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PDBsum entry 1nu5

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protein metals links
Isomerase PDB id
1nu5
Jmol
Contents
Protein chain
369 a.a. *
Metals
_MN ×2
Waters ×287
* Residue conservation analysis
PDB id:
1nu5
Name: Isomerase
Title: Crystal structure of pseudomonas sp. P51 chloromuconate lact enzyme
Structure: Chloromuconate cycloisomerase. Chain: a. Synonym: cl-mle, muconate cycloisomerase ii, chloromuconate lactonizing enzyme. Engineered: yes
Source: Pseudomonas sp.. Organism_taxid: 65067. Strain: p51. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PDB file)
Resolution:
1.95Å     R-factor:   0.200     R-free:   0.231
Authors: T.Kajander,L.Lehtio,A.Goldman
Key ref:
T.Kajander et al. (2003). The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: co-evolution of structure and dynamics with the dehalogenation function. Protein Sci, 12, 1855-1864. PubMed id: 12930985 DOI: 10.1110/ps.0388503
Date:
31-Jan-03     Release date:   30-Dec-03    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P27099  (TCBD_PSESQ) -  Chloromuconate cycloisomerase
Seq:
Struc:
370 a.a.
369 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.5.1.7  - Chloromuconate cycloisomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Muconate Cycloisomerase
      Reaction: 2-chloro-2,5-dihydro-5-oxofuran-2-acetate = 3-chloro-cis,cis-muconate
2-chloro-2,5-dihydro-5-oxofuran-2-acetate
= 3-chloro-cis,cis-muconate
      Cofactor: Manganese
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    Added reference    
 
 
DOI no: 10.1110/ps.0388503 Protein Sci 12:1855-1864 (2003)
PubMed id: 12930985  
 
 
The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: co-evolution of structure and dynamics with the dehalogenation function.
T.Kajander, L.Lehtiö, M.Schlömann, A.Goldman.
 
  ABSTRACT  
 
Bacterial muconate lactonizing enzymes (MLEs) catalyze the conversion of cis,cis-muconate as a part of the beta-ketoadipate pathway, and some MLEs are also able to dehalogenate chlorinated muconates (Cl-MLEs). The basis for the Cl-MLEs dehalogenating activity is still unclear. To further elucidate the differences between MLEs and Cl-MLEs, we have solved the structure of Pseudomonas P51 Cl-MLE at 1.95 A resolution. Comparison of Pseudomonas MLE and Cl-MLE structures reveals the presence of a large cavity in the Cl-MLEs. The cavity may be related to conformational changes on substrate binding in Cl-MLEs, at Gly52. Site-directed mutagenesis on Pseudomonas MLE core positions to the equivalent Cl-MLE residues showed that the variant Thr52Gly was rather inactive, whereas the Thr52Gly-Phe103Ser variant had regained part of the activity. These residues form a hydrogen bond in the Cl-MLEs. The Cl-MLE structure, as a result of the Thr-to-Gly change, is more flexible than MLE: As a mobile loop closes over the active site, a conformational change at Gly52 is observed in Cl-MLEs. The loose packing and structural motions in Cl-MLE may be required for the rotation of the lactone ring in the active site necessary for the dehalogenating activity of Cl-MLEs. Furthermore, we also suggest that differences in the active site mobile loop sequence between MLEs and Cl-MLEs result in lower active site polarity in Cl-MLEs, possibly affecting catalysis. These changes could result in slower product release from Cl-MLEs and make it a better enzyme for dehalogenation of substrate.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. The hydrophobic core packing in MLEs and Cl-MLEs near the active site. MLE (A), P51 Cl-MLE (B; open conformation), and ReCl-MLE (C; closed conformation). h indicates helix 306-319, the arrow indicates the active site capping 53-63 loop, and red lines represent hydrogen bonds (for Glu50 this also indicates the helix cap formed with the helix 306-319), and the second green mesh (labeled with *) in the ReCl-MLE structure represents the volume of the closed active site.
Figure 8.
Figure 8. Loop closure and conformation differences between P51 Cl-MLE and ReCl-MLE. C -trace for P51 Cl-MLE structure is shown in blue and for ReCl-MLE in red. C 's of glycines corresponding to the Thr52 in MLE are shown as dots.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2003, 12, 1855-1864) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17054713 S.Halak, L.Lehtiö, T.Basta, S.Bürger, M.Contzen, A.Stolz, and A.Goldman (2006).
Structure and function of the 3-carboxy-cis,cis-muconate lactonizing enzyme from the protocatechuate degradative pathway of Agrobacterium radiobacter S2.
  FEBS J, 273, 5169-5182.
PDB codes: 2fel 2fen
14675551 R.M.de Jong, and B.W.Dijkstra (2003).
Structure and mechanism of bacterial dehalogenases: different ways to cleave a carbon-halogen bond.
  Curr Opin Struct Biol, 13, 722-730.  
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.