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PDBsum entry 1f0k

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1f0k
Jmol
Contents
Protein chains
351 a.a. *
Ligands
SO4
Waters ×296
* Residue conservation analysis
PDB id:
1f0k
Name: Transferase
Title: The 1.9 angstrom crystal structure of e. Coli murg
Structure: Udp-n-acetylglucosamine-n-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol n- acetylglucosamine transferase. Chain: a, b. Synonym: murg. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.90Å     R-factor:   0.220     R-free:   0.247
Authors: S.Ha,D.Walker,Y.Shi,S.Walker
Key ref: S.Ha et al. (2000). The 1.9 A crystal structure of Escherichia coli MurG, a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis. Protein Sci, 9, 1045-1052. PubMed id: 10892798 DOI: 10.1110/ps.9.6.1045
Date:
16-May-00     Release date:   27-Jul-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P17443  (MURG_ECOLI) -  UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
Seq:
Struc:
355 a.a.
351 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.1.227  - Undecaprenyldiphospho-muramoylpentapeptide beta-N-
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Peptidoglycan Biosynthesis (Part 2)
      Reaction: UDP-N-acetylglucosamine + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D- Ala)-diphosphoundecaprenol = UDP + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma- D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol
UDP-N-acetylglucosamine
+ Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D- Ala)-diphosphoundecaprenol
= UDP
+ GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma- D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     cell cycle   7 terms 
  Biochemical function     UDP-N-acetyl-D-glucosamine:N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol 4-beta-N-acetylglucosaminlytransferase activity     6 terms  

 

 
    Added reference    
 
 
DOI no: 10.1110/ps.9.6.1045 Protein Sci 9:1045-1052 (2000)
PubMed id: 10892798  
 
 
The 1.9 A crystal structure of Escherichia coli MurG, a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis.
S.Ha, D.Walker, Y.Shi, S.Walker.
 
  ABSTRACT  
 
The 1.9 A X-ray structure of a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis is reported. This enzyme, MurG, contains two alpha/beta open sheet domains separated by a deep cleft. Structural analysis suggests that the C-terminal domain contains the UDP-GlcNAc binding site while the N-terminal domain contains the acceptor binding site and likely membrane association site. Combined with sequence data from other MurG homologs, this structure provides insight into the residues that are important in substrate binding and catalysis. We have also noted that a conserved region found in many UDP-sugar transferases maps to a beta/alpha/beta/alpha supersecondary structural motif in the donor binding region of MurG, an observation that may be helpful in glycosyltransferase structure prediction. The identification of a conserved structural motif involved in donor binding in different UDP-sugar transferases also suggests that it may be possible to identify--and perhaps alter--the residues that help determine donor specificity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21240259 M.B.Lazarus, Y.Nam, J.Jiang, P.Sliz, and S.Walker (2011).
Structure of human O-GlcNAc transferase and its complex with a peptide substrate.
  Nature, 469, 564-567.
PDB codes: 3pe3 3pe4
20400947 A.L.Lovering, L.Y.Lin, E.W.Sewell, T.Spreter, E.D.Brown, and N.C.Strynadka (2010).
Structure of the bacterial teichoic acid polymerase TagF provides insights into membrane association and catalysis.
  Nat Struct Mol Biol, 17, 582-589.
PDB codes: 3l7i 3l7j 3l7k 3l7l 3l7m
20644141 A.M.Michaelis, and Z.Gitai (2010).
Dynamic polar sequestration of excess MurG may regulate enzymatic function.
  J Bacteriol, 192, 4597-4605.  
20672277 G.K.Wagner, and T.Pesnot (2010).
Glycosyltransferases and their assays.
  Chembiochem, 11, 1939-1949.  
19656295 B.Henrichfreise, A.Schiefer, T.Schneider, E.Nzukou, C.Poellinger, T.J.Hoffmann, K.L.Johnston, K.Moelleken, I.Wiedemann, K.Pfarr, A.Hoerauf, and H.G.Sahl (2009).
Functional conservation of the lipid II biosynthesis pathway in the cell wall-less bacteria Chlamydia and Wolbachia: why is lipid II needed?
  Mol Microbiol, 73, 913-923.  
19129246 C.Noffz, S.Keppler-Ross, and N.Dean (2009).
Hetero-oligomeric interactions between early glycosyltransferases of the dolichol cycle.
  Glycobiology, 19, 472-478.  
19483088 E.S.Rangarajan, A.Proteau, Q.Cui, S.M.Logan, Z.Potetinova, D.Whitfield, E.O.Purisima, M.Cygler, A.Matte, T.Sulea, and I.C.Schoenhofen (2009).
Structural and functional analysis of Campylobacter jejuni PseG: a udp-sugar hydrolase from the pseudaminic acid biosynthetic pathway.
  J Biol Chem, 284, 20989-21000.
PDB codes: 3hbm 3hbn
19767390 H.M.Eriksson, P.Wessman, C.Ge, K.Edwards, and A.Wieslander (2009).
Massive formation of intracellular membrane vesicles in Escherichia coli by a monotopic membrane-bound lipid glycosyltransferase.
  J Biol Chem, 284, 33904-33914.  
18081839 A.Bouhss, A.E.Trunkfield, T.D.Bugg, and D.Mengin-Lecreulx (2008).
The biosynthesis of peptidoglycan lipid-linked intermediates.
  FEMS Microbiol Rev, 32, 208-233.  
17876818 A.C.Johansson, and E.Lindahl (2008).
Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations.
  Proteins, 70, 1332-1344.  
18627619 C.J.Zea, G.Camci-Unal, and N.L.Pohl (2008).
Thermodynamics of binding of divalent magnesium and manganese to uridine phosphates: implications for diabetes-related hypomagnesaemia and carbohydrate biocatalysis.
  Chem Cent J, 2, 15.  
18518825 L.L.Lairson, B.Henrissat, G.J.Davies, and S.G.Withers (2008).
Glycosyltransferases: structures, functions, and mechanisms.
  Annu Rev Biochem, 77, 521-555.  
18291013 T.den Blaauwen, M.A.de Pedro, M.Nguyen-Distèche, and J.A.Ayala (2008).
Morphogenesis of rod-shaped sacculi.
  FEMS Microbiol Rev, 32, 321-344.  
18809682 X.D.Gao, S.Moriyama, N.Miura, N.Dean, and S.Nishimura (2008).
Interaction between the C termini of Alg13 and Alg14 mediates formation of the active UDP-N-acetylglucosamine transferase complex.
  J Biol Chem, 283, 32534-32541.  
18075661 X.H.Xu, A.E.Trunkfield, T.D.Bugg, and F.L.Qing (2008).
Synthesis of gem-difluorinated nucleoside analogues of the liposidomycins and evaluation as MraY inhibitors.
  Org Biomol Chem, 6, 157-161.  
17379141 B.Ostash, A.Saghatelian, and S.Walker (2007).
A streamlined metabolic pathway for the biosynthesis of moenomycin A.
  Chem Biol, 14, 257-267.  
17376874 D.N.Bolam, S.Roberts, M.R.Proctor, J.P.Turkenburg, E.J.Dodson, C.Martinez-Fleites, M.Yang, B.G.Davis, G.J.Davies, and H.J.Gilbert (2007).
The crystal structure of two macrolide glycosyltransferases provides a blueprint for host cell antibiotic immunity.
  Proc Natl Acad Sci U S A, 104, 5336-5341.
PDB codes: 2iya 2iyf
18063720 J.van Heijenoort (2007).
Lipid intermediates in the biosynthesis of bacterial peptidoglycan.
  Microbiol Mol Biol Rev, 71, 620-635.  
17442341 M.J.Miley, A.K.Zielinska, J.E.Keenan, S.M.Bratton, A.Radominska-Pandya, and M.R.Redinbo (2007).
Crystal structure of the cofactor-binding domain of the human phase II drug-metabolism enzyme UDP-glucuronosyltransferase 2B7.
  J Mol Biol, 369, 498-511.
PDB code: 2o6l
17120230 M.K.Kim, M.K.Cho, H.E.Song, D.Kim, B.H.Park, J.H.Lee, G.B.Kang, S.H.Kim, Y.J.Im, D.S.Lee, and S.H.Eom (2007).
Crystal structure of UDP-N-acetylenolpyruvylglucosamine reductase (MurB) from Thermus caldophilus.
  Proteins, 66, 751-754.
PDB codes: 2gqt 2gqu
17640276 T.Mohammadi, A.Karczmarek, M.Crouvoisier, A.Bouhss, D.Mengin-Lecreulx, and T.den Blaauwen (2007).
The essential peptidoglycan glycosyltransferase MurG forms a complex with proteins involved in lateral envelope growth as well as with proteins involved in cell division in Escherichia coli.
  Mol Microbiol, 65, 1106-1121.  
17501931 V.van Dam, R.Sijbrandi, M.Kol, E.Swiezewska, B.de Kruijff, and E.Breukink (2007).
Transmembrane transport of peptidoglycan precursors across model and bacterial membranes.
  Mol Microbiol, 64, 1105-1114.  
  16511286 D.U.Kim, J.H.Yoo, K.Ryu, and H.S.Cho (2006).
Crystallization and preliminary X-ray crystallographic analysis of the alpha-2,6-sialyltransferase PM0188 from Pasteurella multosida.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 142-144.  
  16946469 M.Barreras, M.A.Bianchet, and L.Ielpi (2006).
Crystallization and preliminary crystallographic characterization of GumK, a membrane-associated glucuronosyltransferase from Xanthomonas campestris required for xanthan polysaccharide synthesis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 880-883.  
17181409 P.Fulco, and R.P.Wenzel (2006).
Ramoplanin: a topical lipoglycodepsipeptide antibacterial agent.
  Expert Rev Anti Infect Ther, 4, 939-945.  
16953575 Y.H.Zhang, C.Ginsberg, Y.Yuan, and S.Walker (2006).
Acceptor substrate selectivity and kinetic mechanism of Bacillus subtilis TagA.
  Biochemistry, 45, 10895-10904.  
16007668 C.J.Zea, and N.L.Pohl (2005).
Unusual sugar nucleotide recognition elements of mesophilic vs. thermophilic glycogen synthases.
  Biopolymers, 79, 106-113.  
15793120 S.Ravishankar, V.P.Kumar, B.Chandrakala, R.K.Jha, S.M.Solapure, and S.M.de Sousa (2005).
Scintillation proximity assay for inhibitors of Escherichia coli MurG and, optionally, MraY.
  Antimicrob Agents Chemother, 49, 1410-1418.  
14730352 C.P.Chiu, A.G.Watts, L.L.Lairson, M.Gilbert, D.Lim, W.W.Wakarchuk, S.G.Withers, and N.C.Strynadka (2004).
Structural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with a substrate analog.
  Nat Struct Mol Biol, 11, 163-170.
PDB codes: 1ro7 1ro8
12874381 A.M.Mulichak, H.C.Losey, W.Lu, Z.Wawrzak, C.T.Walsh, and R.M.Garavito (2003).
Structure of the TDP-epi-vancosaminyltransferase GtfA from the chloroeremomycin biosynthetic pathway.
  Proc Natl Acad Sci U S A, 100, 9238-9243.
PDB codes: 1pn3 1pnv
12655644 B.Eisenhaber, S.Maurer-Stroh, M.Novatchkova, G.Schneider, and F.Eisenhaber (2003).
Enzymes and auxiliary factors for GPI lipid anchor biosynthesis and post-translational transfer to proteins.
  Bioessays, 25, 367-385.  
14646108 C.Horcajada, E.Cid, J.J.Guinovart, N.Verdaguer, and J.C.Ferrer (2003).
Crystallization and preliminary X-ray analysis of the glycogen synthase from Pyrococcus abyssi.
  Acta Crystallogr D Biol Crystallogr, 59, 2322-2324.  
12813070 E.van den Brink-van der Laan, J.W.Boots, R.E.Spelbrink, G.M.Kool, E.Breukink, J.A.Killian, and B.de Kruijff (2003).
Membrane interaction of the glycosyltransferase MurG: a special role for cardiolipin.
  J Bacteriol, 185, 3773-3779.  
12824488 J.Liu, and A.Mushegian (2003).
Three monophyletic superfamilies account for the majority of the known glycosyltransferases.
  Protein Sci, 12, 1418-1431.  
12876312 N.Handa, T.Terada, Y.Kamewari, H.Hamana, J.R.Tame, S.Y.Park, K.Kinoshita, M.Ota, H.Nakamura, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2003).
Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8.
  Protein Sci, 12, 1621-1632.
PDB code: 1uan
12803927 T.D.Butters, H.R.Mellor, K.Narita, R.A.Dwek, and F.M.Platt (2003).
Small-molecule therapeutics for the treatment of glycolipid lysosomal storage disorders.
  Philos Trans R Soc Lond B Biol Sci, 358, 927-945.  
12538870 Y.Hu, L.Chen, S.Ha, B.Gross, B.Falcone, D.Walker, M.Mokhtarzadeh, and S.Walker (2003).
Crystal structure of the MurG:UDP-GlcNAc complex reveals common structural principles of a superfamily of glycosyltransferases.
  Proc Natl Acad Sci U S A, 100, 845-849.
PDB code: 1nlm
14500887 Z.Zhang, S.Kochhar, and M.Grigorov (2003).
Exploring the sequence-structure protein landscape in the glycosyltransferase family.
  Protein Sci, 12, 2291-2302.  
11901475 D.W.Green (2002).
The bacterial cell wall as a source of antibacterial targets.
  Expert Opin Ther Targets, 6, 1.  
12470732 K.Lazar, and S.Walker (2002).
Substrate analogues to study cell-wall biosynthesis and its inhibition.
  Curr Opin Chem Biol, 6, 786-793.  
12022887 L.Chen, H.Men, S.Ha, X.Y.Ye, L.Brunner, Y.Hu, and S.Walker (2002).
Intrinsic lipid preferences and kinetic mechanism of Escherichia coli MurG.
  Biochemistry, 41, 6824-6833.  
12198310 L.Larivière, J.Kurzeck, U.Aschke-Sonnenborn, W.Rüger, and S.Moréra (2002).
Crystallization and preliminary crystallographic study of a ternary complex between the T4 phage beta-glucosyltransferase, uridine diphosphoglucose and a DNA fragment containing an abasic site.
  Acta Crystallogr D Biol Crystallogr, 58, 1484-1486.  
12199709 M.Tenno, S.Toba, F.J.Kézdy, A.P.Elhammer, and A.Kurosaka (2002).
Identification of two cysteine residues involved in the binding of UDP-GalNAc to UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 1 (GalNAc-T1).
  Eur J Biochem, 269, 4308-4316.  
11807274 R.P.Gibson, R.M.Lloyd, S.J.Charnock, and G.J.Davies (2002).
Characterization of Escherichia coli OtsA, a trehalose-6-phosphate synthase from glycosyltransferase family 20.
  Acta Crystallogr D Biol Crystallogr, 58, 349-351.  
11410375 D.Hoffmeister, K.Ichinose, and A.Bechthold (2001).
Two sequence elements of glycosyltransferases involved in urdamycin biosynthesis are responsible for substrate specificity and enzymatic activity.
  Chem Biol, 8, 557-567.  
11398978 E.J.Hehre (2001).
Glycosyl transfer: a history of the concept's development and view of its major contributions to biochemistry.
  Carbohydr Res, 331, 347-368.  
11327854 T.E.Benson, M.S.Harris, G.H.Choi, J.I.Cialdella, J.T.Herberg, J.P.Martin, and E.T.Baldwin (2001).
A structural variation for MurB: X-ray crystal structure of Staphylococcus aureus UDP-N-acetylenolpyruvylglucosamine reductase (MurB).
  Biochemistry, 40, 2340-2350.
PDB code: 1hsk
11717264 V.Chazalet, K.Uehara, R.A.Geremia, and C.Breton (2001).
Identification of essential amino acids in the Azorhizobium caulinodans fucosyltransferase NodZ.
  J Bacteriol, 183, 7067-7075.  
11114903 W.J.Keenleyside, A.J.Clarke, and C.Whitfield (2001).
Identification of residues involved in catalytic activity of the inverting glycosyl transferase WbbE from Salmonella enterica serovar borreze.
  J Bacteriol, 183, 77-85.  
11785761 Y.Bourne, and B.Henrissat (2001).
Glycoside hydrolases and glycosyltransferases: families and functional modules.
  Curr Opin Struct Biol, 11, 593-600.  
11042447 U.M.Unligil, and J.M.Rini (2000).
Glycosyltransferase structure and mechanism.
  Curr Opin Struct Biol, 10, 510-517.  
11032794 U.M.Unligil, S.Zhou, S.Yuwaraj, M.Sarkar, H.Schachter, and J.M.Rini (2000).
X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily.
  EMBO J, 19, 5269-5280.
PDB codes: 1fo8 1fo9 1foa
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 codes are shown on the right.