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PDBsum entry 1ju3

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Hydrolase PDB id
1ju3
Jmol
Contents
Protein chain
570 a.a. *
Ligands
PBC
Waters ×544
* Residue conservation analysis
PDB id:
1ju3
Name: Hydrolase
Title: Bacterial cocaine esterase complex with transition state analog
Structure: Cocaine esterase. Chain: a. Engineered: yes
Source: Rhodococcus sp. Mb1. Organism_taxid: 51612. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.58Å     R-factor:   0.199     R-free:   0.214
Authors: N.A.Larsen,J.M.Turner,J.Stevens,S.J.Rosser,A.Basran, R.A.Lerner,N.C.Bruce,I.A.Wilson
Key ref:
N.A.Larsen et al. (2002). Crystal structure of a bacterial cocaine esterase. Nat Struct Biol, 9, 17-21. PubMed id: 11742345 DOI: 10.1038/nsb742
Date:
23-Aug-01     Release date:   21-Dec-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9L9D7  (COCE_RHOSM) -  Cocaine esterase
Seq:
Struc:
 
Seq:
Struc:
574 a.a.
570 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.1.84  - Cocaine esterase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cocaine + H2O = ecgonine methyl ester + benzoate
Cocaine
+ H(2)O
= ecgonine methyl ester
+ benzoate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     cocaine catabolic process   2 terms 
  Biochemical function     carboxylic ester hydrolase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nsb742 Nat Struct Biol 9:17-21 (2002)
PubMed id: 11742345  
 
 
Crystal structure of a bacterial cocaine esterase.
N.A.Larsen, J.M.Turner, J.Stevens, S.J.Rosser, A.Basran, R.A.Lerner, N.C.Bruce, I.A.Wilson.
 
  ABSTRACT  
 
Here we report the first structure of a cocaine-degrading enzyme. The bacterial esterase, cocE, hydrolyzes pharmacologically active (-)-cocaine to a non-psychoactive metabolite with a rate faster than any other reported cocaine esterase (kcat = 7.8 s-1 and KM = 640 nM). Because of the high catalytic proficiency of cocE, it is an attractive candidate for novel protein-based therapies for cocaine overdose. The crystal structure of cocE, solved by multiple anomalous dispersion (MAD) methods, reveals that cocE is a serine esterase composed of three domains: (i) a canonical alpha/beta hydrolase fold (ii) an alpha-helical domain that caps the active site and (iii) a jelly-roll-like beta-domain that interacts extensively with the other two domains. The active site was identified within the interface of all three domains by analysis of the crystal structures of transition state analog adduct and product complexes, which were refined at 1.58 A and 1.63 A resolution, respectively. These structural studies suggest that substrate recognition arises partly from interactions between the benzoyl moiety of cocaine and a highly evolved specificity pocket.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo views of the active site of cocE. The color scheme and secondary structure is the same as in Fig. 2a. The side chains that contact the bound ligands are shown in brown with red oxygens and blue nitrogens. a, The product complex. Hydrolysis of the acyl enzyme gives the product complex with benzoic acid. After hydrolysis, Ser 117 swings away from the specificity pocket, and His 287 rotates towards DOM3, obliterating the productive catalytic triad configuration. Hydrogen bonds within the triad are mediated by a water molecule. The [A]-weighted^35 2F[o] - F[c] electron density map contoured at 2.0 is shown around the Ser residue and benzoic acid. b, The tetrahedral analog adduct complex. This complex was formed by soaking crystals with phenyl boronic acid. The compound forms a covalent adduct with Ser 117, and the residues of the catalytic triad align themselves in a productive configuration. The [A]-weighted^35 2F[o] - F[c] electron density map contoured at 1.5 is shown around the Ser adduct.
Figure 4.
Figure 4. Proposed mechanism for acyl intermediate hydrolysis. The hydrogens have been assigned according to the hydrogen bond donor-acceptors in the active site. The covalent acyl intermediate (top left) is proposed to go through a tetrahedral transition state (top right) on its way to product (bottom left). The boron inhibitor (bottom right) mimics the tetrahedral transition-state of the acyl enzyme. The pro-R hydroxyl of the boron-adduct is probably positioned where the attacking water would be in the tetrahedral intermediate. In the product complex, whether the water molecule HOH donates or accepts a hydrogen from Ser 117 is unclear.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 17-21) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21289605 G.T.Collins, K.A.Carey, D.Narasimhan, J.Nichols, A.A.Berlin, N.W.Lukacs, R.K.Sunahara, J.H.Woods, and M.C.Ko (2011).
Amelioration of the cardiovascular effects of cocaine in rhesus monkeys by a long-acting mutant form of cocaine esterase.
  Neuropsychopharmacology, 36, 1047-1059.  
20436035 D.Narasimhan, M.R.Nance, D.Gao, M.C.Ko, J.Macdonald, P.Tamburi, D.Yoon, D.M.Landry, J.H.Woods, C.G.Zhan, J.J.Tesmer, and R.K.Sunahara (2010).
Structural analysis of thermostabilizing mutations of cocaine esterase.
  Protein Eng Des Sel, 23, 537-547.
PDB codes: 3i2f 3i2g 3i2h 3i2i 3i2j 3i2k
19857534 J.B.Park, Y.M.Kwon, T.Y.Lee, R.Brim, M.C.Ko, R.K.Sunahara, J.H.Woods, and V.C.Yang (2010).
PEGylation of bacterial cocaine esterase for protection against protease digestion and immunogenicity.
  J Control Release, 142, 174-179.  
18987161 D.Gao, D.L.Narasimhan, J.Macdonald, R.Brim, M.C.Ko, D.W.Landry, J.H.Woods, R.K.Sunahara, and C.G.Zhan (2009).
Thermostable variants of cocaine esterase for long-time protection against cocaine toxicity.
  Mol Pharmacol, 75, 318-323.  
  20161378 F.Zheng, and C.G.Zhan (2009).
Recent progress in protein drug design and discovery with a focus on novel approaches to the development of anticocaine medications.
  Future Med Chem, 1, 515-528.  
19710369 G.T.Collins, R.L.Brim, D.Narasimhan, M.C.Ko, R.K.Sunahara, C.G.Zhan, and J.H.Woods (2009).
Cocaine esterase prevents cocaine-induced toxicity and the ongoing intravenous self-administration of cocaine in rats.
  J Pharmacol Exp Ther, 331, 445-455.  
  20216936 J.S.Stehouwer, and M.M.Goodman (2009).
Fluorine-18 Radiolabeled PET Tracers for Imaging Monoamine Transporters: Dopamine, Serotonin, and Norepinephrine.
  PET Clin, 4, 101-128.  
19217723 M.C.Ko, D.Narasimhan, A.A.Berlin, N.W.Lukacs, R.K.Sunahara, and J.H.Woods (2009).
Effects of cocaine esterase following its repeated administration with cocaine in mice.
  Drug Alcohol Depend, 101, 202-209.  
18710224 F.Zheng, W.Yang, M.C.Ko, J.Liu, H.Cho, D.Gao, M.Tong, H.H.Tai, J.H.Woods, and C.G.Zhan (2008).
Most efficient cocaine hydrolase designed by virtual screening of transition states.
  J Am Chem Soc, 130, 12148-12155.  
18199998 S.Brimijoin, Y.Gao, J.J.Anker, L.A.Gliddon, D.Lafleur, R.Shah, Q.Zhao, M.Singh, and M.E.Carroll (2008).
A cocaine hydrolase engineered from human butyrylcholinesterase selectively blocks cocaine toxicity and reinstatement of drug seeking in rats.
  Neuropsychopharmacology, 33, 2715-2725.  
17337538 G.Rivera-Cancel, D.Bocioaga, and A.G.Hay (2007).
Bacterial degradation of N,N-diethyl-m-toluamide (DEET): cloning and heterologous expression of DEET hydrolase.
  Appl Environ Microbiol, 73, 3105-3108.  
17114567 M.C.Ko, L.D.Bowen, D.Narasimhan, A.A.Berlin, N.W.Lukacs, R.K.Sunahara, Z.D.Cooper, and J.H.Woods (2007).
Cocaine esterase: interactions with cocaine and immune responses in mice.
  J Pharmacol Exp Ther, 320, 926-933.  
  17620715 S.Kim, S.Joo, H.C.Yoon, Y.Ryu, K.K.Kim, and T.D.Kim (2007).
Purification, crystallization and preliminary crystallographic analysis of Est25: a ketoprofen-specific hormone-sensitive lipase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 579-581.  
  18084077 Y.Xie, C.Takemoto, S.Kishishita, T.Uchikubo-Kamo, K.Murayama, L.Chen, Z.J.Liu, B.C.Wang, M.Manzoku, A.Ebihara, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2007).
Structure of the minimized alpha/beta-hydrolase fold protein from Thermus thermophilus HB8.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 993-997.
PDB code: 2dst
17131989 C.J.Rogers, L.M.Eubanks, T.J.Dickerson, and K.D.Janda (2006).
Unexpected acetylcholinesterase activity of cocaine esterases.
  J Am Chem Soc, 128, 15364-15365.  
16847603 C.Zimmer, T.Platz, N.Cadez, F.Giffhorn, and G.W.Kohring (2006).
A cold active (2R,3R)-(-)-di-O-benzoyl-tartrate hydrolyzing esterase from Rhodotorula mucilaginosa.
  Appl Microbiol Biotechnol, 73, 132-140.  
16011362 C.J.Rogers, J.M.Mee, G.F.Kaufmann, T.J.Dickerson, and K.D.Janda (2005).
Toward cocaine esterase therapeutics.
  J Am Chem Soc, 127, 10016-10017.  
15819895 P.Rigolet, X.G.Xi, S.Rety, and J.F.Chich (2005).
The structural comparison of the bacterial PepX and human DPP-IV reveals sites for the design of inhibitors of PepX activity.
  FEBS J, 272, 2050-2059.  
15296741 M.Bartlam, G.Wang, H.Yang, R.Gao, X.Zhao, G.Xie, S.Cao, Y.Feng, and Z.Rao (2004).
Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1.
  Structure, 12, 1481-1488.
PDB codes: 1ve6 1ve7
15319068 Y.Danger, A.Devys, C.Gadjou, H.Galons, D.Blanchard, and G.Folléa (2004).
Development of monoclonal antibodies directed against cocaine and cocaethylene: potential new tools for immunotherapy.
  Hybrid Hybridomics, 23, 212-218.  
12679808 S.Bencharit, C.L.Morton, Y.Xue, P.M.Potter, and M.R.Redinbo (2003).
Structural basis of heroin and cocaine metabolism by a promiscuous human drug-processing enzyme.
  Nat Struct Biol, 10, 349-356.
PDB codes: 1mx5 1mx9
15618752 S.R.Kim, T.Nakamura, Y.Saito, K.Sai, T.Nakajima, H.Saito, K.Shirao, H.Minami, A.Ohtsu, T.Yoshida, N.Saijo, S.Ozawa, and J.Sawada (2003).
Twelve novel single nucleotide polymorphisms in the CES2 gene encoding human carboxylesterase 2 (hCE-2).
  Drug Metab Pharmacokinet, 18, 327-332.  
12057681 D.A.Rathbone, and N.C.Bruce (2002).
Microbial transformation of alkaloids.
  Curr Opin Microbiol, 5, 274-281.  
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.