spacer
spacer

PDBsum entry 1e3a
Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Antibiotic resistance PDB id
1e3a

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
258 a.a. *
560 a.a. *
Ligands
EDO ×3
Metals
_CA
_CL
Waters ×1193
* Residue conservation analysis
PDB id:
1e3a
Name: Antibiotic resistance
Title: A slow processing precursor penicillin acylase from escherichia coli
Structure: Penicillin amidase alpha subunit. Chain: a. Fragment: penicillin amidase residues 29-286. Synonym: pga. Engineered: yes. Penicillin amidase beta subunit. Chain: b. Fragment: penicillin amidase residues 287-846. Synonym: pga.
Source: Escherichia coli. Organism_taxid: 562. Strain: hb101. Atcc: 11105. Cellular_location: periplasm. Gene: pac. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_atcc_number: 11105.
Biol. unit: Hetero-Dimer (from PDB file)
Resolution:
1.80Å     R-factor:   0.149     R-free:   0.197
Authors: L.Hewitt,V.Kasche,K.Lummer,R.J.Lewis,G.N.Murshudov,C.S.Verma, G.G.Dodson,K.S.Wilson
Key ref:
L.Hewitt et al. (2000). Structure of a slow processing precursor penicillin acylase from Escherichia coli reveals the linker peptide blocking the active-site cleft. J Mol Biol, 302, 887-898. PubMed id: 10993730 DOI: 10.1006/jmbi.2000.4105
Date:
07-Jun-00     Release date:   29-Nov-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06875  (PAC_ECOLX) -  Penicillin G acylase from Escherichia coli
Seq:
Struc: 		 
Seq:
Struc: 		846 a.a.
258 a.a.*
Protein chain
Pfam   ArchSchema ?
P06875  (PAC_ECOLX) -  Penicillin G acylase from Escherichia coli
Seq:
Struc: 		 
Seq:
Struc: 		846 a.a.
560 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.3.5.1.11  - penicillin amidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Penicillin Biosynthesis and Metabolism
      Reaction: a penicillin + H2O = 6-aminopenicillanate + a carboxylate
penicillin
 + H2O
 = 6-aminopenicillanate
 + carboxylate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.4105 J Mol Biol 302:887-898 (2000)
PubMed id: 10993730  
 
 
Structure of a slow processing precursor penicillin acylase from Escherichia coli reveals the linker peptide blocking the active-site cleft.
L.Hewitt, V.Kasche, K.Lummer, R.J.Lewis, G.N.Murshudov, C.S.Verma, G.G.Dodson, K.S.Wilson.
 
  ABSTRACT  
 
Penicillin G acylase is a periplasmic protein, cytoplasmically expressed as a precursor polypeptide comprising a signal sequence, the A and B chains of the mature enzyme (209 and 557 residues respectively) joined by a spacer peptide of 54 amino acid residues. The wild-type AB heterodimer is produced by proteolytic removal of this spacer in the periplasm. The first step in processing is believed to be autocatalytic hydrolysis of the peptide bond between the C-terminal residue of the spacer and the active-site serine residue at the N terminus of the B chain. We have determined the crystal structure of a slowly processing precursor mutant (Thr263Gly) of penicillin G acylase from Escherichia coli, which reveals that the spacer peptide blocks the entrance to the active-site cleft consistent with an autocatalytic mechanism of maturation. In this mutant precursor there is, however, an unexpected cleavage at a site four residues from the active-site serine residue. Analyses of the stereochemistry of the 260-261 bond seen to be cleaved in this precursor structure and of the 263-264 peptide bond have suggested factors that may govern the autocatalytic mechanism.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Cartoon of PGA showing the secondary structural elements, a-helices and b-sheets. (a) Mature enzyme [McVey 1999]. (b) Precursor: the A domain is shown in green, the B domain in blue and the linker peptide is in red. The N-terminal nucleophilic serine residue is also drawn in yellow as a ball and stick model. Figure 1, Figure 2, Figure 5 and Figure 7 were created with the program BOBSCRIPT [Esnouf 1997]. 		Figure 7.
Figure 7. Final 2F[o] -F[c] electron density for residues Tyr260 to Met266, contoured at a level of 1s. The extent of the structural rearrangement in the environment surrounding the cleavage between Tyr260 and Pro261, some 8 Å apart, is evident. The electron density for Pro261 is poorly defined and consistent with some disorder and high thermal mobility (B-factor of >40 Å2). The close hydrogen bond between the precursor conformation of the Ser264 Og and Gly263 is shown as a broken line. The rest of the precursor structure is depicted as a C^a trace and coloured according to domain, as in Figure 1.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 302, 887-898) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20128906 H.Maresová, Z.Marková, R.Valesová, J.Sklenár, and P.Kyslík (2010).
Heterologous expression of leader-less pga gene in Pichia pastoris: intracellular production of prokaryotic enzyme.
  BMC Biotechnol, 10, 7.  
20223213 M.Bokhove, H.Yoshida, C.M.Hensgens, J.M.van der Laan, J.D.Sutherland, and B.W.Dijkstra (2010).
Structures of an isopenicillin N converting Ntn-hydrolase reveal different catalytic roles for the active site residues of precursor and mature enzyme.
  Structure, 18, 301-308.
PDB codes: 2x1c 2x1d 2x1e
20080736 M.Bokhove, P.N.Jimenez, W.J.Quax, and B.W.Dijkstra (2010).
The quorum-quenching N-acyl homoserine lactone acylase PvdQ is an Ntn-hydrolase with an unusual substrate-binding pocket.
  Proc Natl Acad Sci U S A, 107, 686-691.
PDB codes: 2wyb 2wyc 2wyd 2wye
20224955 R.Yuryev, V.Kasche, Z.Ignatova, and B.Galunsky (2010).
Improved A. faecalis penicillin amidase mutant retains the thermodynamic and pH stability of the wild type enzyme.
  Protein J, 29, 181-187.  
18334484 K.Michalska, A.Hernandez-Santoyo, and M.Jaskolski (2008).
The mechanism of autocatalytic activation of plant-type L-asparaginases.
  J Biol Chem, 283, 13388-13397.
PDB code: 3c17
18824507 O.D.Ekici, M.Paetzel, and R.E.Dalbey (2008).
Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration.
  Protein Sci, 17, 2023-2037.  
18287282 Y.Sun, and H.C.Guo (2008).
Structural constraints on autoprocessing of the human nucleoporin Nup98.
  Protein Sci, 17, 494-505.
PDB codes: 2q5x 2q5y
17845725 D.A.Cecchini, I.Serra, D.Ubiali, M.Terreni, and A.M.Albertini (2007).
New active site oriented glyoxyl-agarose derivatives of Escherichia coli penicillin G acylase.
  BMC Biotechnol, 7, 54.  
17360274 Y.H.Dong, L.Y.Wang, and L.H.Zhang (2007).
Quorum-quenching microbial infections: mechanisms and implications.
  Philos Trans R Soc Lond B Biol Sci, 362, 1201-1211.  
16461666 J.J.Huang, A.Petersen, M.Whiteley, and J.R.Leadbetter (2006).
Identification of QuiP, the product of gene PA1032, as the second acyl-homoserine lactone acylase of Pseudomonas aeruginosa PAO1.
  Appl Environ Microbiol, 72, 1190-1197.  
16446446 J.K.Kim, I.S.Yang, H.J.Shin, K.J.Cho, E.K.Ryu, S.H.Kim, S.S.Park, and K.H.Kim (2006).
Insight into autoproteolytic activation from the structure of cephalosporin acylase: a protein with two proteolytic chemistries.
  Proc Natl Acad Sci U S A, 103, 1732-1737.
PDB codes: 2adv 2ae3 2ae4 2ae5
17137296 N.Narayanan, Y.Xu, and C.P.Chou (2006).
High-level gene expression for recombinant penicillin acylase production using the araB promoter system in Escherichia coli.
  Biotechnol Prog, 22, 1518-1523.  
16411086 Y.Xu, S.Rosenkranz, C.L.Weng, J.M.Scharer, M.Moo-Young, and C.P.Chou (2006).
Characterization of the T7 promoter system for expressing penicillin acylase in Escherichia coli.
  Appl Microbiol Biotechnol, 72, 529-536.  
16332894 F.Scaramozzino, I.Estruch, P.Rossolillo, M.Terreni, and A.M.Albertini (2005).
Improvement of catalytic properties of Escherichia coli penicillin G acylase immobilized on glyoxyl agarose by addition of a six-amino-acid tag.
  Appl Environ Microbiol, 71, 8937-8940.  
  16508111 P.M.Chandra, J.A.Brannigan, A.Prabhune, A.Pundle, J.P.Turkenburg, G.G.Dodson, and C.G.Suresh (2005).
Cloning, preparation and preliminary crystallographic studies of penicillin V acylase autoproteolytic processing mutants.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 124-127.
PDB code: 2iwm
15870355 S.Y.Park, H.O.Kang, H.S.Jang, J.K.Lee, B.T.Koo, and D.Y.Yum (2005).
Identification of extracellular N-acylhomoserine lactone acylase from a Streptomyces sp. and its application to quorum quenching.
  Appl Environ Microbiol, 71, 2632-2641.  
15801782 V.Kasche, Z.Ignatova, H.Märkl, W.Plate, N.Punckt, D.Schmidt, K.Wiegandt, and B.Ernst (2005).
Ca2+ is a cofactor required for membrane transport and maturation and is a yield-determining factor in high cell density penicillin amidase production.
  Biotechnol Prog, 21, 432-438.  
15028709 B.Galán, J.L.García, and M.A.Prieto (2004).
The PaaX repressor, a link between penicillin G acylase and the phenylacetyl-coenzyme A catabolon of Escherichia coli W.
  J Bacteriol, 186, 2215-2220.  
15128530 G.Cai, S.Zhu, S.Yang, G.Zhao, and W.Jiang (2004).
Cloning, overexpression, and characterization of a novel thermostable penicillin G acylase from Achromobacter xylosoxidans: probing the molecular basis for its high thermostability.
  Appl Environ Microbiol, 70, 2764-2770.  
15133167 G.Flores, X.Soberón, and J.Osuna (2004).
Production of a fully functional, permuted single-chain penicillin G acylase.
  Protein Sci, 13, 1677-1683.  
  15374664 M.A.Prieto, B.Galán, B.Torres, A.Ferrández, C.Fernández, B.Miñambres, J.L.García, and E.Díaz (2004).
Aromatic metabolism versus carbon availability: the regulatory network that controls catabolism of less-preferred carbon sources in Escherichia coli.
  FEMS Microbiol Rev, 28, 503-518.  
14622260 V.Kasche, B.Galunsky, and Z.Ignatova (2003).
Fragments of pro-peptide activate mature penicillin amidase of Alcaligenes faecalis.
  Eur J Biochem, 270, 4721-4728.  
12535081 Y.H.Lin, J.L.Xu, J.Hu, L.H.Wang, S.L.Ong, J.R.Leadbetter, and L.H.Zhang (2003).
Acyl-homoserine lactone acylase from Ralstonia strain XJ12B represents a novel and potent class of quorum-quenching enzymes.
  Mol Microbiol, 47, 849-860.  
12571052 Z.Ignatova, A.Mahsunah, M.Georgieva, and V.Kasche (2003).
Improvement of posttranslational bottlenecks in the production of penicillin amidase in recombinant Escherichia coli strains.
  Appl Environ Microbiol, 69, 1237-1245.  
12207027 H.Suzuki, and H.Kumagai (2002).
Autocatalytic processing of gamma-glutamyltranspeptidase.
  J Biol Chem, 277, 43536-43543.  
11729263 E.Díaz, A.Ferrández, M.A.Prieto, and J.L.García (2001).
Biodegradation of aromatic compounds by Escherichia coli.
  Microbiol Mol Biol Rev, 65, 523.  
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 codes are shown on the right.

 

spacer
spacer