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PDBsum entry 1i29

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protein ligands links
Lyase PDB id
1i29
Jmol
Contents
Protein chain
405 a.a. *
Ligands
LPG-PLP
* Residue conservation analysis
PDB id:
1i29
Name: Lyase
Title: Crystal structure of csdb complexed with l-propargylglycine
Structure: Csdb. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: csdb or sufs. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.80Å     R-factor:   0.209     R-free:   0.233
Authors: H.Mihara,T.Fujii,T.Kurihara,Y.Hata,N.Esaki
Key ref: H.Mihara et al. (2002). Structure of external aldimine of Escherichia coli CsdB, an IscS/NifS homolog: implications for its specificity toward selenocysteine. J Biochem, 131, 679-685. PubMed id: 11983074
Date:
07-Feb-01     Release date:   01-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P77444  (SUFS_ECOLI) -  Cysteine desulfurase
Seq:
Struc:
406 a.a.
405 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.2.8.1.7  - Cysteine desulfurase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-cysteine + acceptor = L-alanine + S-sulfanyl-acceptor
L-cysteine
+ acceptor
=
L-alanine
Bound ligand (Het Group name = LPG)
corresponds exactly
+ S-sulfanyl-acceptor
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
   Enzyme class 2: E.C.4.4.1.16  - Selenocysteine lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-selenocysteine + reduced acceptor = selenide + L-alanine + acceptor
L-selenocysteine
+ reduced acceptor
= selenide
+
L-alanine
Bound ligand (Het Group name = LPG)
corresponds exactly
+ acceptor
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
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     metabolic process   6 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
J Biochem 131:679-685 (2002)
PubMed id: 11983074  
 
 
Structure of external aldimine of Escherichia coli CsdB, an IscS/NifS homolog: implications for its specificity toward selenocysteine.
H.Mihara, T.Fujii, S.Kato, T.Kurihara, Y.Hata, N.Esaki.
 
  ABSTRACT  
 
Escherichia coli CsdB is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes both cysteine desulfuration and selenocysteine deselenation. The enzyme has a high specific activity for L-selenocysteine relative to L-cysteine. On the other hand, its paralog, IscS, exhibits higher activity for L-cysteine, which acts as a sulfur donor during the biosynthesis of the iron-sulfur cluster and 4-thiouridine. The structure of CsdB complexed with L-propargylglycine was determined by X-ray crystallography at 2.8 A resolution. The overall polypeptide fold of the complex is similar to that of the uncomplexed enzyme, indicating that no significant structural change occurs upon formation of the complex. In the complex, propargylglycine forms a Schiff base with PLP, providing the features of the external aldimine formed in the active site. The Cys364 residue, which is essential for the activity of CsdB toward L-cysteine but not toward L-selenocysteine, is clearly visible on a loop of the extended lobe (Thr362-Arg375) in all enzyme forms studied, in contrast to the corresponding disordered loop (Ser321-Arg332) of the Thermotoga maritima NifS-like protein, which is closely related to IscS. The extended lobe of CsdB has an 11-residue deletion compared with that of the NifS-like protein. These facts suggest that the restricted flexibility of the Cys364-anchoring extended lobe in CsdB may be responsible for the ability of the enzyme to discriminate between selenium and sulfur.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20404999 R.Shi, A.Proteau, M.Villarroya, I.Moukadiri, L.Zhang, J.F.Trempe, A.Matte, M.E.Armengod, and M.Cygler (2010).
Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions.
  PLoS Biol, 8, e1000354.
PDB codes: 3lvj 3lvk 3lvl 3lvm
17300176 S.Lima, R.Khristoforov, C.Momany, and R.S.Phillips (2007).
Crystal structure of Homo sapiens kynureninase.
  Biochemistry, 46, 2735-2744.
PDB code: 2hzp
15952888 D.C.Johnson, D.R.Dean, A.D.Smith, and M.K.Johnson (2005).
Structure, function, and formation of biological iron-sulfur clusters.
  Annu Rev Biochem, 74, 247-281.  
15930006 G.Liu, Z.Li, Y.Chiang, T.Acton, G.T.Montelione, D.Murray, and T.Szyperski (2005).
High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.
  Protein Sci, 14, 1597-1608.
PDB code: 1ni7
15688436 R.Prabhakar, K.Morokuma, and D.G.Musaev (2005).
A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment.
  J Comput Chem, 26, 443-446.  
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.