8JT0 | pdb_00008jt0

Dihydrofolate reductase-like enzyme from Leptospira interrogans with additional NADP+

PDB DOI: https://doi.org/10.2210/pdb8JT0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Leptospira interrogans serovar Pomona
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-20 Released: 2024-06-26
Deposition Author(s): Wangkanont, K.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.247 (Depositor), 0.247 (DCC)
R-Value Work:
0.206 (Depositor), 0.206 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 39824401 Search on PubMed
DOI: https://doi.org/10.1016/j.ijbiomac.2025.139931
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 240.53 kDa
Atom Count: 17,041
Modeled Residue Count: 1,972
Deposited Residue Count: 2,030
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase family protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	203	Leptospira interrogans serovar Pomona	Mutation(s): 0 Gene Names: IQB77_11460
UniProt
Find proteins for A0AA40WBR8 (Leptospira interrogans serovar Pomona) Explore A0AA40WBR8 Go to UniProtKB: A0AA40WBR8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AA40WBR8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain CB [auth H] SDF format, chain GB [auth I] SDF format, chain HA [auth E] SDF format, chain M [auth A] SDF format, chain MA [auth F] SDF format, chain OB [auth J] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain UA [auth G] SDF format, chain Z [auth D] MOL2 format, chain CB [auth H] MOL2 format, chain GB [auth I] MOL2 format, chain HA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain OB [auth J] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain UA [auth G] MOL2 format, chain Z [auth D] mmCIF format, chain CB [auth H] mmCIF format, chain GB [auth I] mmCIF format, chain HA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain OB [auth J] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain UA [auth G] mmCIF format, chain Z [auth D]	CB [auth H] GB [auth I] HA [auth E] M [auth A] MA [auth F] CB [auth H], GB [auth I], HA [auth E], M [auth A], MA [auth F], OB [auth J], P [auth B], T [auth C], UA [auth G], Z [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain CB [auth H] Focus chain GB [auth I] Focus chain HA [auth E] Focus chain M [auth A] Focus chain MA [auth F] Focus chain OB [auth J] Focus chain P [auth B] Focus chain T [auth C] Focus chain UA [auth G] Focus chain Z [auth D] Interactions & Density Focus chain CB [auth H] Focus chain GB [auth I] Focus chain HA [auth E] Focus chain M [auth A] Focus chain MA [auth F] Focus chain OB [auth J] Focus chain P [auth B] Focus chain T [auth C] Focus chain UA [auth G] Focus chain Z [auth D]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain BB [auth H] SDF format, chain EB [auth I] SDF format, chain GA [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth F] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain LB [auth J] SDF format, chain MB [auth J] SDF format, chain NB [auth J] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain SA [auth G] SDF format, chain X [auth D] MOL2 format, chain AB [auth H] MOL2 format, chain BB [auth H] MOL2 format, chain EB [auth I] MOL2 format, chain GA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain LB [auth J] MOL2 format, chain MB [auth J] MOL2 format, chain NB [auth J] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain SA [auth G] MOL2 format, chain X [auth D] mmCIF format, chain AB [auth H] mmCIF format, chain BB [auth H] mmCIF format, chain EB [auth I] mmCIF format, chain GA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain LB [auth J] mmCIF format, chain MB [auth J] mmCIF format, chain NB [auth J] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain SA [auth G] mmCIF format, chain X [auth D]	AB [auth H] BB [auth H] EB [auth I] GA [auth E] K [auth A] AB [auth H], BB [auth H], EB [auth I], GA [auth E], K [auth A], KA [auth F], L [auth A], LA [auth F], LB [auth J], MB [auth J], NB [auth J], O [auth B], S [auth C], SA [auth G], X [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain AB [auth H] Focus chain BB [auth H] Focus chain EB [auth I] Focus chain GA [auth E] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain LB [auth J] Focus chain MB [auth J] Focus chain NB [auth J] Focus chain O [auth B] Focus chain S [auth C] Focus chain SA [auth G] Focus chain X [auth D] Interactions & Density Focus chain AB [auth H] Focus chain BB [auth H] Focus chain EB [auth I] Focus chain GA [auth E] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain LB [auth J] Focus chain MB [auth J] Focus chain NB [auth J] Focus chain O [auth B] Focus chain S [auth C] Focus chain SA [auth G] Focus chain X [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain DB [auth H] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain HB [auth I] SDF format, chain IA [auth E] SDF format, chain IB [auth I] SDF format, chain JA [auth E] SDF format, chain JB [auth I] SDF format, chain KB [auth I] SDF format, chain N [auth A] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain PA [auth F] SDF format, chain PB [auth J] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain QB [auth J] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain RB [auth J] SDF format, chain TB [auth J] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain VA [auth G] SDF format, chain W [auth C] SDF format, chain WA [auth G] SDF format, chain XA [auth G] SDF format, chain YA [auth G] SDF format, chain ZA [auth G] SDF format, chain SB [auth J] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain HB [auth I] MOL2 format, chain IA [auth E] MOL2 format, chain IB [auth I] MOL2 format, chain JA [auth E] MOL2 format, chain JB [auth I] MOL2 format, chain KB [auth I] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain PB [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain QB [auth J] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain RB [auth J] MOL2 format, chain TB [auth J] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain YA [auth G] MOL2 format, chain ZA [auth G] MOL2 format, chain SB [auth J] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth H] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain HB [auth I] mmCIF format, chain IA [auth E] mmCIF format, chain IB [auth I] mmCIF format, chain JA [auth E] mmCIF format, chain JB [auth I] mmCIF format, chain KB [auth I] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain PB [auth J] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain QB [auth J] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain RB [auth J] mmCIF format, chain TB [auth J] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth G] mmCIF format, chain W [auth C] mmCIF format, chain WA [auth G] mmCIF format, chain XA [auth G] mmCIF format, chain YA [auth G] mmCIF format, chain ZA [auth G] mmCIF format, chain SB [auth J]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] DB [auth H] AA [auth D], BA [auth D], CA [auth D], DA [auth D], DB [auth H], EA [auth D], FA [auth D], HB [auth I], IA [auth E], IB [auth I], JA [auth E], JB [auth I], KB [auth I], N [auth A], NA [auth F], OA [auth F], PA [auth F], PB [auth J], Q [auth B], QA [auth F], QB [auth J], R [auth B], RA [auth F], RB [auth J], SB [auth J], TB [auth J], U [auth C], V [auth C], VA [auth G], W [auth C], WA [auth G], XA [auth G], YA [auth G], ZA [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain HB [auth I] Focus chain IA [auth E] Focus chain IB [auth I] Focus chain JA [auth E] Focus chain JB [auth I] Focus chain KB [auth I] Focus chain N [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain PB [auth J] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain QB [auth J] Focus chain R [auth B] Focus chain RA [auth F] Focus chain RB [auth J] Focus chain SB [auth J] Focus chain TB [auth J] Focus chain U [auth C] Focus chain V [auth C] Focus chain VA [auth G] Focus chain W [auth C] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain HB [auth I] Focus chain IA [auth E] Focus chain IB [auth I] Focus chain JA [auth E] Focus chain JB [auth I] Focus chain KB [auth I] Focus chain N [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain PB [auth J] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain QB [auth J] Focus chain R [auth B] Focus chain RA [auth F] Focus chain RB [auth J] Focus chain SB [auth J] Focus chain TB [auth J] Focus chain U [auth C] Focus chain V [auth C] Focus chain VA [auth G] Focus chain W [auth C] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain FB [auth I] SDF format, chain TA [auth G] SDF format, chain Y [auth D] MOL2 format, chain FB [auth I] MOL2 format, chain TA [auth G] MOL2 format, chain Y [auth D] mmCIF format, chain FB [auth I] mmCIF format, chain TA [auth G] mmCIF format, chain Y [auth D]	FB [auth I], TA [auth G], Y [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain FB [auth I] Focus chain TA [auth G] Focus chain Y [auth D] Interactions & Density Focus chain FB [auth I] Focus chain TA [auth G] Focus chain Y [auth D]