Crystal structure of renal dipeptidase from Streptomyces coelicolor A3(2)

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

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Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase .

Cummings, J.A.Nguyen, T.T.Fedorov, A.A.Kolb, P.Xu, C.Fedorov, E.V.Shoichet, B.K.Barondeau, D.P.Almo, S.C.Raushel, F.M.

(2010) Biochemistry 49: 611-622

  • DOI: https://doi.org/10.1021/bi901935y
  • Primary Citation of Related Structures:  
    3ID7, 3ITC, 3K5X

  • PubMed Abstract: 

    Human renal dipeptidase, an enzyme associated with glutathione metabolism and the hydrolysis of beta-lactams, is similar in sequence to a cluster of approximately 400 microbial proteins currently annotated as nonspecific dipeptidases within the amidohydrolase superfamily. The closest homologue to the human renal dipeptidase from a fully sequenced microbe is Sco3058 from Streptomyces coelicolor. Dipeptide substrates of Sco3058 were identified by screening a comprehensive series of l-Xaa-l-Xaa, l-Xaa-d-Xaa, and d-Xaa-l-Xaa dipeptide libraries. The substrate specificity profile shows that Sco3058 hydrolyzes a broad range of dipeptides with a marked preference for an l-amino acid at the N-terminus and a d-amino acid at the C-terminus. The best substrate identified was l-Arg-d-Asp (k(cat)/K(m) = 7.6 x 10(5) M(-1) s(-1)). The three-dimensional structure of Sco3058 was determined in the absence and presence of the inhibitors citrate and a phosphinate mimic of l-Ala-d-Asp. The enzyme folds as a (beta/alpha)(8) barrel, and two zinc ions are bound in the active site. Site-directed mutagenesis was used to probe the importance of specific residues that have direct interactions with the substrate analogues in the active site (Asp-22, His-150, Arg-223, and Asp-320). The solvent viscosity and kinetic effects of D(2)O indicate that substrate binding is relatively sticky and that proton transfers do not occurr during the rate-limiting step. A bell-shaped pH-rate profile for k(cat) and k(cat)/K(m) indicated that one group needs to be deprotonated and a second group must be protonated for optimal turnover. Computational docking of high-energy intermediate forms of l/d-Ala-l/d-Ala to the three-dimensional structure of Sco3058 identified the structural determinants for the stereochemical preferences for substrate binding and turnover.

  • Organizational Affiliation

    Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77843, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidase400Streptomyces coelicolorMutation(s): 0 
Gene Names: SCO3058SCBAC19G2.13c
Find proteins for Q93J45 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q93J45 
Go to UniProtKB:  Q93J45
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93J45
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.747α = 90
b = 96.747β = 90
c = 104.721γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations