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PDBsum entry 1nf9

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Hydrolase PDB id
1nf9
Jmol
Contents
Protein chain
207 a.a. *
Ligands
BOG
FMT
Waters ×291
* Residue conservation analysis
PDB id:
1nf9
Name: Hydrolase
Title: Crystal structure of phzd protein from pseudomonas aeruginosa
Structure: Phenazine biosynthesis protein phzd. Chain: a. Synonym: phzd isochorismatase. Engineered: yes
Source: Pseudomonas aeruginosa. Organism_taxid: 287. Gene: phzd. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
1.50Å     R-factor:   0.156     R-free:   0.225
Authors: F.Parsons,K.Calabrese,E.Eisenstein,J.E.Ladner
Key ref:
J.F.Parsons et al. (2003). Structure and mechanism of Pseudomonas aeruginosa PhzD, an isochorismatase from the phenazine biosynthetic pathway. Biochemistry, 42, 5684-5693. PubMed id: 12741825 DOI: 10.1021/bi027385d
Date:
13-Dec-02     Release date:   17-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q7DC80  (Q7DC80_PSEAE) -  Phenazine biosynthesis protein PhzD
Seq:
Struc:
207 a.a.
207 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     2 terms  

 

 
DOI no: 10.1021/bi027385d Biochemistry 42:5684-5693 (2003)
PubMed id: 12741825  
 
 
Structure and mechanism of Pseudomonas aeruginosa PhzD, an isochorismatase from the phenazine biosynthetic pathway.
J.F.Parsons, K.Calabrese, E.Eisenstein, J.E.Ladner.
 
  ABSTRACT  
 
PhzD from Pseudomonas aeruginosa is an isochorismatase involved in phenazine biosynthesis. Phenazines are antimicrobial compounds that provide Pseudomonas with a competitive advantage in certain environments and may be partly responsible for the persistence of Pseudomonas infections. In vivo, PhzD catalyzes the hydrolysis of the vinyl ether functional group of 2-amino-2-deoxyisochorismate, yielding pyruvate and trans-2,3-dihydro-3-hydroxyanthranilic acid, which is then utilized in the phenazine biosynthetic pathway. PhzD also catalyzes hydrolysis of the related vinyl ethers isochorismate, chorismate, and 4-amino-4-deoxychorismate. Here we report the 1.5 A crystal structure of native PhzD, and the 1.6 A structure of the inactive D38A variant in complex with isochorismate. The structures reveal that isochorismate binds to the PhzD active site in a trans-diaxial conformation, and superposition of the structures indicates that the methylene pyruvyl carbon of isochorismate is adjacent to the side chain carboxylate of aspartate 38. The proximity of aspartate 38 to isochorismate and the complete loss of activity resulting from the conversion of aspartate 38 to alanine suggest a mechanism in which the carboxylate acts as a general acid to protonate the substrate, yielding a carbocation/oxocarbonium ion that is then rapidly hydrated to form a hemiketal intermediate, which then decomposes spontaneously to products. The structure of PhzD is remarkably similar to other structures from a subfamily of alpha/beta-hydrolase enzymes that includes pyrazinamidase and N-carbamoylsarcosine amidohydrolase. However, PhzD catalyzes unrelated chemistry and lacks a nucleophilic cysteine found in its close structural relatives. The vinyl ether hydrolysis catalyzed by PhzD represents yet another example of the catalytic diversity seen in the alpha/beta-hydrolase family, whose members are also known to hydrolyze amides, phosphates, phosphonates, epoxides, and C-X bonds.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20846361 P.B.Patil, Y.Zeng, T.Coursey, P.Houston, I.Miller, and S.Chen (2010).
Isolation and characterization of a Nocardiopsisā€ƒsp. from honeybee guts.
  FEMS Microbiol Lett, 312, 110-118.  
20448892 W.M.Abdel-Mageed, B.F.Milne, M.Wagner, M.Schumacher, P.Sandor, W.Pathom-aree, M.Goodfellow, A.T.Bull, K.Horikoshi, R.Ebel, M.Diederich, H.P.Fiedler, and M.Jaspars (2010).
Dermacozines, a new phenazine family from deep-sea dermacocci isolated from a Mariana Trench sediment.
  Org Biomol Chem, 8, 2352-2362.  
19897889 C.Maruyama, and Y.Hamano (2009).
The biological function of the bacterial isochorismatase-like hydrolase SttH.
  Biosci Biotechnol Biochem, 73, 2494-2500.  
19189039 D.A.Fitzpatrick (2009).
Lines of evidence for horizontal gene transfer of a phenazine producing operon into multiple bacterial species.
  J Mol Evol, 68, 171-185.  
19658148 M.Mentel, E.G.Ahuja, D.V.Mavrodi, R.Breinbauer, L.S.Thomashow, and W.Blankenfeldt (2009).
Of two make one: the biosynthesis of phenazines.
  Chembiochem, 10, 2295-2304.  
18523684 D.M.Soanes, I.Alam, M.Cornell, H.M.Wong, C.Hedeler, N.W.Paton, M.Rattray, S.J.Hubbard, S.G.Oliver, and N.J.Talbot (2008).
Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis.
  PLoS ONE, 3, e2300.  
18641136 H.Liang, L.Li, Z.Dong, M.G.Surette, and K.Duan (2008).
The YebC family protein PA0964 negatively regulates the Pseudomonas aeruginosa quinolone signal system and pyocyanin production.
  J Bacteriol, 190, 6217-6227.  
18182490 S.G.Van Lanen, S.Lin, and B.Shen (2008).
Biosynthesis of the enediyne antitumor antibiotic C-1027 involves a new branching point in chorismate metabolism.
  Proc Natl Acad Sci U S A, 105, 494-499.  
18699781 S.Jiang, X.Sun, and S.Zhang (2008).
The ycaC-related protein from the amphioxus Branchiostoma belcheri (BbycaCR) interacts with creatine kinase.
  FEBS J, 275, 4597-4605.  
17512214 F.Song (2007).
A study of noncovalent protein complexes by matrix-assisted laser desorption/ionization.
  J Am Soc Mass Spectrom, 18, 1286-1290.  
17253782 J.F.Parsons, B.T.Greenhagen, K.Shi, K.Calabrese, H.Robinson, and J.E.Ladner (2007).
Structural and functional analysis of the pyocyanin biosynthetic protein PhzM from Pseudomonas aeruginosa.
  Biochemistry, 46, 1821-1828.
PDB code: 2ip2
17880004 S.H.Park, H.B.Oh, W.K.Seong, C.W.Kim, S.Y.Cho, and C.K.Yoo (2007).
Differential analysis of Bacillus anthracis after pX01 plasmid curing and comprehensive data on Bacillus anthracis infection in macrophages and glial cells.
  Proteomics, 7, 3743-3758.  
16719720 D.V.Mavrodi, W.Blankenfeldt, and L.S.Thomashow (2006).
Phenazine compounds in fluorescent Pseudomonas spp. biosynthesis and regulation.
  Annu Rev Phytopathol, 44, 417-445.  
16632253 E.J.Drake, D.A.Nicolai, and A.M.Gulick (2006).
Structure of the EntB multidomain nonribosomal peptide synthetase and functional analysis of its interaction with the EntE adenylation domain.
  Chem Biol, 13, 409-419.
PDB code: 2fq1
16374842 J.D.Pédelacq, B.S.Rho, C.Y.Kim, G.S.Waldo, T.P.Lekin, B.W.Segelke, B.Rupp, L.W.Hung, S.I.Kim, and T.C.Terwilliger (2006).
Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis.
  Proteins, 62, 563-569.
PDB code: 2a2j
16893885 T.Itoh, W.Hashimoto, B.Mikami, and K.Murata (2006).
Crystal structure of unsaturated glucuronyl hydrolase complexed with substrate: molecular insights into its catalytic reaction mechanism.
  J Biol Chem, 281, 29807-29816.
PDB codes: 2ahf 2ahg 2d5j
16641084 Y.Hamano, N.Matsuura, M.Kitamura, and H.Takagi (2006).
A novel enzyme conferring streptothricin resistance alters the toxicity of streptothricin D from broad-spectrum to bacteria-specific.
  J Biol Chem, 281, 16842-16848.  
16199669 J.Caruthers, F.Zucker, E.Worthey, P.J.Myler, F.Buckner, W.Van Voorhuis, C.Mehlin, E.Boni, T.Feist, J.Luft, S.Gulde, A.Lauricella, O.Kaluzhniy, L.Anderson, I.Le Trong, M.A.Holmes, T.Earnest, M.Soltis, K.O.Hodgson, W.G.Hol, and E.A.Merritt (2005).
Crystal structures and proposed structural/functional classification of three protozoan proteins from the isochorismatase superfamily.
  Protein Sci, 14, 2887-2894.
PDB codes: 1x9g 1xn4 1yzv
15983044 T.Jaeger, M.Arsic, and C.Mayer (2005).
Scission of the lactyl ether bond of N-acetylmuramic acid by Escherichia coli "etherase".
  J Biol Chem, 280, 30100-30106.  
15159577 E.G.Ahuja, D.V.Mavrodi, L.S.Thomashow, and W.Blankenfeldt (2004).
Overexpression, purification and crystallization of PhzA, the first enzyme of the phenazine biosynthesis pathway of Pseudomonas fluorescens 2-79.
  Acta Crystallogr D Biol Crystallogr, 60, 1129-1131.  
15502343 J.F.Parsons, K.Calabrese, E.Eisenstein, and J.E.Ladner (2004).
Structure of the phenazine biosynthesis enzyme PhzG.
  Acta Crystallogr D Biol Crystallogr, 60, 2110-2113.
PDB codes: 1t9m 1ty9
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.