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PDBsum entry 3pc4

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protein ligands metals links
Lyase PDB id
3pc4
Jmol
Contents
Protein chain
504 a.a. *
Ligands
HEM
KOU
Metals
_NA
Waters ×598
* Residue conservation analysis
PDB id:
3pc4
Name: Lyase
Title: Full length structure of cystathionine beta-synthase from dr in complex with serine
Structure: Cg1753, isoform a. Chain: a. Synonym: cg1753, isoform b, ld21426p. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: cg1753, dmel_cg1753. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Resolution:
1.70Å     R-factor:   0.180     R-free:   0.203
Authors: M.Koutmos,J.L.Smith
Key ref: M.Koutmos et al. (2010). Structural basis for substrate activation and regulation by cystathionine beta-synthase (CBS) domains in cystathionine {beta}-synthase. Proc Natl Acad Sci U S A, 107, 20958-20963. PubMed id: 21081698
Date:
21-Oct-10     Release date:   01-Dec-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9VRD9  (Q9VRD9_DROME) -  Cystathionine beta-synthase, isoform A
Seq:
Struc:
 
Seq:
Struc:
522 a.a.
504 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.22  - Cystathionine beta-synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-serine + L-homocysteine = L-cystathionine + H2O
L-serine
+ L-homocysteine
= L-cystathionine
+ H(2)O
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = KOU) matches with 65.22% similarity
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     determination of adult lifespan   3 terms 
  Biochemical function     lyase activity     4 terms  

 

 
    reference    
 
 
Proc Natl Acad Sci U S A 107:20958-20963 (2010)
PubMed id: 21081698  
 
 
Structural basis for substrate activation and regulation by cystathionine beta-synthase (CBS) domains in cystathionine {beta}-synthase.
M.Koutmos, O.Kabil, J.L.Smith, R.Banerjee.
 
  ABSTRACT  
 
The catalytic potential for H(2)S biogenesis and homocysteine clearance converge at the active site of cystathionine β-synthase (CBS), a pyridoxal phosphate-dependent enzyme. CBS catalyzes β-replacement reactions of either serine or cysteine by homocysteine to give cystathionine and water or H(2)S, respectively. In this study, high-resolution structures of the full-length enzyme from Drosophila in which a carbanion (1.70 Å) and an aminoacrylate intermediate (1.55 Å) have been captured are reported. Electrostatic stabilization of the zwitterionic carbanion intermediate is afforded by the close positioning of an active site lysine residue that is initially used for Schiff base formation in the internal aldimine and later as a general base. Additional stabilizing interactions between active site residues and the catalytic intermediates are observed. Furthermore, the structure of the regulatory "energy-sensing" CBS domains, named after this protein, suggests a mechanism for allosteric activation by S-adenosylmethionine.