3N2C

Crystal structure of prolidase eah89906 complexed with n-methylphosphonate-l-proline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily .

Xiang, D.F.Patskovsky, Y.Xu, C.Fedorov, A.A.Fedorov, E.V.Sisco, A.A.Sauder, J.M.Burley, S.K.Almo, S.C.Raushel, F.M.

(2010) Biochemistry 49: 6791-6803

  • DOI: 10.1021/bi100897u
  • Primary Citation of Related Structures:  3FEQ, 3MKV, 3MTW

  • PubMed Abstract: 
  • Two uncharacterized enzymes from the amidohydrolase superfamily belonging to cog1228 were cloned, expressed, and purified to homogeneity. The two proteins, Sgx9260c ( gi|44242006 ) and Sgx9260b ( gi|44479596 ), were derived from environmental DNA sam ...

    Two uncharacterized enzymes from the amidohydrolase superfamily belonging to cog1228 were cloned, expressed, and purified to homogeneity. The two proteins, Sgx9260c ( gi|44242006 ) and Sgx9260b ( gi|44479596 ), were derived from environmental DNA samples originating from the Sargasso Sea. The catalytic function and substrate profiles for Sgx9260c and Sgx9260b were determined using a comprehensive library of dipeptides and N-acyl derivative of l-amino acids. Sgx9260c catalyzes the hydrolysis of Gly-l-Pro, l-Ala-l-Pro, and N-acyl derivatives of l-Pro. The best substrate identified to date is N-acetyl-l-Pro with a value of k(cat)/K(m) of 3 x 10(5) M(-1) s(-1). Sgx9260b catalyzes the hydrolysis of l-hydrophobic l-Pro dipeptides and N-acyl derivatives of l-Pro. The best substrate identified to date is N-propionyl-l-Pro with a value of k(cat)/K(m) of 1 x 10(5) M(-1) s(-1). Three-dimensional structures of both proteins were determined by X-ray diffraction methods (PDB codes 3MKV and 3FEQ ). These proteins fold as distorted (beta/alpha)(8)-barrels with two divalent cations in the active site. The structure of Sgx9260c was also determined as a complex with the N-methylphosphonate derivative of l-Pro (PDB code 3N2C ). In this structure the phosphonate moiety bridges the binuclear metal center, and one oxygen atom interacts with His-140. The alpha-carboxylate of the inhibitor interacts with Tyr-231. The proline side chain occupies a small substrate binding cavity formed by residues contributed from the loop that follows beta-strand 7 within the (beta/alpha)(8)-barrel. A total of 38 other proteins from cog1228 are predicted to have the same substrate profile based on conservation of the substrate binding residues. The structure of an evolutionarily related protein, Cc2672 from Caulobacter crecentus, was determined as a complex with the N-methylphosphonate derivative of l-arginine (PDB code 3MTW ).


    Organizational Affiliation

    Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROLIDASE
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
423Burkholderia lata (strain ATCC 17760 / LMG 22485 / NCIMB 9086 / R18194 / 383)N/A
Find proteins for Q393A1 (Burkholderia lata (strain ATCC 17760 / LMG 22485 / NCIMB 9086 / R18194 / 383))
Go to UniProtKB:  Q393A1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
LWY
Query on LWY

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
1-[(R)-hydroxy(methyl)phosphoryl]-L-proline
C6 H12 N O4 P
IIXOSEXCIQDQTO-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LWYKi: 7500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 113.186α = 81.32
b = 108.035β = 80.47
c = 170.772γ = 73.76
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-10-10
    Type: Database references