targets for the control of many human diseases caused by such pathogens as Mycobacteria and Leishmania. Isocitrate lyase catalyses the first committed step in this pathway and the structure of this tetrameric enzyme from Escherichia coli has been determined at 2.1 A resolution. E. coli isocitrate lyase, like the enzyme from other prokaryotes, is located in the cytoplasm, whereas in plants, protozoa, algae and fungi this enzyme is found localized in glyoxysomes. Comparison of the structure of the prokaryotic isocitrate lyase with that from the eukaryote Aspergillus nidulans reveals a different domain structure following the deletion of approximately 100 residues from the larger eukaryotic enzyme. Despite this, the active sites of the prokaryotic and eukaryotic enzymes are very closely related, including the apparent disorder of two equivalent segments of the protein that are known to be involved in a conformational change as part of the enzyme's catalytic cycle.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 (a) A C^ chain trace of the C subunit of E. coli ICL with every 20th residue indicated by a black dot. This figure was produced using the program MIDASPLUS (Ferrin et al., 1988[Ferrin, T. E., Huang, C. C., Jarvis, L. E. & Langridge, R. (1988). J. Mol. Graph. 6, 13-27.]). (b) A single subunit of E. coli ICL with the strands and helices labelled. The strands of the TIM barrel are shown in cyan and the helices in red, except for three regions where small deviations occur between the different subunits (orange). Viewed from the top in an anticlockwise rotation, these regions involve residues 192-200, 290-311 and 318-344. The C-terminal residues which are not observed in any subunit are not shown. Figure prepared using MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.])
Figure 4.
Figure 4 A space-filling representation for the ICL tetramers of (a) E. coli and (b) A. nidulans, with each subunit individually shaded highlighting the loss of the head domain in the simpler prokaryotic enzyme. This diagram was produced using the program MIDASPLUS (Ferrin et al., 1988[Ferrin, T. E., Huang, C. C., Jarvis, L. E. & Langridge, R. (1988). J. Mol. Graph. 6, 13-27.]; Huang et al., 1991[Huang, C. C., Pettersen, E. F., Klein, T. E., Ferrin, T. E. & Langridge, R. (1991). J. Mol. Graph. 9, 230-236.]).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 1209-1218) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19847013 M.Bedhomme, M.Zaffagnini, C.H.Marchand, X.H.Gao, M.Moslonka-Lefebvre, L.Michelet, P.Decottignies, and S.D.Lemaire (2009).
Regulation by glutathionylation of isocitrate lyase from Chlamydomonas reinhardtii.
  J Biol Chem, 284, 36282-36291.  
19684068 M.F.Dunn, J.A.Ramírez-Trujillo, and I.Hernández-Lucas (2009).
Major roles of isocitrate lyase and malate synthase in bacterial and fungal pathogenesis.
  Microbiology, 155, 3166-3175.  
18081320 B.C.Narayanan, W.Niu, Y.Han, J.Zou, P.S.Mariano, D.Dunaway-Mariano, and O.Herzberg (2008).
Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily.
  Biochemistry, 47, 167-182.
PDB code: 3b8i
12837791 F.Schmitzberger, A.G.Smith, C.Abell, and T.L.Blundell (2003).
Comparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (betaalpha)8 phosphoenolpyruvate/pyruvate superfamily.
  J Bacteriol, 185, 4163-4171.  
12906829 F.von Delft, T.Inoue, S.A.Saldanha, H.H.Ottenhof, F.Schmitzberger, L.M.Birch, V.Dhanaraj, M.Witty, A.G.Smith, T.L.Blundell, and C.Abell (2003).
Structure of E. coli ketopantoate hydroxymethyl transferase complexed with ketopantoate and Mg2+, solved by locating 160 selenomethionine sites.
  Structure, 11, 985-996.
PDB code: 1m3u
12897003 T.L.Grimek, H.Holden, I.Rayment, and J.C.Escalante-Semerena (2003).
Residues C123 and D58 of the 2-methylisocitrate lyase (PrpB) enzyme of Salmonella enterica are essential for catalysis.
  J Bacteriol, 185, 4837-4843.  
11728873 K.Höner zu Bentrup, and D.G.Russell (2001).
Mycobacterial persistence: adaptation to a changing environment.
  Trends Microbiol, 9, 597-605.  
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.