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PDBsum entry 2ptq

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protein ligands Protein-protein interface(s) links
Lyase PDB id
2ptq
Jmol
Contents
Protein chains
459 a.a. *
Ligands
FUM ×2
AMP ×2
Waters ×650
* Residue conservation analysis
PDB id:
2ptq
Name: Lyase
Title: Crystal structure of escherichia coli adenylosuccinate lyase h171n with bound amp and fumarate
Structure: Adenylosuccinate lyase. Chain: a, b. Synonym: adenylosuccinate, asl. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: purb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.175     R-free:   0.211
Authors: M.Tsai,P.L.Howell
Key ref:
M.Tsai et al. (2007). Substrate and product complexes of Escherichia coli adenylosuccinate lyase provide new insights into the enzymatic mechanism. J Mol Biol, 370, 541-554. PubMed id: 17531264 DOI: 10.1016/j.jmb.2007.04.052
Date:
08-May-07     Release date:   03-Jul-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AB89  (PUR8_ECOLI) -  Adenylosuccinate lyase
Seq:
Struc:
456 a.a.
459 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.3.2.2  - Adenylosuccinate lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Purine Biosynthesis (late stages)
      Reaction:
1. N6-(1,2-dicarboxyethyl)AMP = fumarate + AMP
2. (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D- ribosyl)imidazole-4-carboxamide
N(6)-(1,2-dicarboxyethyl)AMP
=
fumarate
Bound ligand (Het Group name = FUM)
corresponds exactly
+
AMP
Bound ligand (Het Group name = AMP)
corresponds exactly
(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate
=
fumarate
Bound ligand (Het Group name = FUM)
corresponds exactly
+
5-amino-1-(5-phospho-D- ribosyl)imidazole-4-carboxamide
Bound ligand (Het Group name = AMP)
matches with 87.50% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     'de novo' AMP biosynthetic process   6 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2007.04.052 J Mol Biol 370:541-554 (2007)
PubMed id: 17531264  
 
 
Substrate and product complexes of Escherichia coli adenylosuccinate lyase provide new insights into the enzymatic mechanism.
M.Tsai, J.Koo, P.Yip, R.F.Colman, M.L.Segall, P.L.Howell.
 
  ABSTRACT  
 
Adenylosuccinate lyase (ADL) catalyzes the breakdown of 5-aminoimidazole- (N-succinylocarboxamide) ribotide (SAICAR) to 5-aminoimidazole-4-carboxamide ribotide (AICAR) and fumarate, and of adenylosuccinate (ADS) to adenosine monophosphate (AMP) and fumarate in the de novo purine biosynthetic pathway. ADL belongs to the argininosuccinate lyase (ASL)/fumarase C superfamily of enzymes. Members of this family share several common features including: a mainly alpha-helical, homotetrameric structure; three regions of highly conserved amino acid residues; and a general acid-base catalytic mechanism with the overall beta-elimination of fumarate as a product. The crystal structures of wild-type Escherichia coli ADL (ec-ADL), and mutant-substrate (H171A-ADS) and -product (H171N-AMP.FUM) complexes have been determined to 2.0, 1.85, and 2.0 A resolution, respectively. The H171A-ADS and H171N-AMP.FUM structures provide the first detailed picture of the ADL active site, and have enabled the precise identification of substrate binding and putative catalytic residues. Contrary to previous suggestions, the ec-ADL structures implicate S295 and H171 in base and acid catalysis, respectively. Furthermore, structural alignments of ec-ADL with other superfamily members suggest for the first time a large conformational movement of the flexible C3 loop (residues 287-303) in ec-ADL upon substrate binding and catalysis, resulting in its closure over the active site. This loop movement has been observed in other superfamily enzymes, and has been proposed to be essential for catalysis. The ADL catalytic mechanism is re-examined in light of the results presented here.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo view of the superimposed H171A (pink) and H171N (green) active sites, showing the interactions involving the AMP (a) and fumarate groups (c). The σ[A] weighted F[o]–F[c] omit maps for the substrate (orange) and products (blue) in the H171A and H171N proteins, respectively, are shown contoured at 3σ. Water molecules are shown as spheres. The corresponding schematic representations for the AMP and fumarate groups are shown in (b) and (d), respectively. Hydrogen bonds are represented as red broken lines with the distances indicated in angstroms (Å). Distances for the H171N protein are in bold, and the distances for active site 2 of each protein are given in parentheses. The letter following the residue number denotes the monomer to which each residue belongs, with those for active site 2 of the proteins shown in parentheses. In (b), residues involved in coordinating water molecules are colored blue. Poor electron density did not allow residues S295 and S296 in active site 2 of the H171A protein to be modeled. PyMol was used for Figure preparation.
Figure 3.
Figure 3. Stereo view of the superimposed H171A–ADS (pink), H171N–AMP•FUM (blue) and dδc1-SO[4]^2- (yellow) active sites, showing the conformation of the C3 loop in the proteins. Since the C3 loop in the SeMet protein could not be modeled due to the absence of electron density, the open conformation of the loop observed in the dδc2-S281A mutant^12 is also shown for comparison (green). The side-chains of selected C3 loop residues are shown and numbered according to the E. coli ADL sequence. PyMol was used for Figure preparation.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 370, 541-554) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20549362 G.Allegri, M.J.Fernandes, F.B.Scalco, P.Correia, R.E.Simoni, J.C.Llerena, and M.L.de Oliveira (2010).
Fumaric aciduria: an overview and the first Brazilian case report.
  J Inherit Metab Dis, 33, 411-419.  
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
19007868 A.J.Knox, C.Graham, J.Bleskan, G.Brodsky, and D.Patterson (2009).
Mutations in the Chinese hamster ovary cell GART gene of de novo purine synthesis.
  Gene, 429, 23-30.  
  19724117 G.Kozlov, L.Nguyen, J.Pearsall, and K.Gehring (2009).
The structure of phosphate-bound Escherichia coli adenylosuccinate lyase identifies His171 as a catalytic acid.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 857-861.
PDB code: 3gzh
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.  
18469177 S.Sivendran, and R.F.Colman (2008).
Effect of a new non-cleavable substrate analog on wild-type and serine mutants in the signature sequence of adenylosuccinate lyase of Bacillus subtilis and Homo sapiens.
  Protein Sci, 17, 1162-1174.  
18712276 Y.Zhang, M.Morar, and S.E.Ealick (2008).
Structural biology of the purine biosynthetic pathway.
  Cell Mol Life Sci, 65, 3699-3724.  
17600142 S.Sivendran, M.L.Segall, P.C.Rancy, and R.F.Colman (2007).
Effect of Asp69 and Arg310 on the pK of His68, a key catalytic residue of adenylosuccinate lyase.
  Protein Sci, 16, 1700-1707.  
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.

 

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