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Structure — LDHA (M-type)
Human muscle L-lactate dehydrogenase M chain, ternary complex with NADH and oxamate 1I10, 2.3 Å (Read JA, Winter VJ, Eszes CM, Sessions RB & Brady RL, Proteins 2001, PMID:11276087).
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Structure — LDHB (H-type)
Human heart LDH H chain ternary complex 1I0Z (same authors, same paper, PMID:11276087). M/H folds are indistinguishable; the kinetic split comes from a 0.94 pH-unit His-pKa shift plus peripheral surface charge (Read 2001) — not a different fold. The viewer therefore draws both directions on the single 1I10 frame (same seats, microscopic reverse); isoform panels below cover the kinetic and biological differences.
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① NADH binds
NADH docks with its nicotinamide ring near His192 (LDHB His193); the hydride donor atom (C4, pro-R face) faces the substrate pocket. NADH coordinates from 1I10 (NAI ligand) — obligatory first binder (ordered Bi-Bi).Source: deposited NAI (NADH) coordinates — PDB 1I10 (Read 2001, PMID:11276087); ordered Bi-Bi binding order — Fidelity card / manifest steps
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② Substrate differs by isoform
The initial substrate is not the same per isoform. LDHA binds pyruvate (a keto acid, C=O at C2) and reduces it to lactate; LDHB binds L-lactate (a hydroxy acid, C–OH at C2) and oxidizes it back to pyruvate. Both poses reuse deposited oxamate coordinates with corrected chemistry — carboxyl on the Arg168 salt bridge, keto/carbinol C facing C4, methyl on the amide-N seat — and are labeled [schematic]. Docking closes the mobile loop (residues 98–110), bringing loop-Arg105 in and expelling water (closed state shown; loop static).Source: substrate seats rebuilt from deposited OXM coordinates with corrected chemistry — PDB 1I10 (Read 2001, PMID:11276087) — [schematic] (Fidelity card); loop 98–110 static (drawerNote)
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③ Concerted hydride + proton transfer
[schematic] One event, two hydrogens (Wang–Schramm triple isotope effects, DOI:10.1021/jacs.6b09049): hydride H⁻ (blue ball) flies nicotinamide-C4 → substrate-C2 (pro-R face) while His192-H⁺ (gold ball) hops to the carbonyl oxygen — concerted/synchronous (the ~25 fs separation figure was not re-verified this review — see Kinetics scope), steadied by loop-Arg105 and the Arg168 salt bridge. LDHA: NADH→NAD⁺ + pyruvate→lactate; LDHB: the microscopic reverse.Source: concerted/synchronous H⁻+H⁺ — Wang–Schramm 2016; measured 1I10 contacts: hydride flight 3.29 Å, proton hop 2.90 Å, Arg168 salt bridge 2.72 Å (manifest geomClaims, own 1I10 measurement)
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④ Products released
Ordered Bi-Bi: the acid leaves first, the cofactor second. LDHA: lactate first, NAD⁺ second; LDHB: pyruvate first, NADH second. The loop opens to let them out (narrated — mesh static). Steady state is loop/product-release limited, not chemistry limited. The reaction is freely reversible; net direction follows substrate levels and isoform kinetics.Source: ordered Bi-Bi, reverse of binding order (Fidelity card); loop opening narrated, not animated (drawerNote); release-limited steady state (Kinetics scope card); departures are display poses, no measured exit geometry
Legend & Fidelity
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Mechanism fidelity — measured vs. inferred
The measured layer: the 1I10 human LDHA chain with NADH (NAI) and oxamate (OXM) as deposited heavy-atom coordinates, plus the reproducible mechanism-scene contacts in the manifest geomClaims (hydride flight 3.29 Å · proton hop 2.9 Å · Arg168 salt bridge 2.72 Å · loop–TS contact 3.54 Å · His192·Asp165 dyad 2.64 Å). The inferred layer (all [schematic]): the real substrate/product states — neither pyruvate nor lactate was ever co-crystallized, so they are rebuilt on the deposited oxamate seats (card ②); and the single concerted-event timing (hydride and proton transferred synchronously; QM/MD + triple-isotope evidence, Wang–Schramm 2016 — the ~25 fs separation figure was not re-verified this review) is a quantitative literature result drawn as one beat (card ③), with the stepwise alternative not fully excluded — disclosed, not resolved. Loop closing/opening is narrated, not animated (card ④ and the drawerNote).
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Why is the substrate "[schematic]"?
No co-crystal of LDH with its true substrate (pyruvate or lactate) is deposited — 1I10 / 1I0Z trap oxamate, the isoelectronic pyruvate mimetic. The real-substrate states are therefore built by correcting that mimetic's chemistry on the same seats (details in card ②). What is measured is the scaffold, the NADH, and the oxamate anchor; every substrate-derived state on top of it is a literature-guided reconstruction and carries the [schematic] tag.
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Physiological regulation — LDHA & cancer (Warburg effect)
Most cancer cells rely on aerobic glycolysis (the Warburg effect) rather than oxidative phosphorylation to fuel proliferation; this drives glucose uptake and pyruvate → lactate flux, exactly the LDHA reaction — Vander Heiden MG, Cantley LC & Thompson CB, Science 2009, PMID:19460998. Hypoxia-inducible factor 1 (HIF-1) binds hypoxia response elements in the LDHA promoter and transcriptionally upregulates it, so hypoxic tumors boost LDHA — Semenza GL et al., J Biol Chem 1996, PMID:8955077. Knocking down LDH-A in tumor cells impairs their proliferation under hypoxia and diminishes tumorigenicity, making LDHA a proposed anti-cancer target — Fantin VR, St-Pierre J & Leder P, Cancer Cell 2006, PMID:16766262. (Total serum LDH is a classical, routinely used prognostic/biomarker in clinical oncology — elevated in many advanced solid tumors.)
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Isozymes — why names differ
LDHA (gene LDHA, chromosome 11p15) encodes the M (muscle) subunit; LDHB (gene LDHB, chromosome 12p12) encodes the H (heart) subunit. These are paralogous genes (gene duplication; ~83% amino acid identity). The best-known kinetic difference: a classic active-site-loop sequence difference (an Ala→Gln substitution when the M- and H-chain loops are aligned) is argued to underlie the H-type pattern of inhibition by excess pyruvate (aerobic tissues favor lactate→pyruvate) vs. the M-type resistance (anaerobic tissues favor pyruvate→lactate) — the precise causal assignment is not re-verified this review. Five tetrameric isozymes (LDH-1 H₄ through LDH-5 M₄) reflect the tissue-specific ratio of M and H subunits.
- Kinetics scope (no measured timecourse on this page)The forward (NADH) and reverse (NAD⁺) hydride hops are both drawn; numbers below would be context, not a timecourse. Specific values are withdrawn pending verification: single-turnover chemistry ≈ 7×10² s⁻¹ at pH 5.5 human heart LDH (Wang–Schramm 2016) and the net-reaction ΔG°′ ≈ −25.1 kJ·mol⁻¹ — neither is in UniProt and the sources could not be re-confirmed in the latest review (2026-09-19). Qualitatively: steady state is loop-closure/product-release limited, not chemistry limited; and human LDHA K0.5(pyruvate) is pH-dependent and cooperative at acidic pH (Pasti 2022, PMID:35048959).
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Sequence
LDHA: DNA/gene NCBI Gene 3939 · protein UniProt P00338 · LDHB: DNA/gene NCBI Gene 3945 · protein UniProt P07195
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Sources — bibliography of this page
S1 — PDB 1I10 / 1I0Z: human LDHA with NADH (NAI) and oxamate (OXM) as deposited heavy-atom coordinates — the oxamate trap is the isoelectronic pyruvate mimetic (Read 2001, Proteins, PMID:11276087); substrate/product poses reuse the deposited OXM seats with corrected chemistry (② card) · mechanism-scene contacts reproduced into the manifest geomClaims (shown on the fidelity card)
S2 — Concerted timing: hydride + proton transferred synchronously — QM/MD + triple-isotope evidence, Wang–Schramm 2016 (the ~25 fs separation figure not re-verified this review); stepwise alternative not fully excluded (card ③)
S3 — Regulation & cancer: Vander Heiden MG, Cantley LC & Thompson CB, Science 2009, PMID:19460998 (Warburg effect) · Semenza GL et al., J Biol Chem 1996, PMID:8955077 (HIF-1 upregulates LDHA) · Fantin VR, St-Pierre J & Leder P, Cancer Cell 2006, PMID:16766262 (LDH-A knockdown impairs hypoxic proliferation)
S4 — Isozymes: LDHA (gene 3939, 11p15, M subunit) · LDHB (gene 3945, 12p12, H subunit) — paralogous, ~83% identity; the Ala→Gln loop-substitution argument for H-type pyruvate inhibition is not re-verified this review
S5 — Kinetics scope: the single-turnover and net-reaction ΔG°′ figures (Wang–Schramm 2016) are withdrawn pending verification — values quoted in the Kinetics scope body below (review 2026-09-19) · human LDHA K0.5(pyruvate) pH-dependent / cooperative at acidic pH — Pasti 2022, PMID:35048959
S6 — Sequence: UniProt P00338 (LDHA) · P07195 (LDHB) · EC 1.1.1.27 (BRENDA)
S7 — Repo display conventions: measured layer = the 1I10/1I0Z scaffold, the NADH (NAI) pose and the oxamate anchor (Rule 34 geomClaims, registered in
tools/manifests/ldh.json); every substrate-derived state is [schematic] literature-guided reconstruction (neither pyruvate nor lactate ever co-crystallized) · mobile loop shown closed (deposited state), closing/opening narrated not animated · ordered Bi-Bi off-loading (reverse of binding order); departures are display poses, no measured exit geometry
› Backbone, NADH and oxamate poses are deposited 1I10 coordinates.
Substrate/product poses reuse the oxamate coordinates with corrected chemistry
(carboxyl/keto/methyl seats) and are labeled [schematic]. The mobile loop is
shown closed (the deposited state); its closing/opening is narrated, not animated.