Tài liệu Báo cáo khoa học: Medium-chain dehydrogenases/reductases (MDR) Family characterizations

Medium-chain dehydrogenases/reductases (MDR)

Family characterizations including genome comparisons and active site modelling

Erik Nordling1,2, Hans Jo¨ rnvall1 and Bengt Persson1,2

1

Department of Medical Biochemistry and Biophysics and 2

Stockholm Bioinformatics Centre, Karolinska Institutet, Stockholm,

Sweden

Completed eukaryotic genomes were screened for medium￾chain dehydrogenases/reductases (MDR). In the human

genome, 23 MDR forms were found, a number that prob￾ably will increase, because the genome is not yet fully inter￾preted. Partial sequences already indicate that at least three

furthermembers exist.Within theMDR superfamily, at least

eight families were distinguished. Three families are formed

by dimeric alcohol dehydrogenases (ADH; originally detec￾ted in animals/plants), cinnamyl alcohol dehydrogenases

(originally detected in plants) and tetrameric alcohol dehy￾drogenases (originally detected in yeast). Three further

families are centred around forms initially detected as

mitochondrial respiratory function proteins, acetyl-CoA

reductases of fatty acid synthases, and leukotriene B4

dehydrogenases. The two remaining families with polyol

dehydrogenases (originally detected as sorbitol dehydro￾genase) and quinone reductases (originally detected as

f-crystallin) are also distinct but with variable sequences. The

most abundant families in the human genome are the dimeric

ADH forms and the quinone oxidoreductases. The eukary￾otic patterns are different from those of Escherichia coli.

The different families were further evaluated by molecular

modelling of their active sites as to geometry, hydrophobicity

and volume of substrate-binding pockets. Finally, sequence

patterns were derived that are diagnostic for the different

families and can be used in genome annotations.

Keywords: medium-chain dehydrogenases/reductases;

genome comparisons; polyol dehydrogenase; cinnamyl

alcohol dehydrogenase; quinone oxidoreductase.

Medium-chain dehydrogenases/reductases (MDRs) consti￾tute a large enzyme superfamily with (including species

variants) close to 1000 members [1,2]. The MDR enzymes

represent many different enzyme activities of which alcohol

dehydrogenases (ADHs) are the most closely investigated.

They participate in the oxidation of alcohols, detoxification

of aldehydes/alcohols and the metabolism of bile acids

[3,4]. Another MDR branch has polyol dehydrogenase

(PDH) activities originally detected for sorbitol dehydro￾genase (SDH) [5]. All the corresponding substrates are

widespread in nature because of their derivation from

glucose, fructose, and general metabolism. In some organ￾isms these substrates, such as polyols, can be accumulated

at high concentrations constituting a protection against

environmental stress, such as osmotic shock [6], and

reduced or elevated temperature [7,8]. Polyol accumulation

can, however, be harmful [9], suggesting a further protective

role for these enzymes. An MDR family earlier recognized

is cinnamyl alcohol dehydrogenase, CAD. This enzyme

type in plants catalyses the last step in the biosynthesis of

the monomeric precursors of lignin, the main constituent of

plant cell walls [10]. This enzyme family has been exten￾sively characterized through CAD from plant sources

[11–13], because of its importance for the pulp industry [14].

Down-regulation or inhibition of CAD will reduce wood

lignin content and yield a pulp of high quality [15]. A

further MDR family long since recognized is the quinone

oxidoreductase (QOR)-type, of which one mammalian

form functions as a lens protein (f-crystallin) [16], muta￾tional loss of which may result in cataract formation at

birth. This suggests that f-crystallin has a role in the

protection of the lens against oxidative damage [17]. In

common therefore, as demonstrated by the examples

above, all MDR families appear to have some members

with protective functions in different organismal defences

[2]. All MDR enzymes utilize NAD(H) or NADP(H) as

cofactor and several but not all of the members have one

zinc ion with catalytic function at the active site. Some, in

particular classical, dimeric ADHs, also have a second zinc

ion at a structural site, stabilizing an external loop present

in those forms [18].

The availability of completed genomes provides an

opportunity to evaluate all these members of the MDR

superfamily. We have therefore studied the MDR enzymes

corresponding to the products from available eukaryotic

genomes (and for comparison, the Escherichia coli genome

is also included, but not further analysed because of the

distant relationships). The total number of MDR forms in

each species was evaluated, orthologies were assigned and

evolutionary relationships were characterized. In addition,

separate sequence motifs were defined and the active site

variability was investigated.

Correspondence to B. Persson, Department of Medical Biochemistry

and Biophysics, Karolinska Institutet, S-171 77 Stockholm,

Sweden. Fax: + 46 8 337 462, Tel.: + 46 8 728 7730,

E-mail: [email protected]

Abbreviations: MDR, medium-chain dehydrogenases/reductases;

ADH, alcohol dehydrogenase; CAD, cinnamyl alcohol dehydrogen￾ase; YADH, yeast alcohol dehydrogenase; MRF, mitochondrial

response proteins; PDH, polyol dehydrogenases;

QOR, quinone oxidoreductases; ACR, acyl-CoA reductase;

LTD, leukotriene B4 dehydrogenase.

(Received 12 April 2002, revised 24 June 2002, accepted 15 July 2002)

Eur.J.Biochem. 269, 4267–4276 (2002)
FEBS 2002 doi:10.1046/j.1432-1033.2002.03114.x