PDBsum entry 1ybq

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Hydrolase PDB id
Protein chains
389 a.a. *
BDH ×2
_ZN ×4
Waters ×241
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of escherichia coli isoaspartyl dipeptidas d285n complexed with beta-aspartylhistidine
Structure: Isoaspartyl dipeptidase. Chain: a. Engineered: yes. Mutation: yes. Isoaspartyl dipeptidase. Chain: b. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: iada. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PDB file)
2.00Å     R-factor:   0.185     R-free:   0.243
Authors: R.Marti-Arbona,V.Fresquet,J.B.Thoden,M.L.Davis,H.M.Holden,F.
Key ref:
R.Martí-Arbona et al. (2005). Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli. Biochemistry, 44, 7115-7124. PubMed id: 15882050 DOI: 10.1021/bi050008r
21-Dec-04     Release date:   26-Apr-05    
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Protein chains
Pfam   ArchSchema ?
P39377  (IADA_ECOLI) -  Isoaspartyl dipeptidase
390 a.a.
389 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     proteolysis   1 term 
  Biochemical function     hydrolase activity     7 terms  


DOI no: 10.1021/bi050008r Biochemistry 44:7115-7124 (2005)
PubMed id: 15882050  
Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli.
R.Martí-Arbona, V.Fresquet, J.B.Thoden, M.L.Davis, H.M.Holden, F.M.Raushel.
Isoaspartyl dipeptidase (IAD) is a member of the amidohydrolase superfamily and catalyzes the hydrolytic cleavage of beta-aspartyl dipeptides. Structural studies of the wild-type enzyme have demonstrated that the active site consists of a binuclear metal center positioned at the C-terminal end of a (beta/alpha)(8)-barrel domain. Steady-state kinetic parameters for the hydrolysis of beta-aspartyl dipeptides were obtained at pH 8.1. The pH-rate profiles for the hydrolysis of beta-Asp-Leu were obtained for the Zn/Zn-, Co/Co-, Ni/Ni-, and Cd/Cd-substituted forms of IAD. Bell-shaped profiles were observed for k(cat) and k(cat)/K(m) as a function of pH for all four metal-substituted forms. The pK(a) of the group that must be unprotonated for catalytic activity varied according to the specific metal ion bound in the active site, whereas the pK(a) of the group that must be protonated for catalytic activity was relatively independent of the specific metal ion present. The identity of the group that must be unprotonated for catalytic activity was consistent with the hydroxide that bridges the two divalent cations of the binuclear metal center. The identity of the group that must be protonated for activity was consistent with the free alpha-amino group of the dipeptide substrate. Kinetic constants were obtained for the mutant enzymes at conserved residues Glu77, Tyr137, Arg169, Arg233, Asp285, and Ser289. The catalytic properties of the wild-type and mutant enzymes, coupled with the X-ray crystal structure of the D285N mutant complexed with beta-Asp-His, are consistent with a chemical reaction mechanism for the hydrolysis of dipeptides that is initiated by the polarization of the amide bond via complexation to the beta-metal ion of the binuclear metal center. Nucleophilic attack by the bridging hydroxide is facilitated by abstraction of its proton by the side chain carboxylate of Asp285. Collapse of the tetrahedral intermediate and cleavage of the carbon-nitrogen bond occur with donation of a proton from the protonated form of Asp285.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20000809 J.A.Cummings, T.T.Nguyen, A.A.Fedorov, P.Kolb, C.Xu, E.V.Fedorov, B.K.Shoichet, D.P.Barondeau, S.C.Almo, and F.M.Raushel (2010).
Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase .
  Biochemistry, 49, 611-622.
PDB codes: 3id7 3itc 3k5x
19358546 D.F.Xiang, C.Xu, D.Kumaran, A.C.Brown, J.M.Sauder, S.K.Burley, S.Swaminathan, and F.M.Raushel (2009).
Functional annotation of two new carboxypeptidases from the amidohydrolase superfamily of enzymes.
  Biochemistry, 48, 4567-4576.
PDB code: 2qs8
19281183 D.F.Xiang, Y.Patskovsky, C.Xu, A.J.Meyer, J.M.Sauder, S.K.Burley, S.C.Almo, and F.M.Raushel (2009).
Functional identification of incorrectly annotated prolidases from the amidohydrolase superfamily of enzymes.
  Biochemistry, 48, 3730-3742.
PDB codes: 3be7 3dug
19678710 T.T.Nguyen, A.A.Fedorov, L.Williams, E.V.Fedorov, Y.Li, C.Xu, S.C.Almo, and F.M.Raushel (2009).
The mechanism of the reaction catalyzed by uronate isomerase illustrates how an isomerase may have evolved from a hydrolase within the amidohydrolase superfamily.
  Biochemistry, 48, 8879-8890.
PDB codes: 3hk5 3hk7 3hk8 3hk9 3hka
18702530 J.Kim, P.C.Tsai, S.L.Chen, F.Himo, S.C.Almo, and F.M.Raushel (2008).
Structure of diethyl phosphate bound to the binuclear metal center of phosphotriesterase.
  Biochemistry, 47, 9497-9504.
PDB codes: 2o4q 3cak 3cs2
17567047 R.S.Hall, D.F.Xiang, C.Xu, and F.M.Raushel (2007).
N-Acetyl-D-glucosamine-6-phosphate deacetylase: substrate activation via a single divalent metal ion.
  Biochemistry, 46, 7942-7952.  
16517602 B.Lohkamp, B.Andersen, J.Piskur, and D.Dobritzsch (2006).
The crystal structures of dihydropyrimidinases reaffirm the close relationship between cyclic amidohydrolases and explain their substrate specificity.
  J Biol Chem, 281, 13762-13776.
PDB codes: 2ftw 2fty 2fvk 2fvm
16087890 D.Liu, B.W.Lepore, G.A.Petsko, P.W.Thomas, E.M.Stone, W.Fast, and D.Ringe (2005).
Three-dimensional structure of the quorum-quenching N-acyl homoserine lactone hydrolase from Bacillus thuringiensis.
  Proc Natl Acad Sci U S A, 102, 11882-11887.
PDB code: 2a7m
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