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PDBsum entry 1m21

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protein ligands Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
1m21
Jmol
Contents
Protein chains
487 a.a. *
Ligands
PHE-CSI-LEU-PHA ×2
Waters ×431
* Residue conservation analysis
PDB id:
1m21
Name: Hydrolase/hydrolase inhibitor
Title: Crystal structure analysis of the peptide amidase pam in com the competitive inhibitor chymostatin
Structure: Peptide amidase. Chain: a, b. Synonym: pam. Engineered: yes. Chymostatin. Chain: c, d. Engineered: yes
Source: Stenotrophomonas maltophilia. Organism_taxid: 40324. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes
Resolution:
1.80Å     R-factor:   0.203     R-free:   0.217
Authors: J.Labahn,S.Neumann,G.Buldt,M.-R.Kula,J.Granzin
Key ref:
J.Labahn et al. (2002). An alternative mechanism for amidase signature enzymes. J Mol Biol, 322, 1053-1064. PubMed id: 12367528 DOI: 10.1016/S0022-2836(02)00886-0
Date:
21-Jun-02     Release date:   16-Oct-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8RJN5  (Q8RJN5_STEMA) -  Peptide amidase
Seq:
Struc:
 
Seq:
Struc:
540 a.a.
487 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     carbon-nitrogen ligase activity, with glutamine as amido-N-donor     1 term  

 

 
DOI no: 10.1016/S0022-2836(02)00886-0 J Mol Biol 322:1053-1064 (2002)
PubMed id: 12367528  
 
 
An alternative mechanism for amidase signature enzymes.
J.Labahn, S.Neumann, G.Büldt, M.R.Kula, J.Granzin.
 
  ABSTRACT  
 
The peptide amidase from Stenotrophomonas maltophilia catalyses predominantly the hydrolysis of the C-terminal amide bond in peptide amides. Peptide bonds or amide functions in amino acid side-chains are not hydrolysed. This specificity makes peptide amidase (Pam) interesting for different biotechnological applications. Pam belongs to the amidase signature (AS) family. It is the first protein within this family whose tertiary structure has been solved. The structure of the native Pam has been determined with a resolution of 1.4A and in complex with the competitive inhibitor chymostatin at a resolution of 1.8A. Chymostatin, which forms acyl adducts with many serine proteases, binds non-covalently to this enzyme.Pam folds as a very compact single-domain protein. The AS sequence represents a core domain that is covered by alpha-helices. This AS domain contains the catalytic residues. It is topologically homologous to the phosphoinositol phosphatase domain.The structural data do not support the recently proposed Ser-Lys catalytic dyad mechanism for AS enzymes. Our results are in agreement with the role of Ser226 as the primary nucleophile but differ concerning the roles of Ser202 and Lys123: Ser202, with direct contact both to the substrate molecule and to Ser226, presumably serves as an acid/bases catalyst. Lys123, with direct contact to Ser202 but no contact to Ser226 or the substrate molecule, most likely acts as an acid catalyst.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Fold of Pam: ribbon diagram with b-strands in blue, a-helices in red, and coils in gray. The inhibitor chymostatin (Cst) is colored by atom-type. (a) Stereo view into the active site. The partially disordered loop structure of the native Pam is despicted in black. (b) View rotated 90° around the vertical axis. The channel from Cst(O1) (active site) to the opposite side of the protein is highlighted by a dark blue net. (c) Fold topology of Pam. The amidase signature sequence is indicated by the gray background. The signature domain includes structure elements 5-13.
Figure 4.
Figure 4. (a) Stereo view of an F[o] -F[c] map contoured at 2.5s calculated with native phases for the complex Pam-Cst. (b) Stereo view of the key residues that interact with Cst (molecule A). (c) Bias-reduced electron density (see Materials and Methods) at 1.4s around the nucleophile Ser226 shows no covalent bond of chymostatin to Pam.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 322, 1053-1064) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19889645 K.Yasuhira, N.Shibata, G.Mongami, Y.Uedo, Y.Atsumi, Y.Kawashima, A.Hibino, Y.Tanaka, Y.H.Lee, D.Kato, M.Takeo, Y.Higuchi, and S.Negoro (2010).
X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation.
  J Biol Chem, 285, 1239-1248.
PDB codes: 3a2p 3a2q
19520089 J.Wu, W.Bu, K.Sheppard, M.Kitabatake, S.T.Kwon, D.Söll, and J.L.Smith (2009).
Insights into tRNA-dependent amidotransferase evolution and catalysis from the structure of the Aquifex aeolicus enzyme.
  J Mol Biol, 391, 703-716.
PDB codes: 3h0l 3h0m 3h0r
  19478917 L.Politi, E.Chiancone, L.Giangiacomo, L.Cervoni, A.Scotto D'Abusco, S.Scorsino, and R.Scandurra (2009).
pH-, temperature- and ion-dependent oligomerization of Sulfolobus solfataricus recombinant amidase: a study with site-specific mutants.
  Archaea, 2, 221-231.  
19722626 M.Mileni, J.Garfunkle, J.K.DeMartino, B.F.Cravatt, D.L.Boger, and R.C.Stevens (2009).
Binding and inactivation mechanism of a humanized fatty acid amide hydrolase by alpha-ketoheterocycle inhibitors revealed from cocrystal structures.
  J Am Chem Soc, 131, 10497-10506.
PDB codes: 2wj1 2wj2
19074156 P.F.Wang, A.Yep, G.L.Kenyon, and M.J.McLeish (2009).
Using directed evolution to probe the substrate specificity of mandelamide hydrolase.
  Protein Eng Des Sel, 22, 103-110.  
19801664 S.C.Kim, L.Kang, S.Nagaraj, E.B.Blancaflor, K.S.Mysore, and K.D.Chapman (2009).
Mutations in Arabidopsis fatty acid amide hydrolase reveal that catalytic activity influences growth but not sensitivity to abscisic acid or pathogens.
  J Biol Chem, 284, 34065-34074.  
18942140 S.Heumann, A.Eberl, G.Fischer-Colbrie, H.Pobeheim, F.Kaufmann, D.Ribitsch, A.Cavaco-Paulo, and G.M.Guebitz (2009).
A novel aryl acylamidase from Nocardia farcinica hydrolyses polyamide.
  Biotechnol Bioeng, 102, 1003-1011.  
19085025 W.W.Han, Y.Wang, Y.H.Zhou, Y.Yao, Z.S.Li, and Y.Feng (2009).
Understanding structural/functional properties of amidase from Rhodococcus erythropolis by computational approaches.
  J Mol Model, 15, 481-487.  
17712824 G.Labar, and C.Michaux (2007).
Fatty acid amide hydrolase: from characterization to therapeutics.
  Chem Biodivers, 4, 1882-1902.  
17077089 Y.S.Yun, W.Lee, S.Shin, B.H.Oh, and K.Y.Choi (2006).
Arg-158 is critical in both binding the substrate and stabilizing the transition-state oxyanion for the enzymatic reaction of malonamidase E2.
  J Biol Chem, 281, 40057-40064.  
  16243781 A.S.D'Abusco, R.Casadio, G.Tasco, L.Giangiacomo, A.Giartosio, V.Calamia, S.Di Marco, R.Chiaraluce, V.Consalvi, R.Scandurra, and L.Politi (2005).
Oligomerization of Sulfolobus solfataricus signature amidase is promoted by acidic pH and high temperature.
  Archaea, 1, 411-423.  
16002239 G.Cai, S.Zhu, X.Wang, and W.Jiang (2005).
Cloning, sequence analysis and expression of the gene encoding a novel wide-spectrum amidase belonging to the amidase signature superfamily from Achromobacter xylosoxidans.
  FEMS Microbiol Lett, 249, 15-21.  
15611111 L.Feng, K.Sheppard, D.Tumbula-Hansen, and D.Söll (2005).
Gln-tRNAGln formation from Glu-tRNAGln requires cooperation of an asparaginase and a Glu-tRNAGln kinase.
  J Biol Chem, 280, 8150-8155.  
15480636 L.Krieg, H.Slusarczyk, S.Verseck, and M.R.Kula (2005).
Identification and characterization of a novel D-amidase gene from Variovorax paradoxus and its expression in Escherichia coli.
  Appl Microbiol Biotechnol, 66, 542-550.  
15952893 M.K.McKinney, and B.F.Cravatt (2005).
Structure and function of fatty acid amide hydrolase.
  Annu Rev Biochem, 74, 411-432.  
15901697 N.Shapir, M.J.Sadowsky, and L.P.Wackett (2005).
Purification and characterization of allophanate hydrolase (AtzF) from Pseudomonas sp. strain ADP.
  J Bacteriol, 187, 3731-3738.  
12765833 D.J.Rigden, M.J.Jedrzejas, and M.Y.Galperin (2003).
Amidase domains from bacterial and phage autolysins define a family of gamma-D,L-glutamate-specific amidohydrolases.
  Trends Biochem Sci, 28, 230-234.  
12734197 M.K.McKinney, and B.F.Cravatt (2003).
Evidence for distinct roles in catalysis for residues of the serine-serine-lysine catalytic triad of fatty acid amide hydrolase.
  J Biol Chem, 278, 37393-37399.  
12711609 S.Shin, Y.S.Yun, H.M.Koo, Y.S.Kim, K.Y.Choi, and B.H.Oh (2003).
Characterization of a novel Ser-cisSer-Lys catalytic triad in comparison with the classical Ser-His-Asp triad.
  J Biol Chem, 278, 24937-24943.
PDB codes: 1o9n 1o9o 1o9p 1o9q 1obi 1obj 1obk 1obl 1och 1ock 1ocl 1ocm
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.