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PDBsum entry 1f8i

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1f8i
Jmol
Contents
Protein chains
427 a.a. *
Ligands
GLV ×4
SIN ×4
Metals
_MG ×4
Waters ×1052
* Residue conservation analysis
PDB id:
1f8i
Name: Lyase
Title: Crystal structure of isocitrate lyase:nitropropionate:glyoxylate complex from mycobacterium tuberculosis
Structure: Isocitrate lyase. Chain: a, b, c, d. Synonym: icl. Engineered: yes. Mutation: yes
Source: Mycobacterium tuberculosis h37rv. Organism_taxid: 83332. Strain: h37rv. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.25Å     R-factor:   0.166     R-free:   0.210
Authors: V.Sharma,S.Sharma,K.Hoener Zu Bentrup,J.D.Mckinney, D.G.Russell,W.R.Jacobs Jr.,J.C.Sacchettini,Tb Structural Genomics Consortium (Tbsgc)
Key ref:
V.Sharma et al. (2000). Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis. Nat Struct Biol, 7, 663-668. PubMed id: 10932251 DOI: 10.1038/77964
Date:
30-Jun-00     Release date:   30-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P9WKK6  (ACEA_MYCTO) -  Isocitrate lyase
Seq:
Struc:
428 a.a.
427 a.a.*
Protein chains
Pfam  
P9WKK7  (ACEA_MYCTU) -  Isocitrate lyase
Seq:
Struc:
428 a.a.
427 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.1.3.1  - Isocitrate lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Glyoxylate Cycle
      Reaction: Isocitrate = succinate + glyoxylate
Isocitrate
=
succinate
Bound ligand (Het Group name = SIN)
corresponds exactly
+
glyoxylate
Bound ligand (Het Group name = GLV)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     carboxylic acid metabolic process   3 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1038/77964 Nat Struct Biol 7:663-668 (2000)
PubMed id: 10932251  
 
 
Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis.
V.Sharma, S.Sharma, K.Hoener zu Bentrup, J.D.McKinney, D.G.Russell, W.R.Jacobs, J.C.Sacchettini.
 
  ABSTRACT  
 
Isocitrate lyase (ICL) plays a pivotal role in the persistence of Mycobacterium tuberculosis in mice by sustaining intracellular infection in inflammatory macrophages. The enzyme allows net carbon gain by diverting acetyl-CoA from beta-oxidation of fatty acids into the glyoxylate shunt pathway. Given its potential as a drug target against persistent infections, we solved its structure without ligand and in complex with two inhibitors. Covalent modification of an active site residue, Cys 191, by the inhibitor 3-bromopyruvate traps the enzyme in a catalytic conformation with the active site completely inaccessible to solvent. The structure of a C191S mutant of the enzyme with the inhibitor 3-nitropropionate provides further insight into the reaction mechanism.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Inhibition of ICL activity. a, The reaction catalyzed by ICL can be inhibited by b, 3-bromopyruvate and c, 3-nitropropionate. d -g, The inhibitory effects of 3-nitropropionate on both wild type and a pICL1 complemented mutant strain of M. smegmatis (ICL from M. smegmatis replaced with that from M. tuberculosis) are restricted to growth on acetate and are not observed on glucose. The drug discs shown in each panel are saturated with 30 mM and 60 mM nitropropionate. The M. smegmatis wild type was grown on glucose (d) or acetate (f) and the M. smegmatis icl mutant was defective for growth on fatty acids was rescued by complementation with pICL1^10 and grown on glucose (e) or acetate (g).
Figure 3.
Figure 3. Binding of 3-nitopropionate and glyoxylate. a, Stereo view of the active site of the ternary complex of the ICL C191S mutant with glyoxylate (GA) and 3-nitropropionate (shown as succinate, SA). Since we are unable to resolve the ambiguity of the nitro group, succinate is used to depict the 3-nitropropionate in the figures and the text. The carbon atoms are shown in yellow (protein), green (GA) or cyan (SA). b, Stereo view of the NCS averaged difference Fourier maps (|F[o]| - |F[c]| [c]) contoured at the 2 level showing glyoxylate (green), succinate (cyan), the Mg2+ ion (yellow) and three waters (red) in the active site of ICL. c, Schematic diagram of ICL interactions with glyoxylate and succinate.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 663-668) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20192686 D.M.Estes, S.W.Dow, H.P.Schweizer, and A.G.Torres (2010).
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Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium.
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Rapid model building of alpha-helices in electron-density maps.
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Rapid model building of beta-sheets in electron-density maps.
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Rapid chain tracing of polypeptide backbones in electron-density maps.
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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
18433062 C.J.Liao, K.H.Chin, C.H.Lin, P.S.Tsai, P.C.Lyu, C.C.Young, A.H.Wang, and S.H.Chou (2008).
Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus.
  Proteins, 73, 362-371.
PDB code: 2ze3
20477209 H.Tomioka, Y.Tatano, K.Yasumoto, and T.Shimizu (2008).
Recent advances in antituberculous drug development and novel drug targets.
  Expert Rev Respir Med, 2, 455-471.  
18079742 J.C.Sacchettini, E.J.Rubin, and J.S.Freundlich (2008).
Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis.
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18946503 J.Gonzalo-Asensio, S.Mostowy, J.Harders-Westerveen, K.Huygen, R.Hernández-Pando, J.Thole, M.Behr, B.Gicquel, and C.Martín (2008).
PhoP: a missing piece in the intricate puzzle of Mycobacterium tuberculosis virulence.
  PLoS ONE, 3, e3496.  
18039768 J.H.Lee, D.E.Geiman, and W.R.Bishai (2008).
Role of stress response sigma factor SigG in Mycobacterium tuberculosis.
  J Bacteriol, 190, 1128-1133.  
18275086 R.Kumar, and V.Bhakuni (2008).
Mycobacterium tuberculosis isocitrate lyase (MtbIcl): role of divalent cations in modulation of functional and structural properties.
  Proteins, 72, 892-900.  
17041184 A.Idnurm, S.S.Giles, J.R.Perfect, and J.Heitman (2007).
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17521419 D.J.Beste, T.Hooper, G.Stewart, B.Bonde, C.Avignone-Rossa, M.E.Bushell, P.Wheeler, S.Klamt, A.M.Kierzek, and J.McFadden (2007).
GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism.
  Genome Biol, 8, R89.  
17655757 D.J.Murphy, and J.R.Brown (2007).
Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.
  BMC Infect Dis, 7, 84.  
17244616 Y.Han, H.J.Joosten, W.Niu, Z.Zhao, P.S.Mariano, M.McCalman, J.van Kan, P.J.Schaap, and D.Dunaway-Mariano (2007).
Oxaloacetate hydrolase, the C-C bond lyase of oxalate secreting fungi.
  J Biol Chem, 282, 9581-9590.  
16689789 E.J.Muñoz-Elías, A.M.Upton, J.Cherian, and J.D.McKinney (2006).
Role of the methylcitrate cycle in Mycobacterium tuberculosis metabolism, intracellular growth, and virulence.
  Mol Microbiol, 60, 1109-1122.  
16929102 R.Pai, J.Sacchettini, and T.Ioerger (2006).
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16879647 T.A.Gould, H.van de Langemheen, E.J.Muñoz-Elías, J.D.McKinney, and J.C.Sacchettini (2006).
Dual role of isocitrate lyase 1 in the glyoxylate and methylcitrate cycles in Mycobacterium tuberculosis.
  Mol Microbiol, 61, 940-947.  
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16478688 V.L.Arcus, J.S.Lott, J.M.Johnston, and E.N.Baker (2006).
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  Drug Discov Today, 11, 28-34.  
15895072 E.J.Muñoz-Elías, and J.D.McKinney (2005).
Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence.
  Nat Med, 11, 638-644.  
16239729 E.W.McKee, L.D.Kanbi, K.L.Childs, R.W.Grosse-Kunstleve, P.D.Adams, J.C.Sacchettini, and T.R.Ioerger (2005).
FINDMOL: automated identification of macromolecules in electron-density maps.
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16201909 J.Li, D.Zhu, Z.Yi, Y.He, Y.Chun, Y.Liu, and N.Li (2005).
DNAzymes targeting the icl gene inhibit ICL expression and decrease Mycobacterium tuberculosis survival in macrophages.
  Oligonucleotides, 15, 215-222.  
16151139 M.Brock (2005).
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15822188 Y.Zhang (2005).
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12842039 B.N.Chaudhuri, M.R.Sawaya, C.Y.Kim, G.S.Waldo, M.S.Park, T.C.Terwilliger, and T.O.Yeates (2003).
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  Structure, 11, 753-764.
PDB code: 1oy0
12393860 C.V.Smith, C.C.Huang, A.Miczak, D.G.Russell, J.C.Sacchettini, and K.Höner zu Bentrup (2003).
Biochemical and structural studies of malate synthase from Mycobacterium tuberculosis.
  J Biol Chem, 278, 1735-1743.
PDB codes: 1n8i 1n8w
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.  
12915092 M.Bellinzoni, and G.Riccardi (2003).
Techniques and applications: The heterologous expression of Mycobacterium tuberculosis genes is an uphill road.
  Trends Microbiol, 11, 351-358.  
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.  
12455691 A.Idnurm, and B.J.Howlett (2002).
Isocitrate lyase is essential for pathogenicity of the fungus Leptosphaeria maculans to canola (Brassica napus).
  Eukaryot Cell, 1, 719-724.  
12455685 M.C.Lorenz, and G.R.Fink (2002).
Life and death in a macrophage: role of the glyoxylate cycle in virulence.
  Eukaryot Cell, 1, 657-662.  
12377567 P.Druilhe, P.Hagan, and G.A.Rook (2002).
The importance of models of infection in the study of disease resistance.
  Trends Microbiol, 10, S38-S46.  
12228298 T.H.Rude, D.L.Toffaletti, G.M.Cox, and J.R.Perfect (2002).
Relationship of the glyoxylate pathway to the pathogenesis of Cryptococcus neoformans.
  Infect Immun, 70, 5684-5694.  
11795407 D.Young (2001).
Letting the genome out of the bottle: prospects for new drug development.
  Ann N Y Acad Sci, 953, 146-150.  
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.