5H8K

Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) C158S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants.

Sekula, B.Ruszkowski, M.Malinska, M.Dauter, Z.

(2016) Front Plant Sci 7: 350-350

  • DOI: https://doi.org/10.3389/fpls.2016.00350
  • Primary Citation of Related Structures:  
    5H8I, 5H8J, 5H8K, 5H8L

  • PubMed Abstract: 

    Putrescine, 1,4-diaminobutane, is an intermediate in the biosynthesis of more complexed polyamines, spermidine and spermine. Unlike other eukaryotes, plants have evolved a multistep pathway for putrescine biosynthesis that utilizes arginine. In the final reaction, N-carbamoylputrescine is hydrolyzed to putrescine by N-carbamoylputrescine amidohydrolase (CPA, EC 3.5.1.53). During the hydrolysis, consecutive nucleophilic attacks on the substrate by Cys158 and water lead to formation of putrescine and two by-products, ammonia and carbon dioxide. CPA from the model legume plant, Medicago truncatula (MtCPA), was investigated in this work. Four crystal structures were determined: the wild-type MtCPA in complex with the reaction intermediate, N-(dihydroxymethyl)putrescine as well as with cadaverine, which is a longer analog of putrescine; and also structures of MtCPA-C158S mutant unliganded and with putrescine. MtCPA assembles into octamers, which resemble an incomplete left-handed helical twist. The active site of MtCPA is funnel-like shaped, and its entrance is walled with a contribution of the neighboring protein subunits. Deep inside the catalytic cavity, Glu48, Lys121, and Cys158 form the catalytic triad. In this studies, we have highlighted the key residues, highly conserved among the plant kingdom, responsible for the activity and selectivity of MtCPA toward N-carbamoylputrescine. Moreover, since, according to previous reports, a close MtCPA relative from Arabidopsis thaliana, along with several other nitrilase-like proteins, are subjected to allosteric regulation by substrates, we have used the structural information to indicate a putative secondary binding site. Based on the docking experiment, we postulate that this site is adjacent to the entrance to the catalytic pocket.


  • Organizational Affiliation

    Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology Lodz, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-carbamoylputrescine amidohydrolase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
304Medicago truncatulaMutation(s): 1 
Gene Names: MTR_2g086600
UniProt
Find proteins for G7ITU5 (Medicago truncatula)
Explore G7ITU5 
Go to UniProtKB:  G7ITU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7ITU5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth C],
GB [auth L],
SA [auth G],
YA [auth J]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth K]
BB [auth K]
DA [auth D]
DB [auth L]
AA [auth C],
AB [auth K],
BB [auth K],
DA [auth D],
DB [auth L],
EA [auth D],
EB [auth L],
FA [auth D],
FB [auth L],
GA [auth D],
IA [auth E],
IB [auth M],
JA [auth E],
JB [auth M],
KA [auth E],
KB [auth M],
LA [auth E],
LB [auth N],
MA [auth F],
MB [auth N],
NA [auth F],
NB [auth N],
OA [auth F],
OB [auth N],
PA [auth G],
PB [auth O],
Q [auth A],
QA [auth G],
QB [auth P],
R [auth A],
RA [auth G],
T [auth B],
TA [auth I],
U [auth B],
UA [auth I],
V [auth B],
W [auth B],
WA [auth J],
X [auth B],
XA [auth J],
Y [auth C],
Z [auth C],
ZA [auth K]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth C]
CB [auth K]
HA [auth D]
HB [auth L]
S [auth A]
CA [auth C],
CB [auth K],
HA [auth D],
HB [auth L],
S [auth A],
VA [auth I]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.531α = 90
b = 210.756β = 90
c = 208.723γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
BALBESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2014/12/T/ST5/00136

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description