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PDBsum entry 2bln

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protein ligands Protein-protein interface(s) links
Transferase PDB id
2bln
Jmol
Contents
Protein chains
298 a.a. *
Ligands
FON ×2
U5P ×2
ACT ×2
Waters ×648
* Residue conservation analysis
PDB id:
2bln
Name: Transferase
Title: N-terminal formyltransferase domain of arna in complex with n-5-formyltetrahydrofolate and ump
Structure: Protein yfbg. Chain: a, b. Fragment: formyltransferase domain, residues 1-305. Synonym: udp-d-glucuronate dehydrogenase arna. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: w3310. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.20Å     R-factor:   0.136     R-free:   0.158
Authors: G.J.Williams,S.D.Breazeale,C.R.H.Raetz,J.H.Naismith
Key ref:
G.J.Williams et al. (2005). 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. PubMed id: 15809294 DOI: 10.1074/jbc.M501534200
Date:
07-Mar-05     Release date:   08-Apr-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P77398  (ARNA_ECOLI) -  Bifunctional polymyxin resistance protein ArnA
Seq:
Struc:
 
Seq:
Struc:
660 a.a.
298 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.1.1.1.305  - UDP-glucuronic acid oxidase (UDP-4-keto-hexauronic acid decarboxylating).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: UDP-alpha-D-glucuronate + NAD+ = UDP-beta-L-threo-pentapyranos-4-ulose + CO2 + NADH
UDP-alpha-D-glucuronate
Bound ligand (Het Group name = U5P)
matches with 41.00% similarity
+ NAD(+)
= UDP-beta-L-threo-pentapyranos-4-ulose
+ CO(2)
+ NADH
   Enzyme class 3: E.C.2.1.2.13  - UDP-4-amino-4-deoxy-L-arabinose formyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinose = 5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinose
10-formyltetrahydrofolate
+ UDP-4-amino-4-deoxy-beta-L-arabinose
= 5,6,7,8-tetrahydrofolate
+ UDP-4-deoxy-4-formamido-beta-L-arabinose
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
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biosynthetic process   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M501534200 J Biol Chem 280:23000-23008 (2005)
PubMed id: 15809294  
 
 
Structure and function of both domains of ArnA, a dual function decarboxylase and a formyltransferase, involved in 4-amino-4-deoxy-L-arabinose biosynthesis.
G.J.Williams, S.D.Breazeale, C.R.Raetz, J.H.Naismith.
 
  ABSTRACT  
 
Modification of the lipid A moiety of lipopolysaccharide by the addition of the sugar 4-amino-4-deoxy-L-arabinose (L-Ara4N) 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, because inhibiting its synthesis would render certain pathogens more sensitive to the immune system. The bifunctional enzyme ArnA, which is required for L-Ara4N biosynthesis, 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-L-Ara4N. We now report the crystal structure of the N-terminal formyltransferase domain in a complex with uridine monophosphate and N-5-formyltetrahydrofolate. Using this structure, we identify the active site of formyltransfer in ArnA, including the key catalytic residues Asn(102), His(104), and Asp(140). Additionally, we have shown that residues Ser(433) and Glu(434) of the decarboxylase domain are required for the oxidative decarboxylation of UDP-GlcUA. An E434Q mutant is inactive, suggesting that chemical rather than steric properties of this residue are crucial in the decarboxylation reaction. Our data suggest that the decarboxylase domain catalyzes both hydride abstraction (oxidation) from the C-4' position and the subsequent decarboxylation.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. The assembly process for the modification of LPS by L-Ara4N (22, 24).
Figure 5.
FIG. 5. A plausible mechanism for the catalysis of the decarboxylation reaction. The carboxylic acid group of substrate is shown protonated, although in solution we would have expected it to be deprotonated. However, the E434Q mutant is inactive, and we suggest that it is required to ensure deprotonation of the keto intermediate. The carboxylate form of the keto intermediate is expected to spontaneously decompose without the need for any further catalysis.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 23000-23008) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21370975 M.Bar-Peled, and M.A.O'Neill (2011).
Plant nucleotide sugar formation, interconversion, and salvage by sugar recycling.
  Annu Rev Plant Biol, 62, 127-155.  
18187325 T.Kline, M.S.Trent, C.M.Stead, M.S.Lee, M.C.Sousa, H.B.Felise, H.V.Nguyen, and S.I.Miller (2008).
Synthesis of and evaluation of lipid A modification by 4-substituted 4-deoxy arabinose analogs as potential inhibitors of bacterial polymyxin resistance.
  Bioorg Med Chem Lett, 18, 1507-1510.  
17928292 A.Yan, Z.Guan, and C.R.Raetz (2007).
An undecaprenyl phosphate-aminoarabinose flippase required for polymyxin resistance in Escherichia coli.
  J Biol Chem, 282, 36077-36089.  
17362200 C.R.Raetz, C.M.Reynolds, M.S.Trent, and R.E.Bishop (2007).
Lipid A modification systems in gram-negative bacteria.
  Annu Rev Biochem, 76, 295-329.  
17302813 H.Ren, L.G.Dover, S.T.Islam, D.C.Alexander, J.M.Chen, G.S.Besra, and J.Liu (2007).
Identification of the lipooligosaccharide biosynthetic gene cluster from Mycobacterium marinum.
  Mol Microbiol, 63, 1345-1359.  
17693522 M.Skurnik, M.Biedzka-Sarek, P.S.Lübeck, T.Blom, J.A.Bengoechea, C.Pérez-Gutiérrez, P.Ahrens, and J.Hoorfar (2007).
Characterization and biological role of the O-polysaccharide gene cluster of Yersinia enterocolitica serotype O:9.
  J Bacteriol, 189, 7244-7253.  
17449614 S.R.Murray, R.K.Ernst, D.Bermudes, S.I.Miller, and K.B.Low (2007).
pmrA(Con) confers pmrHFIJKL-dependent EGTA and polymyxin resistance on msbB Salmonella by decorating lipid A with phosphoethanolamine.
  J Bacteriol, 189, 5161-5169.  
16807947 E.Vinogradov, B.Lindner, G.Seltmann, J.Radziejewska-Lebrecht, and O.Holst (2006).
Lipopolysaccharides from Serratia marcescens possess one or two 4-amino-4-deoxy-L-arabinopyranose 1-phosphate residues in the lipid A and D-glycero-D-talo-oct-2-ulopyranosonic acid in the inner core region.
  Chemistry, 12, 6692-6700.  
16936924 J.H.Naismith (2006).
Inferring the chemical mechanism from structures of enzymes.
  Chem Soc Rev, 35, 763-770.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.