spacer
spacer

PDBsum entry 1mdx
Go to PDB code: 
protein ligands links
Transferase PDB id
1mdx

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
366 a.a. *
Ligands
AKG
GOL ×2
Waters ×442
* Residue conservation analysis
PDB id:
1mdx
Name: Transferase
Title: Crystal structure of arnb transferase with pyridoxal 5' phosphate
Structure: Udp-4-amino-4-deoxy-l-arabinose--oxoglutarate aminotransferase. Chain: a. Synonym: polymyxin resistance protein pmrh,udp-(beta-l-threo- pentapyranosyl-4''-ulose diphosphate) aminotransferase,udp-ara4o aminotransferase,udp-4-amino-4-deoxy-l-arabinose aminotransferase. Engineered: yes
Source: Salmonella enterica subsp. Enterica serovar typhimurium. Organism_taxid: 90371. Gene: arnb, pbgp, pbgp1, pmrh, stm2297. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.96Å     R-factor:   0.206     R-free:   0.241
Authors: B.W.Noland,J.M.Newman,J.Hendle,J.Badger,J.A.Christopher,J.Tresser, M.D.Buchanan,T.A.Wright,M.E.Rutter,W.E.Sanderson,H.-J.Muller- Dieckmann,K.S.Gajiwala,J.M.Sauder,S.G.Buchanan
Key ref:
B.W.Noland et al. (2002). Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: a 4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying enzyme. Structure, 10, 1569-1580. PubMed id: 12429098 DOI: 10.1016/S0969-2126(02)00879-1
Date:
07-Aug-02     Release date:   11-Dec-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8ZNF3  (ARNB_SALTY) -  UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Seq:
Struc: 		385 a.a.
366 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.6.1.87  - UDP-4-amino-4-deoxy-L-arabinose aminotransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: UDP-4-amino-4-deoxy-beta-L-arabinose + 2-oxoglutarate = UDP-beta-L-threo- pentopyranos-4-ulose + L-glutamate
UDP-4-amino-4-deoxy-beta-L-arabinose
 +
2-oxoglutarate
Bound ligand (Het Group name = AKG)
corresponds exactly 		= UDP-beta-L-threo- pentopyranos-4-ulose
 + L-glutamate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(02)00879-1 Structure 10:1569-1580 (2002)
PubMed id: 12429098  
 
 
Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: a 4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying enzyme.
B.W.Noland, J.M.Newman, J.Hendle, J.Badger, J.A.Christopher, J.Tresser, M.D.Buchanan, T.A.Wright, M.E.Rutter, W.E.Sanderson, H.J.Müller-Dieckmann, K.S.Gajiwala, S.G.Buchanan.
 
  ABSTRACT  
 
Lipid A modification with 4-amino-4-deoxy-L-arabinose confers on certain pathogenic bacteria, such as Salmonella, resistance to cationic antimicrobial peptides, including those derived from the innate immune system. ArnB catalysis of amino group transfer from glutamic acid to the 4"-position of a UDP-linked ketopyranose molecule to form UDP-4-amino-4-deoxy-L-arabinose represents a key step in the lipid A modification pathway. Structural and functional studies of the ArnB aminotransferase were undertaken by combining X-ray crystallography with biochemical analyses. High-resolution crystal structures were solved for two native forms and one covalently inhibited form of S. typhimurium ArnB. These structures permitted identification of key residues involved in substrate binding and catalysis, including a rarely observed nonprolyl cis peptide bond in the active site.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. Proposed ArnB Enzyme Mechanism(A) The first half-reaction.(B) The second half-reaction. The lysine residue is Lys188.
 
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 1569-1580) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20832292 H.M.Holden, P.D.Cook, and J.B.Thoden (2010).
Biosynthetic enzymes of unusual microbial sugars.
  Curr Opin Struct Biol, 20, 543-550.  
20445930 J.Lowther, B.A.Yard, K.A.Johnson, L.G.Carter, V.T.Bhat, M.C.Raman, D.J.Clarke, B.Ramakers, S.A.McMahon, J.H.Naismith, and D.J.Campopiano (2010).
Inhibition of the PLP-dependent enzyme serine palmitoyltransferase by cycloserine: evidence for a novel decarboxylative mechanism of inactivation.
  Mol Biosyst, 6, 1682-1693.
PDB code: 2xbn
19178182 J.B.Thoden, C.Schäffer, P.Messner, and H.M.Holden (2009).
Structural analysis of QdtB, an aminotransferase required for the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-glucose.
  Biochemistry, 48, 1553-1561.
PDB code: 3frk
18837991 M.H.Karavolos, H.Spencer, D.M.Bulmer, A.Thompson, K.Winzer, P.Williams, J.C.Hinton, and C.M.Khan (2008).
Adrenaline modulates the global transcriptional profile of Salmonella revealing a role in the antimicrobial peptide and oxidative stress resistance responses.
  BMC Genomics, 9, 458.  
18045869 P.D.Cook, and H.M.Holden (2008).
GDP-4-keto-6-deoxy-D-mannose 3-dehydratase, accommodating a sugar substrate in the active site.
  J Biol Chem, 283, 4295-4303.
PDB code: 3b8x
18491919 P.Smith, P.H.Szu, C.Bui, H.W.Liu, and S.C.Tsai (2008).
Structure and mutagenic conversion of E1 dehydrase: at the crossroads of dehydration, amino transfer, and epimerization.
  Biochemistry, 47, 6329-6341.  
18316383 W.B.Wang, I.C.Chen, S.S.Jiang, H.R.Chen, C.Y.Hsu, P.R.Hsueh, W.B.Hsu, and S.J.Liaw (2008).
Role of RppA in the regulation of polymyxin b susceptibility, swarming, and virulence factor expression in Proteus mirabilis.
  Infect Immun, 76, 2051-2062.  
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.  
17630700 E.S.Burgie, and H.M.Holden (2007).
Molecular architecture of DesI: a key enzyme in the biosynthesis of desosamine.
  Biochemistry, 46, 8999-9006.
PDB code: 2po3
17456741 E.S.Burgie, J.B.Thoden, and H.M.Holden (2007).
Molecular architecture of DesV from Streptomyces venezuelae: a PLP-dependent transaminase involved in the biosynthesis of the unusual sugar desosamine.
  Protein Sci, 16, 887-896.
PDB codes: 2oga 2oge
17323931 Q.Wu, Y.N.Liu, H.Chen, E.J.Molitor, and H.W.Liu (2007).
A retro-evolution study of CDP-6-deoxy-D-glycero-L-threo-4-hexulose-3-dehydrase (E1) from Yersinia pseudotuberculosis: implications for C-3 deoxygenation in the biosynthesis of 3,6-dideoxyhexoses.
  Biochemistry, 46, 3759-3767.  
17918933 S.G.Van Lanen, T.J.Oh, W.Liu, E.Wendt-Pienkowski, and B.Shen (2007).
Characterization of the maduropeptin biosynthetic gene cluster from Actinomadura madurae ATCC 39144 supporting a unifying paradigm for enediyne biosynthesis.
  J Am Chem Soc, 129, 13082-13094.  
16894611 B.Popovic, X.Tang, D.Y.Chirgadze, F.Huang, T.L.Blundell, and J.B.Spencer (2006).
Crystal structures of the PLP- and PMP-bound forms of BtrR, a dual functional aminotransferase involved in butirosin biosynthesis.
  Proteins, 65, 220-230.
PDB codes: 2c7t 2c81
16943443 P.D.Cook, J.B.Thoden, and H.M.Holden (2006).
The structure of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: a unique coenzyme B6-dependent enzyme.
  Protein Sci, 15, 2093-2106.
PDB codes: 2gms 2gmu
15608117 A.P.Dubnovitsky, E.G.Kapetaniou, and A.C.Papageorgiou (2005).
Enzyme adaptation to alkaline pH: atomic resolution (1.08 A) structure of phosphoserine aminotransferase from Bacillus alcalophilus.
  Protein Sci, 14, 97.
PDB codes: 1w23 1w3u
15883191 A.P.Dubnovitsky, R.B.Ravelli, A.N.Popov, and A.C.Papageorgiou (2005).
Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage.
  Protein Sci, 14, 1498-1507.
PDB codes: 2bhx 2bi1 2bi2 2bi3 2bi5 2bi9 2bia 2bie 2big
15809294 G.J.Williams, S.D.Breazeale, C.R.Raetz, and J.H.Naismith (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.
PDB codes: 2bll 2bln
16021622 J.Badger, J.M.Sauder, J.M.Adams, S.Antonysamy, K.Bain, M.G.Bergseid, S.G.Buchanan, M.D.Buchanan, Y.Batiyenko, J.A.Christopher, S.Emtage, A.Eroshkina, I.Feil, E.B.Furlong, K.S.Gajiwala, X.Gao, D.He, J.Hendle, A.Huber, K.Hoda, P.Kearins, C.Kissinger, B.Laubert, H.A.Lewis, J.Lin, K.Loomis, D.Lorimer, G.Louie, M.Maletic, C.D.Marsh, I.Miller, J.Molinari, H.J.Muller-Dieckmann, J.M.Newman, B.W.Noland, B.Pagarigan, F.Park, T.S.Peat, K.W.Post, S.Radojicic, A.Ramos, R.Romero, M.E.Rutter, W.E.Sanderson, K.D.Schwinn, J.Tresser, J.Winhoven, T.A.Wright, L.Wu, J.Xu, and T.J.Harris (2005).
Structural analysis of a set of proteins resulting from a bacterial genomics project.
  Proteins, 60, 787-796.
PDB codes: 1o60 1o61 1o62 1o63 1o64 1o65 1o66 1o67 1o68 1o69 1o6b 1o6c 1o6d 1vgt 1vgu 1vgv 1vgw 1vgx 1vgy 1vgz 1vh0 1vh1 1vh2 1vh3 1vh4 1vh5 1vh6 1vh7 1vh8 1vh9 1vha 1vhc 1vhd 1vhe 1vhf 1vhg 1vhj 1vhk 1vhl 1vhm 1vho 1vhq 1vhs 1vht 1vhu 1vhv 1vhw 1vhx 1vhy 1vhz 1vi0 1vi1 1vi2 1vi3 1vi4 1vi5 1vi6 1vi8 1vi9 1via 1vic 1vim 1viq 1vis 1viu 1viv 1vix 1viy 1viz
15939024 P.Z.Gatzeva-Topalova, A.P.May, and M.C.Sousa (2005).
Structure and mechanism of ArnA: conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance.
  Structure, 13, 929-942.
PDB codes: 1z73 1z74 1z75 1z7b 1z7e
15695810 S.D.Breazeale, A.A.Ribeiro, A.L.McClerren, and C.R.Raetz (2005).
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.  
15634672 T.E.Carver, B.Bordeau, M.D.Cummings, E.C.Petrella, M.J.Pucci, L.E.Zawadzke, B.A.Dougherty, J.A.Tredup, J.W.Bryson, J.Yanchunas, M.L.Doyle, M.R.Witmer, M.I.Nelen, R.L.DesJarlais, E.P.Jaeger, H.Devine, E.D.Asel, B.A.Springer, R.Bone, F.R.Salemme, and M.J.Todd (2005).
Decrypting the biochemical function of an essential gene from Streptococcus pneumoniae using ThermoFluor technology.
  J Biol Chem, 280, 11704-11712.  
15498941 A.Paiardini, F.Bossa, and S.Pascarella (2004).
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes.
  Protein Sci, 13, 2992-3005.  
15052329 M.S.Trent (2004).
Biosynthesis, transport, and modification of lipid A.
  Biochem Cell Biol, 82, 71-86.  
12704196 S.D.Breazeale, A.A.Ribeiro, and C.R.Raetz (2003).
Origin of lipid A species modified with 4-amino-4-deoxy-L-arabinose in polymyxin-resistant mutants of Escherichia coli. An aminotransferase (ArnB) that generates UDP-4-deoxyl-L-arabinose.
  J Biol Chem, 278, 24731-24739.  
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. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

spacer
spacer