Structure of L-3-hydroxyacyl-coenzyme A dehydrogenase: preliminary chain tracing at 2.8-A resolution.

Birktoft, Jens J.; Holden, Hazel M.; Hamlin, R.; Xuong, N.-H.; Banaszak, Leonard J.

doi:10.1073/pnas.84.23.8262

Cited by 40 publications

(37 citation statements)

References 25 publications

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“…1), was observed by alignment of BHBD from strain ATCC 824 with the pig and rat HAD enzymes (data not shown). This observation is in agreement with an X-ray crystallographic study of crystallized porcine HAD at 2.8 Å (0.28 nm) which suggests that the NAD-binding site of this enzyme is located within the amino-terminal domain (6).…”

Section: Discussionsupporting

confidence: 79%

Cloning, sequencing, and expression of clustered genes encoding beta-hydroxybutyryl-coenzyme A (CoA) dehydrogenase, crotonase, and butyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824

1996

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The enzymes ␤-hydroxybutyryl-coenzyme A (CoA) dehydrogenase (BHBD), crotonase, and butyryl-CoA dehydrogenase (BCD) from Clostridium acetobutylicum are responsible for the formation of butyryl-CoA from acetoacetyl-CoA. These enzymes are essential to both acid formation and solvent formation by clostridia. Clustered genes encoding BHBD, crotonase, BCD, and putative electron transfer flavoprotein ␣ and ␤ subunits have been cloned and sequenced. The nucleotide sequence of the crt gene indicates that it encodes crotonase, a protein with 261 amino acid residues and a calculated molecular mass of 28.2 kDa; the hbd gene encodes BHBD, with 282 residues and a molecular mass of 30.5 kDa. Three open reading frames (bcd, etfB, and etfA) are located between crt and hbd. The nucleotide sequence of bcd indicates that it encodes BCD, which consists of 379 amino acid residues and has high levels of homology with various acyl-CoA dehydrogenases. Open reading frames etfB and etfA, located downstream of bcd, encode 27.2-and 36.1-kDa proteins, respectively, and show homology with the fixAB genes and the ␣ and ␤ subunits of the electron transfer flavoprotein. These findings suggest that BCD in clostridia might interact with the electron transfer flavoprotein in its redox function. Primer extension analysis identified a promoter consensus sequence upstream of the crt gene, suggesting that the clustered genes are transcribed as a transcriptional unit and form a BCS (butyryl-CoA synthesis) operon. A DNA fragment containing the entire BCS operon was subcloned into an Escherichia coli-C. acetobutylicum shuttle vector. Enzyme activity assays showed that crotonase and BHBD were highly overproduced in cell extracts from E. coli harboring the subclone. In C. acetobutylicum harboring the subclone, the activities of the enzymes crotonase, BHBD, and BCD were elevated.

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Section: Discussionsupporting

confidence: 79%

Cloning, sequencing, and expression of clustered genes encoding beta-hydroxybutyryl-coenzyme A (CoA) dehydrogenase, crotonase, and butyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824

1996

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“…8) is quite distinct from that described for the known dehydrogenase structures. Best known is the lactate dehydrogenase-like class, including LDH (16), malate dehydrogenase (25), alcohol dehydrogenase (26), glyceraldehyde-3-phosphate dehydrogenase (27), and L-3-hydroxyacyl CoA dehydrogenase (28). Although the catalytic domains vary in structure, the nucleotide-binding domains of these enzymes all have a very similar structure, the LDH fold, and all bind the cofactor in a similar manner.…”

Section: Discussionmentioning

confidence: 99%

Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase.

Hurley

Thorsness

Ramalingam

et al. 1989

Proc. Natl. Acad. Sci. U.S.A.

211

213

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The structure of isocitrate dehydrogenase [threo-Ds- The enzyme was shown to be phosphorylated (6, 7) and the phosphorylation was shown to occur on a serine residue (8). Although there is some loss of activity when Ser-113 is replaced by a number ofamino acids (Ala, Cys, Thr, Tyr), the replacement by aspartic acid causes complete inactivation (9). Hence, it is the negative charge introduced by phosphorylation that causes inactivation (9).There is no significant sequence conservation between IDH and any of the dehydrogenases for which threedimensional structures are known. The sequence of E. coli IDH shows significant conservation only with isopropylmalate dehydrogenase (IMDH) (9). A preliminary x-ray diffraction pattern has been reported for IMDH (10). Aligned residues of IDH and IMDH sequences (11-14) are 25-29% identical, varying among species.The structures of dehydrogenases have been the subject of much interest because the nucleotide-binding domains of many of these enzymes retain much structural similarity, despite relatively little sequence conservation, as first observed by Rossman et al. (15). This nucleotide-binding fold is referred to as the lactate dehydrogenase (LDH) fold, for the first enzyme in which it was described (16). The same fold has been described, with small modifications, in many other structures, frequently in a nucleotide-binding domain. As IDH shows no sequence conservation with dehydrogenases of known structure, the IDH structure is of interest as a potential alternative solution to the same evolutionary challenge. § Structure Determination IDH was purified by a modification of the procedure described by Reeves et al. (17) from a strain of E. coli in which IDH was expressed as described by LaPorte et al. (18). Crystals were grown in a solution containing dephosphorylated IDH (28 mg/ml), 34% saturated ammonium sulfate, 100 mM NaCl, 35 mM Na2HPO4, 9 mM citric acid, and 0. Diffraction was observed to 2.5 A with Cu Ka radiation from a rotating anode x-ray source at room temperature. All diffraction data were collected on a Nicolet area detector and reduced with the XENGEN data reduction package. One isomorphous heavy atom derivative was prepared by a 5-day soak in 1% saturated p-chloromercuribenzenesulfonic acid (PCMBS). The position of one major site was determined from the heavy-atom difference Patterson map, with a second site subsequently located from an error residual map. Heavy atom parameters were refined by the method of Dickerson et al. (19) and a single isomorphous replacement electron density map was calculated. Crystallographic statistics as a function of resolution are summarized in Fig. 1.Density modification (20) resulted in a dramatic improvement of the electron density map. The unusually large solvent fraction of 0.73 facilitated the use of density modification in phasing. The phases calculated by a first round of density modification were fixed and used for further refinement of heavy atom parameters; a second single isomorphous replacement map was used in a...

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“…Hence, human brain L-3-hydroxyacyl-CoA dehydrogenase is a homotetramer. In contrast, mitochondrial L-3-hydroxyacyl-CoA dehydrogenase from pig heart is composed of two identical 33-kDa subunits (28) (Figs. 1 and 4).…”

Section: Structural Features Of Human Brain Short Chain L-3-hydroxyacmentioning

confidence: 99%

A Human Brain l-3-Hydroxyacyl-coenzyme A Dehydrogenase Is Identical to an Amyloid β-Peptide-binding Protein Involved in Alzheimer's Disease

He¹,

Schulz²,

Yang³

1998

Journal of Biological Chemistry

115

109

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A novel L-3-hydroxyacyl-CoA dehydrogenase from human brain has been cloned, expressed, purified, and characterized. This enzyme is a homotetramer with a molecular mass of 108 kDa. Its subunit consists of 261 amino acid residues and has structural features characteristic of short chain dehydrogenases. It was found that the amino acid sequence of this human brain enzyme is identical to that of an endoplasmic reticulum amyloid ␤-peptide-binding protein (ERAB), which mediates neurotoxicity in Alzheimer's disease (Yan, S. D., Fu, J., Soto, C., Chen, X., Zhu, H., Al-Mohanna, F., Collison, K., Zhu, A., Stern, E., Saido, T., Tohyama, M., Ogawa, S., Roher, A., and Stern, D. (1997) Nature 389, 689 -695). The purification of human brain short chain L-3-hydroxyacyl-CoA dehydrogenase made it possible to characterize the structural and catalytic properties of ERAB. This NAD ؉ -dependent dehydrogenase catalyzes the reversible oxidation of L-3-hydroxyacyl-CoAs to form 3-ketoacyl-CoAs, but it does not act on the D-isomers. The catalytic rate constant of the purified enzyme was estimated to be 37 s ؊1 with apparent K m values of 89 and 20 M for acetoacetyl-CoA and NADH, respectively. The activity ratio of this enzyme for substrates with chain lengths of C 4 , C 8 , and C 16 was ϳ1:2:2. The human short chain L-3-hydroxyacyl-CoA dehydrogenase gene is organized into six exons and five introns and maps to chromosome Xp11.2. The amino-terminal NAD-binding region of the dehydrogenase is encoded by the first three exons, whereas the other exons code for the carboxyl-terminal substratebinding region harboring putative catalytic residues. The results of this study lead to the conclusion that ERAB involved in neuronal dysfunction is encoded by the human short chain L-3-hydroxyacyl-CoA dehydrogenase gene.L-3-Hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) catalyzes the third step of the fatty acid ␤-oxidation pathway: L-3-hydroxyacyl-CoA ϩ NAD ϩ i 3-ketoacyl-CoA ϩ NADH ϩ H ϩ (1). This reaction is known to be catalyzed by mitochondrial monofunctional L-3-hydroxyacyl-CoA dehydrogenase and by prokaryotic and eukaryotic multifunctional ␤-oxidation enzymes that possess an L-3-hydroxyacyl-CoA dehydrogenase functional domain (2, 3). The catalytic residue of this kind of dehydrogenase was recently identified to be a conserved histidine (4), and a conserved glutamate residue is also required for high catalytic efficiency (5). The catalytic residue of L-3-hydroxyacyl-CoA dehydrogenase was proposed to interact with the conserved glutamate, and this electrostatic interaction seemed to be strengthened by the binding of substrate (5). However, we were surprised to see that a catalytic His-Glu pair is not present in the newly isolated bovine liver type II dehydrogenase (6, 7), which is not homologous to any of the known L-3-hydroxyacylCoA dehydrogenases. More interestingly, it was reported that this new type of L-3-hydroxyacyl-CoA dehydrogenase was not found in human liver by either Northern blot or immunoblot analysis (6, 7). As a result, several important q...

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Structure of L-3-hydroxyacyl-coenzyme A dehydrogenase: preliminary chain tracing at 2.8-A resolution.

Cited by 40 publications

References 25 publications

Cloning, sequencing, and expression of clustered genes encoding beta-hydroxybutyryl-coenzyme A (CoA) dehydrogenase, crotonase, and butyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824

Cloning, sequencing, and expression of clustered genes encoding beta-hydroxybutyryl-coenzyme A (CoA) dehydrogenase, crotonase, and butyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824

Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase.

A Human Brain l-3-Hydroxyacyl-coenzyme A Dehydrogenase Is Identical to an Amyloid β-Peptide-binding Protein Involved in Alzheimer's Disease

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