PDBsum entry 4jn6

Lyase/oxidoreductase

PDB id: 4jn6

Contents

Protein chains

338 a.a.

296 a.a.

Ligands

OXL ×2

Metals

_MN ×2

_NA

Waters ×353

PDB id:

4jn6

Name:

Lyase/oxidoreductase

Title:

Crystal structure of the aldolase-dehydrogenase complex from mycobacterium tuberculosis hrv37

Structure:

4-hydroxy-2-oxovalerate aldolase. Chain: a, c. Synonym: hoa, 4-hydroxy-2-keto-pentanoic acid aldolase, 4-hydroxy-2- oxopentanoate aldolase. Engineered: yes. Acetaldehyde dehydrogenase. Chain: b, d. Synonym: acetaldehyde dehydrogenase [acetylating]. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Strain: hrv37. Gene: rv3534c, mt3638. Expressed in: rhodococcus jostii. Expression_system_taxid: 132919. Gene: mhpf, rv3535c, mt3639.

Resolution:

1.93Å R-factor: 0.176 R-free: 0.206

Authors:

J.Carere,S.E.Mckenna,M.S.Kimber,S.Y.K.Seah

Key ref:

J.Carere et al. (2013). Characterization of an aldolase-dehydrogenase complex from the cholesterol degradation pathway of Mycobacterium tuberculosis. Biochemistry, 52, 3502-3511. PubMed id: 23614353 DOI: 10.1021/bi400351h

Date:

14-Mar-13 Release date: 08-May-13

Protein chains

P9WMK5  (HOA_MYCTU) -  4-hydroxy-2-oxohexanoate aldolase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 346 a.a.

Struc: 338 a.a.

Protein chains

P9WQH3  (ACDH_MYCTU) -  Propanal dehydrogenase (CoA-propanoylating) from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 303 a.a.

Struc: 296 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, C: E.C.4.1.3.39 - 4-hydroxy-2-oxovalerate aldolase.
• Reaction: (S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate

(S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate (Bound ligand (Het Group name = OXL) matches with 71.43% similarity)

• Cofactor: Mn(2+)
• Enzyme class 2: Chains A, C: E.C.4.1.3.43 - 4-hydroxy-2-oxohexanoate aldolase.
• Reaction: (S)-4-hydroxy-2-oxohexanoate = propanal + pyruvate

(S)-4-hydroxy-2-oxohexanoate = propanal + pyruvate (Bound ligand (Het Group name = OXL) matches with 71.43% similarity)

• Cofactor: Mn(2+)
• Enzyme class 3: Chains B, D: E.C.1.2.1.10 - acetaldehyde dehydrogenase (acetylating).
• Reaction: acetaldehyde + NAD⁺ + CoA = acetyl-CoA + NADH + H⁺

acetaldehyde (Bound ligand (Het Group name = OXL) matches with 50.00% similarity) + NAD(+) + CoA = acetyl-CoA + NADH + H(+)

• Enzyme class 4: Chains B, D: E.C.1.2.1.87 - propanal dehydrogenase (CoA-propanoylating).
• Reaction: propanal + NAD⁺ + CoA = propanoyl-CoA + NADH + H⁺

propanal + NAD(+) + CoA (Bound ligand (Het Group name = OXL) matches with 42.86% similarity) = propanoyl-CoA + NADH + H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1021/bi400351h

Biochemistry 52:3502-3511 (2013)

PubMed id: 23614353

Characterization of an aldolase-dehydrogenase complex from the cholesterol degradation pathway of Mycobacterium tuberculosis.

J.Carere, S.E.McKenna, M.S.Kimber, S.Y.Seah.

ABSTRACT

HsaF and HsaG are an aldolase and dehydrogenase from the cholesterol degradation pathway of Mycobacterium tuberculosis. HsaF could be heterologously expressed and purified as a soluble dimer, but the enzyme was inactive in the absence of HsaG. HsaF catalyzes the aldol cleavage of 4-hydroxy-2-oxoacids to produce pyruvate and an aldehyde. The enzyme requires divalent metals for activity, with a preference for Mn(2+). The Km values for 4-hydroxy-2-oxoacids were about 20-fold lower than observed for the aldolase homologue, BphI from the polychlorinated biphenyl degradation pathway. Acetaldehyde and propionaldehyde were channeled directly to the dehydrogenase, HsaG, without export to the bulk solvent where they were transformed to acyl-CoA in an NAD(+) and coenzyme A dependent reaction. HsaG is able to utilize aldehydes up to five carbons in length as substrates, with similar catalytic efficiencies. The HsaF-HsaG complex was crystallized and its structure was determined to a resolution of 1.93 Å. Substitution of serine 41 in HsaG with isoleucine or aspartate resulted in about 35-fold increase in Km for CoA but only 4-fold increase in Km dephospho-CoA, suggesting that this residue interacts with the 3'-ribose phosphate of CoA. A second protein annotated as a 4-hydroxy-2-oxopentanoic acid aldolase in M. tuberculosis (MhpE, Rv3469c) was expressed and purified, but was found to lack aldolase activity. Instead this enzyme was found to possess oxaloacetate decarboxylase activity, consistent with the conservation (with the 4-hydroxy-2-oxoacid aldolases) of residues involved in pyruvate enolate stabilization.