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PDBsum entry 2v8d

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protein metals Protein-protein interface(s) links
Hydrolase PDB id
2v8d
Jmol
Contents
Protein chains
437 a.a. *
Metals
_ZN ×4
Waters ×58
* Residue conservation analysis
PDB id:
2v8d
Name: Hydrolase
Title: Crystal structure of mutant e159a of beta-alanine synthase from saccharomyces kluyveri
Structure: Beta-alanine synthase. Chain: a, b. Fragment: residues 2-455. Engineered: yes. Mutation: yes
Source: Saccharomyces kluyveri. Yeast. Organism_taxid: 4934. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
2.30Å     R-factor:   0.232     R-free:   0.276
Authors: S.Lundgren,B.Andersen,J.Piskur,D.Dobritzsch
Key ref:
S.Lundgren et al. (2007). Crystal structures of yeast beta-alanine synthase complexes reveal the mode of substrate binding and large scale domain closure movements. J Biol Chem, 282, 36037-36047. PubMed id: 17916556 DOI: 10.1074/jbc.M705517200
Date:
07-Aug-07     Release date:   02-Oct-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q96W94  (Q96W94_LACKL) -  Beta-alanine synthase
Seq:
Struc:
455 a.a.
437 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.5.1.6  - Beta-ureidopropionase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: N-carbamoyl-beta-alanine + H2O = beta-alanine + CO2 + NH3
N-carbamoyl-beta-alanine
+ H(2)O
= beta-alanine
+ CO(2)
+ NH(3)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M705517200 J Biol Chem 282:36037-36047 (2007)
PubMed id: 17916556  
 
 
Crystal structures of yeast beta-alanine synthase complexes reveal the mode of substrate binding and large scale domain closure movements.
S.Lundgren, B.Andersen, J.Piskur, D.Dobritzsch.
 
  ABSTRACT  
 
Beta-alanine synthase is the final enzyme of the reductive pyrimidine catabolic pathway, which is responsible for the breakdown of uracil and thymine in higher organisms. The fold of the homodimeric enzyme from the yeast Saccharomyces kluyveri identifies it as a member of the AcyI/M20 family of metallopeptidases. Its subunit consists of a catalytic domain harboring a di-zinc center and a smaller dimerization domain. The present site-directed mutagenesis studies identify Glu(159) and Arg(322) as crucial for catalysis and His(262) and His(397) as functionally important but not essential. We determined the crystal structures of wild-type beta-alanine synthase in complex with the reaction product beta-alanine, and of the mutant E159A with the substrate N-carbamyl-beta-alanine, revealing the closed state of a dimeric AcyI/M20 metallopeptidase-like enzyme. Subunit closure is achieved by a approximately 30 degrees rigid body domain rotation, which completes the active site by integration of substrate binding residues that belong to the dimerization domain of the same or the partner subunit. Substrate binding is achieved via a salt bridge, a number of hydrogen bonds, and coordination to one of the zinc ions of the di-metal center.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Open and closed conformation of SkβAS. a, stereoview of the homodimer of SkβAS-E159A (E159A_NCβA). The two subunits are colored differently. Substrate molecules bound in the respective active sites and Bicine molecules bound close to the hinge region are shown as ball-and-stick models with white and yellow carbon atoms, respectively. Zinc ions are represented as black spheres. b, stereoview of the extended, open enzyme conformation as observed for SkβAS-R322A (R322A). The distance separating the C[ ]-atom positions of D192 from both monomers in this enzyme state is given. Zinc ions are shown as black spheres. c, schematic view of the subunit backbones of E159A_NCβA (magenta), WT-βAla (white), E159A (yellow), and R322A (blue) after superposition of the respective catalytic domains. The rigid body hinge movement of the dimerization domain from the open to the closed state is indicated by an arrow and the approximate rotation angle is given. d, stereoview of the domain interface in the open state (R322A). The two subunits per homodimer are shown in white (A) and yellow (B) cartoon representation, respectively. Residue stretches interacting with each other in the closed but not in the open state are colored identically (red: amino acids 118, 120, 160, 162 from subunit A and 305-310 from subunit B; green: 189, 190, 192 (A) and 192, 306 (B); bright green: 229, 231, 235 (A) and 262, 265, 269 (B); blue: 247, 249, 322, 365, 393-396, 403 (A) and 264 (B); cyan: 419-422 (A) and 259-261, 309-310 (B); orange: 166, 359-360 (A); magenta: 161, 167, 249, 251 (A)). Residues H262, R322, N309, and D192 are shown as stick models. Black spheres represent zinc ions. e, stereoview of the domain interface in the closed state (E159A_NCβA). The orientation of the catalytic domain in monomer A is the same as in d. All representations and color codes correspond to those used in d.NCβA is shown as stick model with oxygen atoms in red, nitrogen atoms in blue, and carbon atoms in yellow.
Figure 3.
FIGURE 3. Comparison of SkβAS with PepV. a, stereoview of the superimposed crystal structures of monomeric PepV (gray) and dimeric E159A_NCβA. From the latter only one complete subunit (yellow) and the dimerization domain of the partner subunit (green) are shown. Stick models of NCβA (red), and a transition state mimic bound to PepV (cyan) are included in the figure. Zinc ions are represented as spheres, for SkβAS in orange and for PepV in blue. b, stereoview of the superimposed active sites of SkβAS (E159A_NCβA) and PepV. The dimensions of the substrate binding cavities are outlined by the white surface for PepV and by the orange surface for E159A_NCβA. The latter was calculated after modeling of a glutamate at position 159 to correspond to the active site of the wild-type enzyme. Zinc ions are represented as orange (E159A_NCβA) and green spheres (PepV). Stick models of substrate- and zinc-binding residues as well as some other residues lining the cavity walls are shown with green carbon atoms for PepV and yellow carbon atoms for the SkβAS complex. For clarity, only the latter are labeled. The transition state mimic Asp [PO[2]CH[2]]AlaOH bound to PepV is depicted with thicker sticks and carbon atoms in cyan, while those of NCβA are shown in orange.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 36037-36047) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20610394 T.S.Girish, and B.Gopal (2010).
Crystal structure of Staphylococcus aureus metallopeptidase (Sapep) reveals large domain motions between the manganese-bound and apo-states.
  J Biol Chem, 285, 29406-29415.
PDB codes: 3khx 3khz 3ki9
19011069 A.I.Martínez-Gómez, S.Martínez-Rodríguez, J.Pozo-Dengra, D.Tessaro, S.Servi, J.M.Clemente-Jiménez, F.Rodríguez-Vico, and F.J.Las Heras-Vázquez (2009).
Potential application of N-carbamoyl-beta-alanine amidohydrolase from Agrobacterium tumefaciens C58 for beta-amino acid production.
  Appl Environ Microbiol, 75, 514-520.  
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