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PDBsum entry 1gzg

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1gzg
Jmol
Contents
Protein chains
329 a.a. *
Ligands
LAF ×5
SO4 ×2
Metals
_MG ×2
_NA ×2
__K ×2
Waters ×671
* Residue conservation analysis
PDB id:
1gzg
Name: Lyase
Title: Complex of a mg2-dependent porphobilinogen synthase from pseudomonas aeruginosa (mutant d139n) with 5-fluorolevulinic acid
Structure: Delta-aminolevulinic acid dehydratase. Chain: a, b. Synonym: porphobilinogen synthase, alad, aladh. Engineered: yes. Mutation: yes. Other_details: schiff base links between atoms nz of lys205 and lys260 and atoms c5 of 5-fluorolevulinic acid
Source: Pseudomonas aeruginosa. Organism_taxid: 287. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Octamer (from PDB file)
Resolution:
1.66Å     R-factor:   0.175     R-free:   0.198
Authors: F.Frere,W.-D.Schubert,F.Stauffer,N.Frankenberg,R.Neier, D.Jahn,D.W.Heinz
Key ref:
F.Frère et al. (2002). Structure of porphobilinogen synthase from Pseudomonas aeruginosa in complex with 5-fluorolevulinic acid suggests a double Schiff base mechanism. J Mol Biol, 320, 237-247. PubMed id: 12079382 DOI: 10.1016/S0022-2836(02)00472-2
Date:
21-May-02     Release date:   27-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q59643  (HEM2_PSEAE) -  Delta-aminolevulinic acid dehydratase
Seq:
Struc:
337 a.a.
329 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.4.2.1.24  - Porphobilinogen synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Porphyrin Biosynthesis (early stages)
      Reaction: 2 5-aminolevulinate = porphobilinogen + 2 H2O
2 × 5-aminolevulinate
Bound ligand (Het Group name = LAF)
matches with 70.00% similarity
= porphobilinogen
+ 2 × H(2)O
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     tetrapyrrole biosynthetic process   4 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S0022-2836(02)00472-2 J Mol Biol 320:237-247 (2002)
PubMed id: 12079382  
 
 
Structure of porphobilinogen synthase from Pseudomonas aeruginosa in complex with 5-fluorolevulinic acid suggests a double Schiff base mechanism.
F.Frère, W.D.Schubert, F.Stauffer, N.Frankenberg, R.Neier, D.Jahn, D.W.Heinz.
 
  ABSTRACT  
 
All natural tetrapyrroles, including hemes, chlorophylls and vitamin B12, share porphobilinogen (PBG) as a common precursor. Porphobilinogen synthase (PBGS) synthesizes PBG through the asymmetric condensation of two molecules of aminolevulinic acid (ALA). Crystal structures of PBGS from various sources confirm the presence of two distinct binding sites for each ALA molecule, termed A and P. We have solved the structure of the active-site variant D139N of the Mg2+-dependent PBGS from Pseudomonas aeruginosa in complex with the inhibitor 5-fluorolevulinic acid at high resolution. Uniquely, full occupancy of both substrate binding sites each by a single substrate-like molecule was observed. Both inhibitor molecules are covalently bound to two conserved, active-site lysine residues, Lys205 and Lys260, through Schiff bases. The active site now also contains a monovalent cation that may critically enhance enzymatic activity. Based on these structural data, we postulate a catalytic mechanism for P. aeruginosa PBGS initiated by a C-C bond formation between A and P-side ALA, followed by the formation of the intersubstrate Schiff base yielding the product PBG.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. A representation of A-site and P-site 5F-LA in the active site of PBGS monomer A. The P-site and A-site substrate recognition pockets are underlaid in green and purple, respectively. Hydrogen bonding interactions are indicated by dotted blue lines and hydrophobic interactions by dotted orange lines. Protein bonds are in black, the P-site 5F-LA molecule in green, the A-site 5F-LA in red, fluorine atoms in white, and the monovalent cation in the A-site in yellow.
Figure 6.
Figure 6. Proposed catalytic mechanism of PBGS from P. aeruginosa. P-site and A-site ALA are shown in green and red, respectively. The steps in the condensation of A and P-side ALA to form PBG are indicated by roman numerals. (I) Binding of P-side ALA. (II) Binding of A-side ALA. (III) Abstraction of H^+ from C3 of A-side ALA, yielding the A-site enamine. (IV) Aldole addition forming the C–C bond between A- and P-side-ALA. (V–VII) Schiff-base exchange producing a C–N bond between A-side and P-side ALA. (VIII) Transfer of H^+ to Lys260. (IX) Trans-elimination of P-site lysine. (X) Abstraction of the pro-R-H^+ from C5 of P-side ALA, aromatization and release of PBG.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 320, 237-247) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21514151 N.Iwai, K.Nakayama, J.Oku, and T.Kitazume (2011).
Synthesis and antibacterial activity of alaremycin derivatives for the porphobilinogen synthase.
  Bioorg Med Chem Lett, 21, 2812-2815.  
20354739 N.Sawada, N.Nagahara, F.Arisaka, K.Mitsuoka, and M.Minami (2011).
Redox and metal-regulated oligomeric state for human porphobilinogen synthase activation.
  Amino Acids, 41, 173-180.  
20506125 G.Layer, J.Reichelt, D.Jahn, and D.W.Heinz (2010).
Structure and function of enzymes in heme biosynthesis.
  Protein Sci, 19, 1137-1161.  
19822707 I.U.Heinemann, C.Schulz, W.D.Schubert, D.W.Heinz, Y.G.Wang, Y.Kobayashi, Y.Awa, M.Wachi, D.Jahn, and M.Jahn (2010).
Structure of the heme biosynthetic Pseudomonas aeruginosa porphobilinogen synthase in complex with the antibiotic alaremycin.
  Antimicrob Agents Chemother, 54, 267-272.
PDB code: 2woq
  20865533 U.D.Ramirez, F.Myachina, L.Stith, and E.K.Jaffe (2010).
Docking to large allosteric binding sites on protein surfaces.
  Adv Exp Med Biol, 680, 481-488.  
17516138 I.H.Ciğerci, S.E.Korcan, M.Konuk, and S.Oztürk (2008).
Comparison of ALAD activities of Citrobacter and Pseudomonas strains and their usage as biomarker for Pb contamination.
  Environ Monit Assess, 139, 41-48.  
18559269 S.H.Lawrence, U.D.Ramirez, L.Tang, F.Fazliyez, L.Kundrat, G.D.Markham, and E.K.Jaffe (2008).
Shape shifting leads to small-molecule allosteric drug discovery.
  Chem Biol, 15, 586-596.  
17311232 S.Gacond, F.Frère, M.Nentwich, J.P.Faurite, N.Frankenberg-Dinkel, and R.Neier (2007).
Synthesis of bisubstrate inhibitors of porphobilinogen synthase from Pseudomonas aeruginosa.
  Chem Biodivers, 4, 189-202.  
16023348 E.K.Jaffe (2005).
Morpheeins--a new structural paradigm for allosteric regulation.
  Trends Biochem Sci, 30, 490-497.  
15747133 N.Sawada, N.Nagahara, T.Sakai, Y.Nakajima, M.Minami, and T.Kawada (2005).
The activation mechanism of human porphobilinogen synthase by 2-mercaptoethanol: intrasubunit transfer of a reserve zinc ion and coordination with three cysteines in the active center.
  J Biol Inorg Chem, 10, 199-207.  
16131755 P.T.Erskine, L.Coates, R.Newbold, A.A.Brindley, F.Stauffer, G.D.Beaven, R.Gill, A.Coker, S.P.Wood, M.J.Warren, P.M.Shoolingin-Jordan, R.Neier, and J.B.Cooper (2005).
Structure of yeast 5-aminolaevulinic acid dehydratase complexed with the inhibitor 5-hydroxylaevulinic acid.
  Acta Crystallogr D Biol Crystallogr, 61, 1222-1226.
PDB code: 1w31
15555082 D.W.Bollivar, C.Clauson, R.Lighthall, S.Forbes, B.Kokona, R.Fairman, L.Kundrat, and E.K.Jaffe (2004).
Rhodobacter capsulatus porphobilinogen synthase, a high activity metal ion independent hexamer.
  BMC Biochem, 5, 17.  
14638682 S.Dhanasekaran, N.R.Chandra, B.K.Chandrasekhar Sagar, P.N.Rangarajan, and G.Padmanaban (2004).
Delta-aminolevulinic acid dehydratase from Plasmodium falciparum: indigenous versus imported.
  J Biol Chem, 279, 6934-6942.  
12573695 E.K.Jaffe (2003).
An unusual phylogenetic variation in the metal ion binding sites of porphobilinogen synthase.
  Chem Biol, 10, 25-34.  
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.