PDBsum entry 5a1t

Oxidoreductase

PDB id: 5a1t

Contents

Protein chains

331 a.a.

Ligands

NAI ×2

OXM ×2

Waters ×655

PDB id:

5a1t

Name:

Oxidoreductase

Title:

Trichomonas vaginalis lactate dehydrogenase in complex with nadh and oxamate

Structure:

L-lactate dehydrogenase. Chain: a, b. Engineered: yes

Source:

Trichomonas vaginalis. Organism_taxid: 5722. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.97Å R-factor: 0.204 R-free: 0.250

Authors:

P.A.Steindel,E.H.Chen,D.L.Theobald

Key ref:

P.A.Steindel et al. (2016). Gradual neofunctionalization in the convergent evolution of trichomonad lactate and malate dehydrogenases. Protein Sci, 25, 1319-1331. PubMed id: 26889885 DOI: 10.1002/pro.2904

Date:

05-May-15 Release date: 02-Mar-16

Protein chains

O96445  (O96445_TRIVA) -  L-lactate dehydrogenase from Trichomonas vaginalis

Seq: 333 a.a.

Struc: 331 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.27 - L-lactate dehydrogenase.
• Reaction: (S)-lactate + NAD⁺ = pyruvate + NADH + H⁺

(S)-lactate (Bound ligand (Het Group name = OXM) matches with 71.43% similarity) + NAD(+) (Bound ligand (Het Group name = NAI) corresponds exactly) = pyruvate + NADH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1002/pro.2904

Protein Sci 25:1319-1331 (2016)

PubMed id: 26889885

Gradual neofunctionalization in the convergent evolution of trichomonad lactate and malate dehydrogenases.

P.A.Steindel, E.H.Chen, J.D.Wirth, D.L.Theobald.

ABSTRACT

Lactate and malate dehydrogenases (LDH and MDH) are homologous, core metabolic enzymes common to nearly all living organisms. LDHs have evolved convergently from MDHs at least four times, achieving altered substrate specificity by a different mechanism each time. For instance, the LDH of anaerobic trichomonad parasites recently evolved independently from an ancestral trichomonad MDH by gene duplication. LDH plays a central role in trichomonad metabolism by catalyzing the reduction of pyruvate to lactate, thereby regenerating the NAD+ required for glycolysis. Using ancestral reconstruction methods, we identified the biochemical and evolutionary mechanisms responsible for this convergent event. The last common ancestor of these enzymes was a highly specific MDH, similar to modern trichomonad MDHs. In contrast, the LDH lineage evolved promiscuous activity by relaxing specificity in a gradual process of neofunctionalization involving one highly detrimental substitution at the "specificity residue" (R91L) and many additional mutations of small effect. L91 has different functional consequences in LDHs and in MDHs, indicating a prominent role for epistasis. Crystal structures of modern-day and ancestral enzymes show that the evolution of substrate specificity paralleled structural changes in dimerization and α-helix orientation. The relatively small "specificity residue" of the trichomonad LDHs can accommodate a range of substrate sizes and may permit solvent to access the active site, both of which promote substrate promiscuity. The trichomonad LDHs present a multi-faceted counterpoint to the independent evolution of LDHs in other organisms and illustrate the diverse mechanisms by which protein function, structure, and stability coevolve.