PDBsum entry 2nsf

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Isomerase PDB id
Protein chain
240 a.a. *
SO4 ×3
Waters ×229
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of the mycothiol-dependent maleylpyruvate
Structure: Hypothetical protein cgl3021. Chain: a. Synonym: maleylpyruvate isomerase. Engineered: yes
Source: Corynebacterium glutamicum. Organism_taxid: 1718. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.75Å     R-factor:   0.230     R-free:   0.234
Authors: W.R.Chang,R.Wang
Key ref:
R.Wang et al. (2007). Crystal Structures and Site-directed Mutagenesis of a Mycothiol-dependent Enzyme Reveal a Novel Folding and Molecular Basis for Mycothiol-mediated Maleylpyruvate Isomerization. J Biol Chem, 282, 16288-15294. PubMed id: 17428791 DOI: 10.1074/jbc.M610347200
04-Nov-06     Release date:   10-Apr-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q8NLC1  (Q8NLC1_CORGL) -  Putative uncharacterized protein Cgl3021
241 a.a.
240 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     sterol binding     2 terms  


DOI no: 10.1074/jbc.M610347200 J Biol Chem 282:16288-15294 (2007)
PubMed id: 17428791  
Crystal Structures and Site-directed Mutagenesis of a Mycothiol-dependent Enzyme Reveal a Novel Folding and Molecular Basis for Mycothiol-mediated Maleylpyruvate Isomerization.
R.Wang, Y.J.Yin, F.Wang, M.Li, J.Feng, H.M.Zhang, J.P.Zhang, S.J.Liu, W.R.Chang.
Mycothiol (MSH) is the major low molecular mass thiols in many Gram-positive bacteria such as Mycobacterium tuberculosis and Corynebacterium glutamicum. The physiological roles of MSH are believed to be equivalent to those of GSH in Gram-negative bacteria, but current knowledge of MSH is limited to detoxification of alkalating chemicals and protection from host cell defense/killing systems. Recently, an MSH-dependent maleylpyruvate isomerase (MDMPI) was discovered from C. glutamicum, and this isomerase represents one example of many putative MSH-dependent enzymes that take MSH as cofactor. In this report, fourteen mutants of MDMPI were generated. The wild type and mutant (H52A) MDMPIs were crystallized and their structures were solved at 1.75 and 2.05A resolution, respectively. The crystal structures reveal that this enzyme contains a divalent metal-binding domain and a C-terminal domain possessing a novel folding pattern (alphabetaalphabetabetaalpha fold). The divalent metal-binding site is composed of residues His(52), Glu(144), and His(148) and is located at the bottom of a surface pocket. Combining the structural and site-directed mutagenesis studies, it is proposed that this surface pocket including the metal ion and MSH moiety formed the putative catalytic center.
  Selected figure(s)  
Figure 4.
FIGURE 4. The side chain of Arg^222 (NH1) at the C-terminal domain interacts with Asp^151 (OD2) of the N-terminal domain through a salt bridge. The N-terminal domain is shown in yellow, C-terminal domain in cyan, and interdomain coil in gray. Asp^151 and Arg^222 are represented in stick model (carbon atoms are colored the same as the domain they locate at) and the metal ion by a sphere (gray). Salt bridge is shown by dashed line. The figure was created by PyMol.
Figure 6.
FIGURE 6. The stereo view of the conformation differences in the putative active pocket between the wild type and the mutant (H52A) MDMPI. Mutant H52A is shown in purple and native MDMPI in green. Conformation differences were found at the side chains of Arg^82 and Trp^44. In H52A the metal ion was missing and a glycerol occupied the position of the metal ion, and the location of SO^2–[4] also changed. Furthermore, there is no obvious conformation changes observed, when compared with that of the wild type. The image was created by PyMol.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 16288-15294) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21181154 T.T.Liu, Y.Xu, H.Liu, S.Luo, Y.J.Yin, S.J.Liu, and N.Y.Zhou (2011).
Functional characterization of a gene cluster involved in gentisate catabolism in Rhodococcus sp. strain NCIMB 12038.
  Appl Microbiol Biotechnol, 90, 671-678.  
  20208147 D.R.Cooper, K.Grelewska, C.Y.Kim, A.Joachimiak, and Z.S.Derewenda (2010).
The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 219-224.
PDB code: 3gor
20922372 Y.J.Yin, B.J.Wang, C.Y.Jiang, Y.M.Luo, J.H.Jin, and S.J.Liu (2010).
Identification and quantification of mycothiol in Actinobacteria by a novel enzymatic method.
  Appl Microbiol Biotechnol, 88, 1393-1401.  
19286650 E.Ordóñez, K.Van Belle, G.Roos, S.De Galan, M.Letek, J.A.Gil, L.Wyns, L.M.Mateos, and J.Messens (2009).
Arsenate reductase, mycothiol, and mycoredoxin concert thiol/disulfide exchange.
  J Biol Chem, 284, 15107-15116.  
18772286 G.L.Newton, N.Buchmeier, and R.C.Fahey (2008).
Biosynthesis and functions of mycothiol, the unique protective thiol of Actinobacteria.
  Microbiol Mol Biol Rev, 72, 471-494.  
18004771 K.Nagata, J.Ohtsuka, M.Takahashi, A.Asano, H.Iino, A.Ebihara, and M.Tanokura (2008).
Crystal structure of TTHA0303 (TT2238), a four-helix bundle protein with an exposed histidine triad from Thermus thermophilus HB8 at 2.0 A.
  Proteins, 70, 1103-1107.
PDB code: 2yqy
19030604 V.K.Jothivasan, and C.J.Hamilton (2008).
Mycothiol: synthesis, biosynthesis and biological functions of the major low molecular weight thiol in actinomycetes.
  Nat Prod Rep, 25, 1091-1117.  
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.