Short-chain dehydrogenases/reductases (SDR)

Jörnvall, Hans; Persson, Bengt; Krook, Maria; Atrian, Sı́lvia; Gonzàlez‐Duarte, Roser; Jeffery, Jonathan; Ghosh, Debashis

doi:10.1021/bi00018a001

Cited by 1,220 publications

(1,176 citation statements)

References 88 publications

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“…This represents a modified version of the classic Rossmann fold observed in many dinucleotide-binding proteins in that an α helix and a β strand are donated to the Rossmann fold by the C-terminal subdomain (Figure 4). The smaller C-terminal subdomain is formed by residues A 511 -I 540 and N 567 -T 656 and consists of four strands of pleated β sheet and three α helices.The structure of ArnA decarboxylase shown here represents the unliganded form of the enzyme and clearly shows that ArnA decarboxylase belongs to the SDR superfamily (25,26). This group of proteins is characterized by high structural similarity and the presence of specific sequence motifs despite low overall sequence identity (15-30% …”

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confidence: 88%

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,

2004

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Gram-negative bacteria including Escherichia coli, Salmonella typhimurium, and Pseudomonas aeruginosa can modify the structure of lipid A in their outer membrane with 4-amino-4-deoxy-Larabinose (Ara4N). Such modification results in resistance to cationic antimicrobial peptides of the innate immune system and antibiotics such as polymyxin. ArnA is a key enzyme in the lipid A modification pathway, and its deletion abolishes both the Ara4N-lipid A modification and polymyxin resistance. ArnA is a bifunctional enzyme. It can catalyze (i) the NAD + -dependent decarboxylation of UDP-glucuronic acid to UDP-4-keto-arabinose and (ii) the N-10-formyltetrahydrofolatedependent formylation of UDP-4-amino-4-deoxy-L-arabinose. We show that the NAD + -dependent decarboxylating activity is contained in the 360 amino acid C-terminal domain of ArnA. This domain is separable from the N-terminal fragment, and its activity is identical to that of the full-length enzyme. The crystal structure of the ArnA decarboxylase domain from E. coli is presented here. The structure confirms that the enzyme belongs to the short-chain dehydrogenase/reductase (SDR) family. On the basis of sequence and structure comparisons of the ArnA decarboxylase domain with other members of the short-chain dehydrogenase/reductase (SDR) family, we propose a binding model for NAD + and UDP-glucuronic acid and the involvement of residues T 432 , Y 463 , K 467 ,R 619 , and S 433 in the mechanism of NAD + -dependent oxidation of the 4″-OH of the UDP-glucuronic acid and decarboxylation of the UDP-4-keto-glucuronic acid intermediate.In the process of establishing infections, bacteria must overcome the host defense mechanism including the bactericidal action of cationic antimicrobial peptides (CAMPs). 1 These are small, amphipathic, positively charged peptides that destroy bacteria through membrane permeabilization and constitute a phylogenetically conserved branch of the innate immune system (1-4). In the case of Gram-negative bacteria, CAMPs bind to the bacterial cell surface through electrostatic interactions with the negatively charged groups of the lipopolysaccharide (LPS), the immunogenic glycolipid in the outer membrane in Gram-negative bacteria (5,6). They then traverse to the inner membrane and form a pore, which leads to membrane permeabilization and cell death (7)(8)(9). In addition to their function as a key member of the innate immune system, CAMPs represent an important class of clinical antimicrobials. They have both intrinsic bactericidal activity and appear to enhance the activity of other antibiotics, presumably by facilitating their entry into the microbe (3,10,11 21). The N-terminal domain (residues 1-313) is similar in sequence to other enzymes involved in formyl transfer. However, the relevance of this reaction in the biosynthesis of Ara4N-lipid A is unclear. ArnA is also responsible for the C-4″ oxidation of UDP-GlcA to UDP-4-keto-glucuronic acid and its decarboxylation to yield UDP-4-keto-arabinose (boxed in Figure 1) (20). The C terminus o...

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confidence: 88%

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,

2004

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“…Both structures exhibit the typical Rossmann nucleotide-binding fold of alternating b/a secondary structure (a seven parallel b-strand core surrounded by six a-helices) common across this family. 2,6 Q9HYA2 exists as a tetramer in solution as judged by size exclusion chromatography (SEC; data not shown), and tetramers were observed in both crystal forms. However, the apo enzyme crystal form contained only a dimer in its asymmetric unit, with the tetramer formed via crystallographic twofold symmetry.…”

Section: Resultsmentioning

confidence: 99%

“…During cloning, the restriction sites NdeI and XhoI were engineered onto the 5 0 and 3 0 ends, respectively, of the PCR-amplified fragment. The gene was subcloned into a customized pETDuet vector (Novagen) containing a N-terminal (His) 6 -SUMO affinity tag using these restriction sites. 20 The expression cassette of the pQ9HYA2-SUMO plasmid was confirmed by DNA sequencing.…”

Section: Expression and Purificationmentioning

confidence: 99%

The short‐chain oxidoreductase Q9HYA2 from Pseudomonas aeruginosa PAO1 contains an atypical catalytic center

et al. 2010

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The characteristic oxidation or reduction reaction mechanisms of short-chain oxidoreductase (SCOR) enzymes involve a highly conserved Asp-Ser-Tyr-Lys catalytic tetrad. The SCOR enzyme Q9HYA2 from the pathogenic bacterium Pseudomonas aeruginosa was recognized to possess an atypical catalytic tetrad composed of Lys118-Ser146-Thr159-Arg163. Orthologs of Q9HYA2 containing the unusual catalytic tetrad along with conserved substrate and cofactor recognition residues were identified in 27 additional species, the majority of which are bacterial pathogens. However, this atypical catalytic tetrad was not represented within the Protein Data Bank. The crystal structures of unligated and NADPH-complexed Q9HYA2 were determined at 2.3 Å resolution. Structural alignment to a polyketide ketoreductase (KR), a typical SCOR, demonstrated that Q9HYA2's Lys118, Ser146, and Arg163 superimposed upon the KR's catalytic Asp114, Ser144, and Lys161, respectively. However, only the backbone of Q9HYA2's Thr159 overlapped KR's catalytic Tyr157. The Thr159 hydroxyl in apo Q9HYA2 is poorly positioned for participating in catalysis. In the Q9HYA2-NADPH complex, the Thr159 side chain was modeled in two alternate rotamers, one of which is positioned to interact with other members of the tetrad and the bound cofactor. A chloride ion is bound at the position normally occupied by the catalytic tyrosine hydroxyl. The putative active site of Q9HYA2 contains a chemical moiety at each catalytically important position of a typical SCOR enzyme. This is the first observation of a SCOR protein with this alternate catalytic center that includes threonine replacing the catalytic tyrosine and an ion replacing the hydroxyl moiety of the catalytic tyrosine.

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“…Total RNA samples of human tissues were purchased from Sawady Technology (Tokyo, Japan). The antibodies against the purified dimeric DD of Japanese monkey kidney were prepared as described previously [17].…”

Section: Experimental Materialsmentioning

confidence: 99%

“…short-chain dehydrogenase\reductase family [17], but the primary structure of the dimeric enzyme has not been determined.…”

Section: Introductionmentioning

confidence: 99%

Cloning and sequencing of the cDNA species for mammalian dimeric dihydrodiol dehydrogenases

Arimitsu

Aoki

Ishikura

et al. 1999

Biochemical Journal

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Cynomolgus and Japanese monkey kidneys, dog and pig livers and rabbit lens contain dimeric dihydrodiol dehydrogenase (EC 1.3.1.20) associated with high carbonyl reductase activity. Here we have isolated cDNA species for the dimeric enzymes by reverse transcriptase-PCR from human intestine in addition to the above five animal tissues. The amino acid sequences deduced from the monkey, pig and dog cDNA species perfectly matched the partial sequences of peptides digested from the respective enzymes of these animal tissues, and active recombinant proteins were expressed in a bacterial system from the monkey and human cDNA species. Northern blot analysis revealed the existence of a single 1.3 kb mRNA species for the enzyme in these animal tissues. The human enzyme shared 94%, 85%, 84% and 82% amino acid identity with the enzymes of the two monkey strains (their sequences were identical), the dog, the pig and the rabbit respectively. The sequences of the primate enzymes consisted of 335 amino acid residues and lacked one amino acid compared with the other animal enzymes. In contrast with previous reports that other types of dihydrodiol dehydrogenase, carbonyl reductases and enzymes with either activity belong to the aldo-keto reductase family or the short-chain dehydrogenase/reductase family, dimeric dihydrodiol dehydrogenase showed no sequence similarity with the members of the two protein families. The dimeric enzyme aligned with low degrees of identity (14-25%) with several prokaryotic proteins, in which 47 residues are strictly or highly conserved. Thus dimeric dihydrodiol dehydrogenase has a primary structure distinct from the previously known mammalian enzymes and is suggested to constitute a novel protein family with the prokaryotic proteins.

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Short-chain dehydrogenases/reductases (SDR)

Cited by 1,220 publications

References 88 publications

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,

The short‐chain oxidoreductase Q9HYA2 from Pseudomonas aeruginosa PAO1 contains an atypical catalytic center

Cloning and sequencing of the cDNA species for mammalian dimeric dihydrodiol dehydrogenases

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Short-chain dehydrogenases/reductases (SDR)

Cited by 1,220 publications

References 88 publications

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance,

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance,

The short‐chain oxidoreductase Q9HYA2 from Pseudomonas aeruginosa PAO1 contains an atypical catalytic center

Cloning and sequencing of the cDNA species for mammalian dimeric dihydrodiol dehydrogenases

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Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,