7NRZ | pdb_00007nrz

Crystal structure of malate dehydrogenase from Trypanosoma cruzi

PDB DOI: https://doi.org/10.2210/pdb7NRZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Trypanosoma cruzi strain CL Brener
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-03-04 Released: 2022-02-16
Deposition Author(s): Sonani, R.R., Kurpiewska, K., Lewinski, K., Dubin, G.
Funding Organization(s): Polish National Science Centre, Foundation for Polish Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.216 (Depositor), 0.217 (DCC)
R-Value Work:
0.203 (Depositor), 0.206 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Distinct sequence and structural feature of trypanosoma malate dehydrogenase.

Sonani, R.R., Kurpiewska, K., Lewinski, K., Dubin, G.

(2021) Biochem Biophys Res Commun 557: 288-293

PubMed: 33894416 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2021.04.033
Primary Citation Related Structures:
7NRZ

PubMed Abstract:
Glycosomal malate dehydrogenase from Trypanosoma cruzi (tcgMDH) catalyzes the oxidation/reduction of malate/oxaloacetate, a crucial step of the glycolytic process occurring in the glycosome of the human parasite. Inhibition of tcgMDH is considered a druggable trait for the development of trypanocidal drugs. Sequence comparison of MDHs from different organisms revealed a distinct insertion of a prolin rich 9-mer (62-KLPPVPRDP-70) in tcgMDH as compared to other eukaryotic MDHs. Crystal structure of tcgMDH is solved here at 2.6 Å resolution with R _work/R _free values of 0.206/0.216. The tcgMDH forms homo-dimer with the solvation free energy (ΔG ^o) gain of -9.77 kcal/mol. The dimeric form is also confirmed in solution by biochemical assays, chemical-crosslinking and dynamic light scattering. The inserted 9-mer adopts a structure of a solvent accessible loop in the vicinity of NAD ⁺ binding site. The distinct sequence and structural feature of tcgMDH, revealed in the present report, provides an anchor point for the development of inhibitors specific for tcgMDH, possible trypanocidal agents of the future.

Organizational Affiliation

Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland.

Macromolecule Content

Total Structure Weight: 279.01 kDa
Atom Count: 19,867
Modeled Residue Count: 2,584
Deposited Residue Count: 2,584
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	323	Trypanosoma cruzi strain CL Brener	Mutation(s): 0 Gene Names: Tc00.1047053506503.69 EC: 1.1.1.37
UniProt
Find proteins for Q4DRD8 (Trypanosoma cruzi (strain CL Brener)) Explore Q4DRD8 Go to UniProtKB: Q4DRD8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4DRD8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain MB [auth E] MOL2 format, chain BB [auth D] MOL2 format, chain MB [auth E] mmCIF format, chain BB [auth D] mmCIF format, chain MB [auth E]	BB [auth D], MB [auth E]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Focus chain MB [auth E] Interactions & Density Focus chain BB [auth D] Focus chain MB [auth E]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain O [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain O [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain O [auth A]	O [auth A], Z [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain Z [auth A] Interactions & Density Focus chain O [auth A] Focus chain Z [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain VB [auth F] SDF format, chain OA [auth C] SDF format, chain N [auth A] SDF format, chain AA [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain VB [auth F] MOL2 format, chain OA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain VB [auth F] mmCIF format, chain OA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain AA [auth A]	AA [auth A], GA [auth B], N [auth A], OA [auth C], VB [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain GA [auth B] Focus chain N [auth A] Focus chain OA [auth C] Focus chain VB [auth F] Interactions & Density Focus chain AA [auth A] Focus chain GA [auth B] Focus chain N [auth A] Focus chain OA [auth C] Focus chain VB [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain AC [auth F] SDF format, chain BA [auth B] SDF format, chain BC [auth F] SDF format, chain CB [auth D] SDF format, chain DC [auth F] SDF format, chain GB [auth D] SDF format, chain GC [auth G] SDF format, chain HA [auth B] SDF format, chain HC [auth G] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain IB [auth D] SDF format, chain IC [auth G] SDF format, chain JA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain NA [auth B] SDF format, chain QC [auth H] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain S [auth A] SDF format, chain SB [auth F] SDF format, chain SC [auth H] SDF format, chain TA [auth C] SDF format, chain TB [auth F] SDF format, chain U [auth A] SDF format, chain WB [auth F] SDF format, chain X [auth A] SDF format, chain XA [auth C] SDF format, chain XB [auth F] SDF format, chain YA [auth D] SDF format, chain YB [auth F] SDF format, chain ZB [auth F] SDF format, chain ZA [auth D] SDF format, chain Y [auth A] SDF format, chain WA [auth C] SDF format, chain W [auth A] SDF format, chain VA [auth C] SDF format, chain V [auth A] SDF format, chain UB [auth F] SDF format, chain UA [auth C] SDF format, chain T [auth A] SDF format, chain SA [auth C] SDF format, chain RC [auth H] SDF format, chain RB [auth F] SDF format, chain QB [auth F] SDF format, chain QA [auth C] SDF format, chain Q [auth A] SDF format, chain PC [auth H] SDF format, chain PB [auth F] SDF format, chain PA [auth C] SDF format, chain P [auth A] SDF format, chain OB [auth E] SDF format, chain NC [auth G] SDF format, chain NB [auth E] SDF format, chain MC [auth G] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LC [auth G] SDF format, chain LB [auth E] SDF format, chain KC [auth G] SDF format, chain KB [auth E] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JC [auth G] SDF format, chain JB [auth D] SDF format, chain J [auth A] SDF format, chain HB [auth D] SDF format, chain FC [auth G] SDF format, chain FB [auth D] SDF format, chain FA [auth B] SDF format, chain EC [auth G] SDF format, chain EB [auth D] SDF format, chain EA [auth B] SDF format, chain DB [auth D] SDF format, chain DA [auth B] SDF format, chain CC [auth F] SDF format, chain CA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain AC [auth F] MOL2 format, chain BA [auth B] MOL2 format, chain BC [auth F] MOL2 format, chain CB [auth D] MOL2 format, chain DC [auth F] MOL2 format, chain GB [auth D] MOL2 format, chain GC [auth G] MOL2 format, chain HA [auth B] MOL2 format, chain HC [auth G] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth D] MOL2 format, chain IC [auth G] MOL2 format, chain JA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain QC [auth H] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain SB [auth F] MOL2 format, chain SC [auth H] MOL2 format, chain TA [auth C] MOL2 format, chain TB [auth F] MOL2 format, chain U [auth A] MOL2 format, chain WB [auth F] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain XB [auth F] MOL2 format, chain YA [auth D] MOL2 format, chain YB [auth F] MOL2 format, chain ZB [auth F] MOL2 format, chain ZA [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain UB [auth F] MOL2 format, chain UA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain RC [auth H] MOL2 format, chain RB [auth F] MOL2 format, chain QB [auth F] MOL2 format, chain QA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain PC [auth H] MOL2 format, chain PB [auth F] MOL2 format, chain PA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth E] MOL2 format, chain NC [auth G] MOL2 format, chain NB [auth E] MOL2 format, chain MC [auth G] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LC [auth G] MOL2 format, chain LB [auth E] MOL2 format, chain KC [auth G] MOL2 format, chain KB [auth E] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JC [auth G] MOL2 format, chain JB [auth D] MOL2 format, chain J [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain FC [auth G] MOL2 format, chain FB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain EC [auth G] MOL2 format, chain EB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain CC [auth F] MOL2 format, chain CA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain AC [auth F] mmCIF format, chain BA [auth B] mmCIF format, chain BC [auth F] mmCIF format, chain CB [auth D] mmCIF format, chain DC [auth F] mmCIF format, chain GB [auth D] mmCIF format, chain GC [auth G] mmCIF format, chain HA [auth B] mmCIF format, chain HC [auth G] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth D] mmCIF format, chain IC [auth G] mmCIF format, chain JA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain QC [auth H] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain SB [auth F] mmCIF format, chain SC [auth H] mmCIF format, chain TA [auth C] mmCIF format, chain TB [auth F] mmCIF format, chain U [auth A] mmCIF format, chain WB [auth F] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth C] mmCIF format, chain XB [auth F] mmCIF format, chain YA [auth D] mmCIF format, chain YB [auth F] mmCIF format, chain ZB [auth F] mmCIF format, chain ZA [auth D] mmCIF format, chain Y [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain UB [auth F] mmCIF format, chain UA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain RC [auth H] mmCIF format, chain RB [auth F] mmCIF format, chain QB [auth F] mmCIF format, chain QA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain PC [auth H] mmCIF format, chain PB [auth F] mmCIF format, chain PA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth E] mmCIF format, chain NC [auth G] mmCIF format, chain NB [auth E] mmCIF format, chain MC [auth G] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LC [auth G] mmCIF format, chain LB [auth E] mmCIF format, chain KC [auth G] mmCIF format, chain KB [auth E] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JC [auth G] mmCIF format, chain JB [auth D] mmCIF format, chain J [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain FC [auth G] mmCIF format, chain FB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain EC [auth G] mmCIF format, chain EB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain CC [auth F] mmCIF format, chain CA [auth B]	AB [auth D] AC [auth F] BA [auth B] BC [auth F] CA [auth B] AB [auth D], AC [auth F], BA [auth B], BC [auth F], CA [auth B], CB [auth D], CC [auth F], DA [auth B], DB [auth D], DC [auth F], EA [auth B], EB [auth D], EC [auth G], FA [auth B], FB [auth D], FC [auth G], GB [auth D], GC [auth G], HA [auth B], HB [auth D], HC [auth G], I [auth A], IA [auth B], IB [auth D], IC [auth G], J [auth A], JA [auth B], JB [auth D], JC [auth G], K [auth A], KA [auth B], KB [auth E], KC [auth G], L [auth A], LA [auth B], LB [auth E], LC [auth G], M [auth A], MA [auth B], MC [auth G], NA [auth B], NB [auth E], NC [auth G], OB [auth E], P [auth A], PA [auth C], PB [auth F], PC [auth H], Q [auth A], QA [auth C], QB [auth F], QC [auth H], R [auth A], RA [auth C], RB [auth F], RC [auth H], S [auth A], SA [auth C], SB [auth F], SC [auth H], T [auth A], TA [auth C], TB [auth F], U [auth A], UA [auth C], UB [auth F], V [auth A], VA [auth C], W [auth A], WA [auth C], WB [auth F], X [auth A], XA [auth C], XB [auth F], Y [auth A], YA [auth D], YB [auth F], ZA [auth D], ZB [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain AC [auth F] Focus chain BA [auth B] Focus chain BC [auth F] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain CC [auth F] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain DC [auth F] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain EC [auth G] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain FC [auth G] Focus chain GB [auth D] Focus chain GC [auth G] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain HC [auth G] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain IC [auth G] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain JC [auth G] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth E] Focus chain KC [auth G] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth E] Focus chain LC [auth G] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MC [auth G] Focus chain NA [auth B] Focus chain NB [auth E] Focus chain NC [auth G] Focus chain OB [auth E] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth F] Focus chain PC [auth H] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth F] Focus chain QC [auth H] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth F] Focus chain RC [auth H] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth F] Focus chain SC [auth H] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth F] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth F] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain WB [auth F] Focus chain X [auth A] Focus chain XA [auth C] Focus chain XB [auth F] Focus chain Y [auth A] Focus chain YA [auth D] Focus chain YB [auth F] Focus chain ZA [auth D] Focus chain ZB [auth F] Interactions & Density Focus chain AB [auth D] Focus chain AC [auth F] Focus chain BA [auth B] Focus chain BC [auth F] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain CC [auth F] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain DC [auth F] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain EC [auth G] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain FC [auth G] Focus chain GB [auth D] Focus chain GC [auth G] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain HC [auth G] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain IC [auth G] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain JC [auth G] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth E] Focus chain KC [auth G] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth E] Focus chain LC [auth G] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MC [auth G] Focus chain NA [auth B] Focus chain NB [auth E] Focus chain NC [auth G] Focus chain OB [auth E] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth F] Focus chain PC [auth H] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth F] Focus chain QC [auth H] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth F] Focus chain RC [auth H] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth F] Focus chain SC [auth H] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth F] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth F] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain WB [auth F] Focus chain X [auth A] Focus chain XA [auth C] Focus chain XB [auth F] Focus chain Y [auth A] Focus chain YA [auth D] Focus chain YB [auth F] Focus chain ZA [auth D] Focus chain ZB [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain OC [auth G] MOL2 format, chain OC [auth G] mmCIF format, chain OC [auth G]	OC [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain OC [auth G] Interactions & Density Focus chain OC [auth G]