3MKV

Crystal structure of amidohydrolase eaj56179


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.5 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, 3N2C, 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 samples originating from the Sargasso Sea ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE AMIDOHYDROLASEA, B, C, D, E, F, G, H426unidentifiedMutation(s): 0 
Gene Names: EAJ56179
UniProt
Find proteins for B2T4I1 (Paraburkholderia phytofirmans (strain DSM 17436 / LMG 22146 / PsJN))
Explore B2T4I1 
Go to UniProtKB:  B2T4I1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth E] , CA [auth E] , IA [auth G] , K [auth A] , L [auth A] , MA [auth H] , NA [auth H] , O [auth B] , 
BA [auth E],  CA [auth E],  IA [auth G],  K [auth A],  L [auth A],  MA [auth H],  NA [auth H],  O [auth B],  OA [auth H],  P [auth B],  S [auth C],  W [auth D],  X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
T [auth C], Y [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth E] , DA [auth F] , EA [auth F] , GA [auth G] , HA [auth G] , I [auth A] , J [auth A] , KA [auth H] , 
AA [auth E],  DA [auth F],  EA [auth F],  GA [auth G],  HA [auth G],  I [auth A],  J [auth A],  KA [auth H],  LA [auth H],  M [auth B],  N [auth B],  Q [auth C],  R [auth C],  U [auth D],  V [auth D],  Z [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download Ideal Coordinates CCD File 
FA [auth F], JA [auth G]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D, E, F, G, HL-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.022α = 90
b = 198.599β = 107.76
c = 104.294γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-10-10
    Changes: Database references
  • Version 1.3: 2014-04-02
    Changes: Source and taxonomy
  • Version 1.4: 2018-11-21
    Changes: Data collection, Structure summary
  • Version 1.5: 2021-02-10
    Changes: Database references, Derived calculations, Structure summary