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PDBsum entry 1j3u

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protein Protein-protein interface(s) links
Lyase PDB id
1j3u
Jmol
Contents
Protein chains
462 a.a. *
Waters ×213
* Residue conservation analysis
PDB id:
1j3u
Name: Lyase
Title: Crystal structure of aspartase from bacillus sp. Ym55-1
Structure: Aspartase. Chain: a, b. Engineered: yes
Source: Bacillus sp. Ym55-1. Organism_taxid: 96471. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PDB file)
Resolution:
2.50Å     R-factor:   0.221     R-free:   0.266
Authors: T.Fujii,H.Sakai,Y.Kawata,Y.Hata
Key ref:
T.Fujii et al. (2003). Crystal structure of thermostable aspartase from Bacillus sp. YM55-1: structure-based exploration of functional sites in the aspartase family. J Mol Biol, 328, 635-654. PubMed id: 12706722 DOI: 10.1016/S0022-2836(03)00310-3
Date:
16-Feb-03     Release date:   06-May-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9LCC6  (Q9LCC6_9BACI) -  Aspartase
Seq:
Struc:
468 a.a.
462 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.4.3.1.1  - Aspartate ammonia-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-aspartate = fumarate + NH3
L-aspartate
= fumarate
+ NH(3)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     tricarboxylic acid cycle enzyme complex   1 term 
  Biological process     fumarate metabolic process   3 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S0022-2836(03)00310-3 J Mol Biol 328:635-654 (2003)
PubMed id: 12706722  
 
 
Crystal structure of thermostable aspartase from Bacillus sp. YM55-1: structure-based exploration of functional sites in the aspartase family.
T.Fujii, H.Sakai, Y.Kawata, Y.Hata.
 
  ABSTRACT  
 
The crystal structure of the thermostable aspartase from Bacillus sp. YM55-1 has been solved and refined for 2.5A resolution data with an R-factor of 22.1%. The present enzyme is a homotetramer with subunits composed of three domains. It exhibits no allosteric effects, in contrast to the Escherichia coli aspartase, which is activated by divalent metal cation and L-aspartate, but is four-times more active than the E.coli enzyme. The overall folding of the present enzyme subunit is similar to those of the E.coli aspartase and the E.coli fumarase C, both of which belong to the same superfamily as the present enzyme. A local structural comparison of these three enzymes revealed seven structurally different regions. Five of the regions were located around putative functional sites, suggesting the involvement of these regions into the functions characteristic of the enzymes. Of these regions, the region of Gln96-Gly100 is proposed as a part of the recognition site of the alpha-amino group in L-aspartate for aspartase and the hydroxyl group in L-malate for fumarase. The region of Gln315-Gly323 is a flexible loop with a well-conserved sequence that is suggested to be involved in the catalytic reaction. The region of Lys123-Lys128 corresponds to a part of the putative activator-binding site in the E.coli fumarase C. The region in the Bacillus aspartase, however, adopts a main-chain conformation that prevents the activator binding. The regions of Gly228-Glu241 and Val265-Asp272, which form a part of the active-site wall, are suggested to be involved in the allosteric activation of the E.coli aspartase by the binding of the metal ion and the activator. Moreover, an increase in the numbers of intersubunit hydrogen bonds and salt-bridges is observed in the Bacillus aspartase relative to those of the E.coli enzyme, implying a contribution to the thermostability of the present aspartase.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo drawings of two independent active sites of BsAsp. (a) The active site composed of the A-chain, the B-chain, and the C-chain. An unknown ligand is shown as a green lump of s[A]-weighted F[o] -F[c] electron density contoured at the 3.5 s level. (b) The active site composed of the B-chain, the C-chain, and the D-chain. The water molecule bound to the active site is shown by a large red ball. In (a) and (b), hydrogen bonds are shown by broken lines colored red for the interactions between the water molecule and the protein and blue for other interactions.
Figure 6.
Figure 6. Stereo drawings of active sites of (a) Ecfum and (b) EcAsp. The orientations of the molecules are almost the same as those in Figure 3. The molecules were superimposed onto that of BsAsp by least-squares C^a-fitting of the corresponding residues labeled here. The hydrogen bonds are shown by broken lines colored red for interactions between the water molecule and the protein and blue for other interactions. In (a), the citrate molecule bound to the active site is drawn with green-colored thin bonds and small balls.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 328, 635-654) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20693687 P.K.Fyfe, A.Dawson, M.T.Hutchison, S.Cameron, and W.N.Hunter (2010).
Structure of Staphylococcus aureus adenylosuccinate lyase (PurB) and assessment of its potential as a target for structure-based inhibitor discovery.
  Acta Crystallogr D Biol Crystallogr, 66, 881-888.
PDB code: 2x75
19490103 V.Puthan Veetil, H.Raj, W.J.Quax, D.B.Janssen, and G.J.Poelarends (2009).
Site-directed mutagenesis, kinetic and inhibition studies of aspartate ammonia lyase from Bacillus sp. YM55-1.
  FEBS J, 276, 2994-3007.  
17512708 M.J.Wagemaker, D.C.Eastwood, C.van der Drift, M.S.Jetten, K.Burton, L.J.Van Griensven, and H.J.Op den Camp (2007).
Argininosuccinate synthetase and argininosuccinate lyase: two ornithine cycle enzymes from Agaricus bisporus.
  Mycol Res, 111, 493-502.  
15857789 Y.Asano, I.Kira, and K.Yokozeki (2005).
Alteration of substrate specificity of aspartase by directed evolution.
  Biomol Eng, 22, 95.  
15502303 P.Bhaumik, M.K.Koski, U.Bergmann, and R.K.Wierenga (2004).
Structure determination and refinement at 2.44 A resolution of argininosuccinate lyase from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 60, 1964-1970.
PDB code: 1tj7
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.