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PDBsum entry 1n8i

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protein ligands metals links
Lyase PDB id
1n8i
Jmol
Contents
Protein chain
701 a.a. *
Ligands
GLV
Metals
_MG
Waters ×450
* Residue conservation analysis
PDB id:
1n8i
Name: Lyase
Title: Biochemical and structural studies of malate synthase from mycobacterium tuberculosis
Structure: Probable malate synthase g. Chain: a. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: glcb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.10Å     R-factor:   0.185     R-free:   0.231
Authors: C.V.Smith,C.C.Huang,A.Miczak,D.G.Russell,J.C.Sacchettini, K.Honer Zu Bentrup,Tb Structural Genomics Consortium (Tbsgc
Key ref:
C.V.Smith et al. (2003). Biochemical and structural studies of malate synthase from Mycobacterium tuberculosis. J Biol Chem, 278, 1735-1743. PubMed id: 12393860 DOI: 10.1074/jbc.M209248200
Date:
20-Nov-02     Release date:   18-Dec-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam  
P9WK16  (MASZ_MYCTO) -  Malate synthase G
Seq:
Struc:
 
Seq:
Struc:
741 a.a.
701 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.3.9  - Malate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Glyoxylate Cycle
      Reaction: Acetyl-CoA + H2O + glyoxylate = (S)-malate + CoA
Acetyl-CoA
+ H(2)O
+
glyoxylate
Bound ligand (Het Group name = GLV)
corresponds exactly
= (S)-malate
+ CoA
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     glyoxylate cycle   2 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M209248200 J Biol Chem 278:1735-1743 (2003)
PubMed id: 12393860  
 
 
Biochemical and structural studies of malate synthase from Mycobacterium tuberculosis.
C.V.Smith, C.C.Huang, A.Miczak, D.G.Russell, J.C.Sacchettini, K.Höner zu Bentrup.
 
  ABSTRACT  
 
Establishment or maintenance of a persistent infection by Mycobacterium tuberculosis requires the glyoxylate pathway. This is a bypass of the tricarboxylic acid cycle in which isocitrate lyase and malate synthase (GlcB) catalyze the net incorporation of carbon during growth of microorganisms on acetate or fatty acids as the primary carbon source. The glcB gene from M. tuberculosis, which encodes malate synthase, was cloned, and GlcB was expressed in Escherichia coli. The influence of media conditions on expression in M. tuberculosis indicated that this enzyme is regulated differentially to isocitrate lyase. Purified GlcB had K(m) values of 57 and 30 microm for its substrates glyoxylate and acetyl coenzyme A, respectively, and was inhibited by bromopyruvate, oxalate, and phosphoenolpyruvate. The GlcB structure was solved to 2.1-A resolution in the presence of glyoxylate and magnesium. We also report the structure of GlcB in complex with the products of the reaction, coenzyme A and malate, solved to 2.7-A resolution. Coenzyme A binds in a bent conformation, and the details of its interactions are described, together with implications on the enzyme mechanism.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. a, simulated-annealing omitted F[o] F[c] map of coenzyme A. The map was contoured at 3 sigma. b, the interactions between coenzyme A and GlcB. The coenzyme A is shown in white, and the carbons of the interacting amino acids are in gold. The malate and magnesium ion in the active site are also shown. c, binding of coenzyme A to the active site of GlcB. Surfaces were made around the protein atoms and colored according to the electrostatic potential, red for acidic, and blue for basic residues, and were made using the program SPOCK (66). Mg2+ in the active site is shown as a blue sphere.
Figure 3.
Fig. 3. a, active site of the GlcB-glyoxylate binary complex. Mg2+ is held in an octahedral coordination by the carboxylate side chains of Glu-434 and Asp-462, one carboxylate oxygen, one aldehyde oxygen of glyoxylate- and two water molecules. b, active site of GlcB-malate-CoA ternary complex. A water molecule that is seen coordinating Mg2+ in GlcB-glyoxylate is replaced by the hydroxyl of malate.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 1735-1743) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20306314 R.Kumar, and V.Bhakuni (2010).
A functionally active dimer of Mycobacterium tuberculosis Malate synthase G.
  Eur Biophys J, 39, 1557-1562.  
20047909 T.J.Erb, L.Frerichs-Revermann, G.Fuchs, and B.E.Alber (2010).
The apparent malate synthase activity of Rhodobacter sphaeroides is due to two paralogous enzymes, (3S)-Malyl-coenzyme A (CoA)/{beta}-methylmalyl-CoA lyase and (3S)- Malyl-CoA thioesterase.
  J Bacteriol, 192, 1249-1258.  
19549344 B.Roucourt, N.Minnebo, P.Augustijns, K.Hertveldt, G.Volckaert, and R.Lavigne (2009).
Biochemical characterization of malate synthase G of P. aeruginosa.
  BMC Biochem, 10, 20.  
19767422 J.C.Micklinghoff, K.J.Breitinger, M.Schmidt, R.Geffers, B.J.Eikmanns, and F.C.Bange (2009).
Role of the transcriptional regulator RamB (Rv0465c) in the control of the glyoxylate cycle in Mycobacterium tuberculosis.
  J Bacteriol, 191, 7260-7269.  
19052159 K.R.Steingart, N.Dendukuri, M.Henry, I.Schiller, P.Nahid, P.C.Hopewell, A.Ramsay, M.Pai, and S.Laal (2009).
Performance of purified antigens for serodiagnosis of pulmonary tuberculosis: a meta-analysis.
  Clin Vaccine Immunol, 16, 260-276.  
  19888806 P.F.Zambuzzi-Carvalho, A.H.Cruz, L.K.Santos-Silva, A.M.Goes, C.M.Soares, and M.Pereira (2009).
The malate synthase of Paracoccidioides brasiliensis Pb01 is required in the glyoxylate cycle and in the allantoin degradation pathway.
  Med Mycol, 47, 734-744.  
19481971 T.R.Ioerger, and J.C.Sacchettini (2009).
Structural genomics approach to drug discovery for Mycobacterium tuberculosis.
  Curr Opin Microbiol, 12, 318-325.  
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.  
18714089 J.R.Lohman, A.C.Olson, and S.J.Remington (2008).
Atomic resolution structures of Escherichia coli and Bacillus anthracis malate synthase A: comparison with isoform G and implications for structure-based drug discovery.
  Protein Sci, 17, 1935-1945.
PDB codes: 3cux 3cuz 3cv1 3cv2
17041184 A.Idnurm, S.S.Giles, J.R.Perfect, and J.Heitman (2007).
Peroxisome function regulates growth on glucose in the basidiomycete fungus Cryptococcus neoformans.
  Eukaryot Cell, 6, 60-72.  
17577419 K.Singh, and V.Bhakuni (2007).
Cation induced differential effect on structural and functional properties of Mycobacterium tuberculosis alpha-isopropylmalate synthase.
  BMC Struct Biol, 7, 39.  
18166139 M.F.Rabahi, A.P.Junqueira-Kipnis, M.C.Dos Reis, W.Oelemann, and M.B.Conde (2007).
Humoral response to HspX and GlcB to previous and recent infection by Mycobacterium tuberculosis.
  BMC Infect Dis, 7, 148.  
16677310 A.G.Kinhikar, D.Vargas, H.Li, S.B.Mahaffey, L.Hinds, J.T.Belisle, and S.Laal (2006).
Mycobacterium tuberculosis malate synthase is a laminin-binding adhesin.
  Mol Microbiol, 60, 999.  
16877713 D.M.Anstrom, and S.J.Remington (2006).
The product complex of M. tuberculosis malate synthase revisited.
  Protein Sci, 15, 2002-2007.
PDB code: 2gq3
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.  
16846242 L.P.de Carvalho, and J.S.Blanchard (2006).
Kinetic and chemical mechanism of alpha-isopropylmalate synthase from Mycobacterium tuberculosis.
  Biochemistry, 45, 8988-8999.  
17005277 T.L.Sorensen, K.E.McAuley, R.Flaig, and E.M.Duke (2006).
New light for science: synchrotron radiation in structural medicine.
  Trends Biotechnol, 24, 500-508.  
16478688 V.L.Arcus, J.S.Lott, J.M.Johnston, and E.N.Baker (2006).
The potential impact of structural genomics on tuberculosis drug discovery.
  Drug Discov Today, 11, 28-34.  
15687206 M.Meister, S.Saum, B.E.Alber, and G.Fuchs (2005).
L-malyl-coenzyme A/beta-methylmalyl-coenzyme A lyase is involved in acetate assimilation of the isocitrate lyase-negative bacterium Rhodobacter capsulatus.
  J Bacteriol, 187, 1415-1425.  
15389729 R.P.Tripathi, N.Tewari, N.Dwivedi, and V.K.Tiwari (2005).
Fighting tuberculosis: an old disease with new challenges.
  Med Res Rev, 25, 93.  
16075427 V.Tugarinov, and L.E.Kay (2005).
Methyl groups as probes of structure and dynamics in NMR studies of high-molecular-weight proteins.
  Chembiochem, 6, 1567-1577.  
15159544 N.Koon, C.J.Squire, and E.N.Baker (2004).
Crystal structure of LeuA from Mycobacterium tuberculosis, a key enzyme in leucine biosynthesis.
  Proc Natl Acad Sci U S A, 101, 8295-8300.
PDB codes: 1sr9 3fig
14623960 J.Timm, F.A.Post, L.G.Bekker, G.B.Walther, H.C.Wainwright, R.Manganelli, W.T.Chan, L.Tsenova, B.Gold, I.Smith, G.Kaplan, and J.D.McKinney (2003).
Differential expression of iron-, carbon-, and oxygen-responsive mycobacterial genes in the lungs of chronically infected mice and tuberculosis patients.
  Proc Natl Acad Sci U S A, 100, 14321-14326.  
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.  
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 codes are shown on the right.