4OYT

Crystal structure of ternary complex of Plasmodium vivax SHMT with D-serine and folinic acid

  • Classification: TRANSFERASE
  • Organism(s): Plasmodium vivax Sal-1
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2014-02-13 Released: 2014-12-10 
  • Deposition Author(s): Chitnumsub, P., Jaruwat, A., Leartsakulpanich, U.
  • Funding Organization(s): Cluster Program and Management Office, National Science and Technology development Agency, the Cluster Program and Management Office for Discovery based Development Grant, Synchron Light Research Institute-Public Organization, The Thailand Research Fund

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structures of Plasmodium vivax serine hydroxymethyltransferase: implications for ligand-binding specificity and functional control.

Chitnumsub, P.Jaruwat, A.Riangrungroj, P.Ittarat, W.Noytanom, K.Oonanant, W.Vanichthanankul, J.Chuankhayan, P.Maenpuen, S.Chen, C.J.Chaiyen, P.Yuthavong, Y.Leartsakulpanich, U.

(2014) Acta Crystallogr D Biol Crystallogr 70: 3177-3186

  • DOI: 10.1107/S1399004714023128
  • Primary Citation of Related Structures:  
    4OYT, 4PFF, 4PFN

  • PubMed Abstract: 
  • Plasmodium parasites, the causative agent of malaria, rely heavily on de novo folate biosynthesis, and the enzymes in this pathway have therefore been explored extensively for antimalarial development. Serine hydroxymethyltransferase (SHMT) from Plasmodium spp ...

    Plasmodium parasites, the causative agent of malaria, rely heavily on de novo folate biosynthesis, and the enzymes in this pathway have therefore been explored extensively for antimalarial development. Serine hydroxymethyltransferase (SHMT) from Plasmodium spp., an enzyme involved in folate recycling and dTMP synthesis, has been shown to catalyze the conversion of L- and D-serine to glycine (Gly) in a THF-dependent reaction, the mechanism of which is not yet fully understood. Here, the crystal structures of P. vivax SHMT (PvSHMT) in a binary complex with L-serine and in a ternary complex with D-serine (D-Ser) and (6R)-5-formyltetrahydrofolate (5FTHF) provide clues to the mechanism underlying the control of enzyme activity. 5FTHF in the ternary-complex structure was found in the 6R form, thus differing from the previously reported structures of SHMT-Gly-(6S)-5FTHF from other organisms. This suggested that the presence of D-Ser in the active site can alter the folate-binding specificity. Investigation of binding in the presence of D-Ser and the (6R)- or (6S)-5FTHF enantiomers indicated that both forms of 5FTHF can bind to the enzyme but that only (6S)-5FTHF gives rise to a quinonoid intermediate. Likewise, a large surface area with a highly positively charged electrostatic potential surrounding the PvSHMT folate pocket suggested a preference for a polyglutamated folate substrate similar to the mammalian SHMTs. Furthermore, as in P. falciparum SHMT, a redox switch created from a cysteine pair (Cys125-Cys364) was observed. Overall, these results assert the importance of features such as stereoselectivity and redox status for control of the activity and specificity of PvSHMT.


    Organizational Affiliation

    National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine hydroxymethyltransferase, putativeA, B, C442Plasmodium vivax Sal-1Mutation(s): 0 
Gene Names: PVX_100730
EC: 2.1.2.1
UniProt
Find proteins for A5K8L9 (Plasmodium vivax (strain Salvador I))
Explore A5K8L9 
Go to UniProtKB:  A5K8L9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K8L9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FON
Query on FON

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C]
N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid
C20 H23 N7 O7
VVIAGPKUTFNRDU-OLZOCXBDSA-N
 Ligand Interaction
1W9
Query on 1W9

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
K [auth C]
(2R)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-oxidanyl-propanoic acid
C11 H15 N2 O8 P
ZTQZHYMXYBDMIL-RZTFRGLUSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
M [auth C]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
ETF
Query on ETF

Download Ideal Coordinates CCD File 
N [auth C]TRIFLUOROETHANOL
C2 H3 F3 O
RHQDFWAXVIIEBN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.619α = 90
b = 58.115β = 90
c = 236.614γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cluster Program and Management Office, National Science and Technology development AgencyThailandCPMO-P-00-20029
the Cluster Program and Management Office for Discovery based Development GrantThailandCPMO-DD/P-10-11274
Synchron Light Research Institute-Public OrganizationThailand2-2549/LS01
Synchron Light Research Institute-Public OrganizationThailand2551/08
The Thailand Research FundThailandRTA5680001

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-01-07
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy