Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) in complex with cadaverine

Experimental Data Snapshot

  • Resolution: 2.19 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

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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 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.

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): 0 
Gene Names: MTR_2g086600
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
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PGE

Download Ideal Coordinates CCD File 
C6 H14 O4
Query on PEG

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CB [auth L],
OA [auth G],
S [auth A]
C4 H10 O3
Query on N2P

Download Ideal Coordinates CCD File 
BB [auth L]
DA [auth D]
EB [auth M]
GA [auth E]
IB [auth N]
BB [auth L],
DA [auth D],
EB [auth M],
GA [auth E],
IB [auth N],
KA [auth F],
LB [auth O],
NA [auth G],
V [auth B],
VA [auth J],
XA [auth K],
Y [auth C]
C5 H14 N2
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
EA [auth D]
FB [auth M]
GB [auth M]
AA [auth C],
BA [auth C],
EA [auth D],
FB [auth M],
GB [auth M],
HA [auth E],
HB [auth M],
IA [auth E],
JA [auth F],
JB [auth N],
LA [auth F],
MB [auth O],
NB [auth O],
PA [auth G],
Q [auth A],
QA [auth H],
R [auth A],
RA [auth I],
SA [auth I],
T [auth A],
TA [auth I],
W [auth B],
YA [auth K],
Z [auth C],
ZA [auth K]
C3 H8 O3
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth K]
CA [auth C]
DB [auth L]
FA [auth D]
KB [auth N]
AB [auth K],
CA [auth C],
DB [auth L],
FA [auth D],
KB [auth N],
MA [auth F],
U [auth A],
UA [auth I],
WA [auth J]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.19 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.269α = 90
b = 211.041β = 90
c = 208.822γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction

Structure Validation

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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: 2017-11-01
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description