8JSV | pdb_00008jsv

Dihydrofolate reductase-like enzyme from Leptospira interrogans (selenomethionine derivative)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.234 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure and catalytic activity of a dihydrofolate reductase-like enzyme from Leptospira interrogans.

Chandit, C.Hengphasatporn, K.Donsuy, P.Shigeta, Y.Wangkanont, K.

(2025) Int J Biol Macromol 298: 139931-139931

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.139931
  • Primary Citation of Related Structures:  
    8JSV, 8JSY, 8JT0

  • PubMed Abstract: 

    A dihydrofolate reductase (DHFR)-like enzyme from Leptospira interrogans (LiDHFRL) was cloned and the recombinant protein was characterized. Sequence alignment suggested that the enzyme lacked the conserved catalytic residues found in DHFR. Indeed, LiDHFRL did not catalyze the reduction of dihydrofolate by either NADH or NADPH. X-ray crystallography revealed that LiDHFRL bound NADP(H) tightly, but its active site architecture was vastly different from that of Escherichia coli DHFR (EcDHFR) and other DHFRLs. Interestingly, vanillin could serve as a substrate for LiDHFRL, demonstrating that LiDHFRL is a functional enzyme. A putative vanillin binding mode was proposed.


  • Organizational Affiliation
    • Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductase family protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
203Leptospira interrogans serovar PomonaMutation(s): 0 
Gene Names: IQB77_11460
UniProt
Find proteins for A0AA40WBR8 (Leptospira interrogans serovar Pomona)
Explore A0AA40WBR8 
Go to UniProtKB:  A0AA40WBR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AA40WBR8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
EB [auth H]
FA [auth D]
IB [auth I]
LA [auth E]
M [auth A]
EB [auth H],
FA [auth D],
IB [auth I],
LA [auth E],
M [auth A],
PB [auth J],
Q [auth B],
QA [auth F],
X [auth C],
YA [auth G]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
DA [auth D]
DB [auth H]
EA [auth D]
HB [auth I]
IA [auth E]
DA [auth D],
DB [auth H],
EA [auth D],
HB [auth I],
IA [auth E],
JA [auth E],
K [auth A],
KA [auth E],
L [auth A],
MB [auth J],
NB [auth J],
OA [auth F],
OB [auth J],
P [auth B],
PA [auth F],
U [auth C],
V [auth C],
VA [auth G],
W [auth C],
WA [auth G],
XA [auth G]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth G]
BA [auth C]
BB [auth G]
CA [auth C]
AA [auth C],
AB [auth G],
BA [auth C],
BB [auth G],
CA [auth C],
CB [auth G],
FB [auth H],
GA [auth D],
GB [auth H],
HA [auth D],
JB [auth I],
KB [auth I],
LB [auth I],
MA [auth E],
N [auth A],
NA [auth E],
O [auth A],
QB [auth J],
R [auth B],
RA [auth F],
RB [auth J],
S [auth B],
SA [auth F],
SB [auth J],
T [auth B],
TA [auth F],
TB [auth J],
UA [auth F],
Y [auth C],
Z [auth C],
ZA [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.9α = 90
b = 138.329β = 90
c = 236.699γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentThailand--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Structure summary
  • Version 1.2: 2025-01-29
    Changes: Database references
  • Version 1.3: 2025-02-05
    Changes: Database references