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Information on EC 2.1.2.13 - UDP-4-amino-4-deoxy-L-arabinose formyltransferase and Organism(s) Escherichia coli and UniProt Accession P77398
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2.1.2.13 UDP-4-amino-4-deoxy-L-arabinose formyltransferaseIUBMB Comments
The activity is part of a bifunctional enzyme also performing the reaction of EC 1.1.1.305 [UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating)].
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The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
ArnA, ArnA formyltransferase, ArnAFT, Pmrl, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
ArnA
ArnAFT
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ArnA is a bifunctional enzyme, ArnAFT protein consists of the first 304 amino acids of ArnA, with Asn-305 converted to a stop codon
SYSTEMATIC NAME
IUBMB Comments
10-formyltetrahydrofolate:UDP-4-amino-4-deoxy-beta-L-arabinose N-formyltransferase
The activity is part of a bifunctional enzyme also performing the reaction of EC 1.1.1.305 [UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating)].
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
additional information
?
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F4SGI5
the bifunctional enzyme has N- and C-terminal domains catalyzing formylation and oxidative decarboxylation reactions, respectively
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-
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10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
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-
-
?
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
ArnA is a key enzyme in the 4-amino-4-deoxy-L-arabinose-lipid A modification pathway. It is a bifunctional enzyme catalyzing the oxidative decarboxylation of UDP-glucuronic acid to the UDP-4''-ketopentose (UDP-beta-L-threo-pentapyranosyl-4''-ulose) and the N-10-formyltetrahydrofolate-dependent formylation of UDP-4-amino-4-deoxy-L-arabinose. The transformylase activity of the Escherichia coli ArnA is contained in its 300 N-terminal residues
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-
?
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
modification of the lipid A moiety of lipopolysaccharide by the addition of the sugar 4-amino-4-deoxy-L-arabinose is a strategy adopted by pathogenic Gram-negative bacteria to evade cationic antimicrobial peptides produced by the innate immune system. The bifunctional enzyme ArnA is required for 4-amino-4-deoxy-L-arabinose biosynthesis and catalyzes the NAD+-dependent oxidative decarboxylation of UDP-glucuronic acid to generate a UDP-4'-keto-pentose sugar and also catalyzes transfer of a formyl group from N-10-formyltetrahydrofolate to the 4'-amine of UDP-4-amino-4-deoxy-L-arabinose
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-
?
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
ArnA is a key enzyme in the 4-amino-4-deoxy-L-arabinose-lipid A modification pathway. It is a bifunctional enzyme catalyzing the oxidative decarboxylation of UDP-glucuronic acid to the UDP-4''-ketopentose (UDP-beta-L-threo-pentapyranosyl-4''-ulose) and the N-10-formyltetrahydrofolate-dependent formylation of UDP-4-amino-4-deoxy-L-arabinose. The transformylase activity of the Escherichia coli ArnA is contained in its 300 N-terminal residues. A mechanism for the transformylation reaction is proposed, catalyzed by ArnA involving residues N102, H104, and D140
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-
?
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
modification of the lipid A moiety of lipopolysaccharide by the addition of the sugar 4-amino-4-deoxy-L-arabinose is a strategy adopted by pathogenic Gram-negative bacteria to evade cationic antimicrobial peptides produced by the innate immune system. The bifunctional enzyme ArnA is required for 4-amino-4-deoxy-L-arabinose biosynthesis and catalyzes the NAD+-dependent oxidative decarboxylation of UDP-glucuronic acid to generate a UDP-4'-keto-pentose sugar and also catalyzes transfer of a formyl group from N-10-formyltetrahydrofolate to the 4'-amine of UDP-4-amino-4-deoxy-L-arabinose. The active site of formyltransfer in ArnA includes the key catalytic residues Asn102, His104, and Asp140
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-
?
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
F4SGI5
-
-
-
?
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
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bi-functional enzyme, the oxidative decarboxylation of UDP-glucuronic acid is catalyzed by the 345-residue C-terminal domain of ArnA. The 304-residue N-terminal domain catalyzes the N-10-formyltetrahydrofolate-dependent formylation of the 4''-amine of UDP-4-amino-4-deoxy-L-arabinose, generating the sugar nucleotide, uridine 5'-diphospho-beta-(4-deoxy-4-formamido-L-arabinose). The two domains of ArnA are expressed independently as active proteins in Escherichia coli. Both are required for maintenance of polymyxin resistance and L-4-amino-4-deoxy-L-arabinose modification of lipid A. Only the formylated sugar nucleotide is converted in vitro to an undecaprenyl phosphate-linked form by the enzyme ArnC
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-
?
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
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ArnA is a bi-functional enzyme. The oxidative decarboxylation of UDP-glucuronic acid is catalyzed by the 345-residue C-terminal domain of ArnA. The 304-residue N-terminal domain catalyzes the N-10-formyltetrahydrofolate-dependent formylation of the 4''-amine of UDP-L-4-amino-4-deoxy-L-arabinose, generating the sugar nucleotide, uridine 5'-diphospho-beta-(4-deoxy-4-formamido-L-arabinose)
the major isomer is the cis-formamido rotamer
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?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
-
-
-
?
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
ArnA is a key enzyme in the 4-amino-4-deoxy-L-arabinose-lipid A modification pathway. It is a bifunctional enzyme catalyzing the oxidative decarboxylation of UDP-glucuronic acid to the UDP-4''-ketopentose (UDP-beta-L-threo-pentapyranosyl-4''-ulose) and the N-10-formyltetrahydrofolate-dependent formylation of UDP-4-amino-4-deoxy-L-arabinose. The transformylase activity of the Escherichia coli ArnA is contained in its 300 N-terminal residues
-
-
?
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
modification of the lipid A moiety of lipopolysaccharide by the addition of the sugar 4-amino-4-deoxy-L-arabinose is a strategy adopted by pathogenic Gram-negative bacteria to evade cationic antimicrobial peptides produced by the innate immune system. The bifunctional enzyme ArnA is required for 4-amino-4-deoxy-L-arabinose biosynthesis and catalyzes the NAD+-dependent oxidative decarboxylation of UDP-glucuronic acid to generate a UDP-4'-keto-pentose sugar and also catalyzes transfer of a formyl group from N-10-formyltetrahydrofolate to the 4'-amine of UDP-4-amino-4-deoxy-L-arabinose
-
-
?
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
F4SGI5
-
-
-
?
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose
5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
-
bi-functional enzyme, the oxidative decarboxylation of UDP-glucuronic acid is catalyzed by the 345-residue C-terminal domain of ArnA. The 304-residue N-terminal domain catalyzes the N-10-formyltetrahydrofolate-dependent formylation of the 4''-amine of UDP-4-amino-4-deoxy-L-arabinose, generating the sugar nucleotide, uridine 5'-diphospho-beta-(4-deoxy-4-formamido-L-arabinose). The two domains of ArnA are expressed independently as active proteins in Escherichia coli. Both are required for maintenance of polymyxin resistance and L-4-amino-4-deoxy-L-arabinose modification of lipid A. Only the formylated sugar nucleotide is converted in vitro to an undecaprenyl phosphate-linked form by the enzyme ArnC
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
F4SGI5
the enzyme is involved in the formation of 4-amino-4-deoxy-L-arabinose. The addition of this sugar to the lipid A moiety of the lipopolysaccharide of pathogenic Gram-negative bacteria allows these organisms to evade the cationic antimicrobial peptides of the host immune system
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallization of native and Se-Met decarboxylase protein. Good quality crystals are obtained with a precipitant solution of 3.2 M NaCl, 0.1 M Bistris, pH 5.2, using a drop containing 0.004 ml of protein and 0.004 ml of precipitant equilibrated against a reservoir of 0.1 ml of precipitant. Space group as P4(1)3(2), with cell dimensions a = b = c = 149.4 A, beta = gamma = 90°
hanging drop vapor diffusion method, crystal structure of the ArnA transformylase domain is solved to 1.7 A resolution
hanging drop vapor diffusion method, crystal structure of the full-length bifunctional ArnA with UDP-glucuronic acid and ATP bound to the dehydrogenase domain. Binding of UDP-glucuronic acid triggers a 17 A conformational change in ArnA_DH that opens the NAD+ binding site while trapping UDP-glucuronic acid
structure of apo-ArnA and comparison with its ATP- and UDP-glucuronic acid-bound counterparts. In the crystal structure, a binding pocket at the centre of each ArnA trimer in its apo state pocket is occupied by a dithiothreitol molecule. Formation of the pocket is linked to a cascade of structural rearrangements that emerge from the NAD+-binding site. A small effector molecule is postulated that binds to the central pocket and modulates the catalytic properties of ArnA
N-formyltransferase domain of the enzyme in complex with N5-formyltetrahydrofolate and UDP-4-amino-4-deoxy-beta-L-arabinopyranose, hanging drop vapor diffusion method, using 20-22% poly(ethyleneglycol) 5000, 50 mM MgCl2, 100 mM HEPES (pH 8.0) at 21°C
F4SGI5
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E434Q
mutant is inactive, suggesting that chemical rather than steric properties of this residue are crucial in the decarboxylation reaction
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
overexpression of native and selenomethionine decarboxylase and formyltransferase domains of ArnA
overexpression of ArnA as a hexahistidine fusion protein, cloning and expression the separate domains in pET28b and pWSK29
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
modification of the lipid A moiety of lipopolysaccharide by the addition of the sugar 4-amino-4-deoxy-L-arabinose is a strategy adopted by pathogenic Gram-negative bacteria to evade cationic antimicrobial peptides produced by the innate immune system. L-Ara4N biosynthesis is therefore a potential anti-infective target
synthesis
engineering of Escherichia coli to ynthesize the plant-specific flavonoid O-pentosides quercetin 3-O-xyloside and quercetin 3-O-arabinoside. For UDP-xylose biosynthesis, genes UXS (UDP-xylose synthase) from Arabidopsis thaliana and ugd (UDP-glucose dehydrogenase) from E.scherichia coli, are overexpressed. The gene encoding ArnA, which competes with UXS for UDP-glucuronic acid, is deleted. For UDP-arabinose biosynthesis, UXE (UDP-xylose epimerase) i overexpressed. UDP-dependent glycosyltransferases are engineered to ensure specificity for UDP-xylose and UDP-arabinose. The srains thus obtained synthesize approximately 160 mg/liter of quercetin 3-O-xyloside and quercetin 3-O-arabinoside
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Gatzeva-Topalova, P.Z.; May, A.P.; Sousa, M.C.
Crystal structure and mechanism of the Escherichia coli ArnA (PmrI) transformylase domain. An enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance
Biochemistry
44
5328-5338
2005
Escherichia coli (P77398)
Breazeale, S.D.; Ribeiro, A.A.; Raetz, C.R.
Oxidative decarboxylation of UDP-glucuronic acid in extracts of polymyxin-resistant Escherichia coli. Origin of lipid a species modified with 4-amino-4-deoxy-L-arabinose
J. Biol. Chem.
277
2886-2896
2001
Escherichia coli (P77398)
Breazeale, S.D.; Ribeiro, A.A.; McClerren, A.L.; Raetz, C.R.
A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-Amino-4-deoxy-L-arabinose. Identification and function oF UDP-4-deoxy-4-formamido-L-arabinose
J. Biol. Chem.
280
14154-14167
2005
Escherichia coli
Williams, G.J.; Breazeale, S.D.; Raetz. C.R.; Naismith. J.H.
Structure and function of both domains of ArnA, a dual function decarboxylase and a formyltransferase, involved in 4-amino-4-deoxy-L-arabinose biosynthesis
J. Biol. Chem.
280
23000-23008
2005
Escherichia coli (P77398)
Gatzeva-Topalova, P.Z.; May, A.P.; Sousa, M.C.
Structure and mechanism of ArnA: conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance.
Structure
13
929-942
2005
Escherichia coli (P77398)
Fischer, U.; Hertlein, S.; Grimm, C.
The structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic cooperativity
Acta Crystallogr. Sect. D
71
687-696
2015
Escherichia coli (P77398)
Han, S.H.; Kim, B.G.; Yoon, J.A.; Chong, Y.; Ahn, J.H.
Synthesis of flavonoid O-pentosides by Escherichia coli through engineering of nucleotide sugar pathways and glycosyltransferase
Appl. Environ. Microbiol.
80
2754-2762
2014
Escherichia coli (A0A140N587)
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