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PDBsum entry 1g1l

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1g1l
Jmol
Contents
Protein chains
(+ 2 more) 292 a.a. *
Ligands
SO4 ×23
DAU ×16
CIT ×2
Waters ×2971
* Residue conservation analysis
PDB id:
1g1l
Name: Transferase
Title: The structural basis of the catalytic mechanism and regulati glucose-1-phosphate thymidylyltransferase (rmla). Tdp-gluco complex.
Structure: Glucose-1-phosphate thymidylyltransferase. Chain: a, b, c, d, e, f, g, h. Synonym: glucose-1-phosphate thymidylyltransferase (rmla). Engineered: yes
Source: Pseudomonas aeruginosa. Organism_taxid: 287. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.77Å     R-factor:   0.159     R-free:   0.215
Authors: W.Blankenfeldt,M.Asuncion,J.S.Lam,J.H.Naimsmith
Key ref:
W.Blankenfeldt et al. (2000). The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA). EMBO J, 19, 6652-6663. PubMed id: 11118200 DOI: 10.1093/emboj/19.24.6652
Date:
12-Oct-00     Release date:   27-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9HU22  (Q9HU22_PSEAE) -  Glucose-1-phosphate thymidylyltransferase
Seq:
Struc:
293 a.a.
292 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.24  - Glucose-1-phosphate thymidylyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
6-Deoxyhexose Biosynthesis
      Reaction: dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-alpha-D-glucose
dTTP
+ alpha-D-glucose 1-phosphate
= diphosphate
+
dTDP-alpha-D-glucose
Bound ligand (Het Group name = DAU)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biosynthetic process   2 terms 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1093/emboj/19.24.6652 EMBO J 19:6652-6663 (2000)
PubMed id: 11118200  
 
 
The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA).
W.Blankenfeldt, M.Asuncion, J.S.Lam, J.H.Naismith.
 
  ABSTRACT  
 
The synthesis of deoxy-thymidine di-phosphate (dTDP)-L-rhamnose, an important component of the cell wall of many microorganisms, is a target for therapeutic intervention. The first enzyme in the dTDP-L-rhamnose biosynthetic pathway is glucose-1-phosphate thymidylyltransferase (RmlA). RmlA is inhibited by dTDP-L-rhamnose thereby regulating L-rhamnose production in bacteria. The structure of Pseudomonas aeruginosa RmlA has been solved to 1.66 A resolution. RmlA is a homotetramer, with the monomer consisting of three functional subdomains. The sugar binding and dimerization subdomains are unique to RmlA-like enzymes. The sequence of the core subdomain is found not only in sugar nucleotidyltransferases but also in other nucleotidyltransferases. The structures of five distinct enzyme substrate- product complexes reveal the enzyme mechanism that involves precise positioning of the nucleophile and activation of the electrophile. All the key residues are within the core subdomain, suggesting that the basic mechanism is found in many nucleotidyltransferases. The dTDP-L-rhamnose complex identifies how the protein is controlled by its natural inhibitor. This work provides a platform for the design of novel drugs against pathogenic bacteria.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 (A) The mechanism of the reaction catalysed by RmlA. (B) The distinct chemical groups that form the ternary complex with the protein.
Figure 2.
Figure 2 (A) Stereo ribbon diagram of the RmlA monomer with location of secondary structure elements. The different colours denote the three subdomains. Yellow is the core binding subdomain, light blue is the sugar-binding subdomain and magenta the dimerization subdomain. The character represents a 3[10] helix, and and have their normal meaning. Secondary structure was assigned with DSSP (Kabsch and Sander, 1983). (B) A ribbon representation of the RmlA tetramer. The monomers are coloured red, monomer A; blue, monomer B; yellow, monomer A'; and light blue, monomer B'. G-1-P (black) and dTTP (green) are shown at the active sites in ball-and-stick format. dTDP–L-rhamnose (magenta) is shown in the secondary binding sites, again as a ball-and-stick diagram. (C) Same as (B), rotated by 90° around the y-axis. All molecular representations are prepared with BOBSCRIPT (Esnouf, 1997) through the GL_RENDER interface (L.Esser and J.Deisenhofer, unpublished data) and were rendered with POV-Ray™.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 6652-6663) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21498076 R.S.Reis, A.G.Pereira, B.C.Neves, and D.M.Freire (2011).
Gene regulation of rhamnolipid production in Pseudomonas aeruginosa--a review.
  Bioresour Technol, 102, 6377-6384.  
19919534 H.Denton, S.Fyffe, and T.K.Smith (2010).
GDP-mannose pyrophosphorylase is essential in the bloodstream form of Trypanosoma brucei.
  Biochem J, 425, 603-614.  
20238176 H.Kim, J.Choi, T.Kim, N.K.Lokanath, S.C.Ha, S.W.Suh, H.Y.Hwang, and K.K.Kim (2010).
Structural basis for the reaction mechanism of UDP-glucose pyrophosphorylase.
  Mol Cells, 29, 397-405.
PDB codes: 3juj 3juk
18807197 D.Simkhada, T.J.Oh, E.M.Kim, J.C.Yoo, and J.K.Sohng (2009).
Cloning and characterization of CalS7 from Micromonospora echinospora sp. calichensis as a glucose-1-phosphate nucleotidyltransferase.
  Biotechnol Lett, 31, 147-153.  
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.  
17893902 D.J.McNally, I.C.Schoenhofen, R.S.Houliston, N.H.Khieu, D.M.Whitfield, S.M.Logan, H.C.Jarrell, and J.R.Brisson (2008).
CMP-pseudaminic acid is a natural potent inhibitor of PseB, the first enzyme of the pseudaminic acid pathway in Campylobacter jejuni and Helicobacter pylori.
  ChemMedChem, 3, 55-59.  
18219417 M.P.Huestis, G.A.Aish, J.P.Hui, E.C.Soo, and D.L.Jakeman (2008).
Lipophilic sugar nucleotide synthesis by structure-based design of nucleotidylyltransferase substrates.
  Org Biomol Chem, 6, 477-484.  
18387352 R.Moretti, and J.S.Thorson (2008).
A comparison of sugar indicators enables a universal high-throughput sugar-1-phosphate nucleotidyltransferase assay.
  Anal Biochem, 377, 251-258.  
18199755 S.K.Hwang, Y.Nagai, D.Kim, and T.W.Okita (2008).
Direct appraisal of the potato tuber ADP-glucose pyrophosphorylase large subunit in enzyme function by study of a novel mutant form.
  J Biol Chem, 283, 6640-6647.  
18446454 S.L.Rivera, E.Vargas, M.I.Ramírez-Díaz, J.Campos-García, and C.Cervantes (2008).
Genes related to chromate resistance by Pseudomonas aeruginosa PAO1.
  Antonie Van Leeuwenhoek, 94, 299-305.  
17046787 C.Dong, L.L.Major, V.Srikannathasan, J.C.Errey, M.F.Giraud, J.S.Lam, M.Graninger, P.Messner, M.R.McNeil, R.A.Field, C.Whitfield, and J.H.Naismith (2007).
RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation.
  J Mol Biol, 365, 146-159.
PDB codes: 2ixc 2ixh 2ixi 2ixj 2ixk 2ixl
17786898 C.Schäffer, R.Novotny, S.Küpcü, S.Zayni, A.Scheberl, J.Friedmann, U.B.Sleytr, and P.Messner (2007).
Novel biocatalysts based on S-layer self-assembly of Geobacillus stearothermophilus NRS 2004/3a: a nanobiotechnological approach.
  Small, 3, 1549-1559.  
17434970 D.Aragão, A.M.Fialho, A.R.Marques, E.P.Mitchell, I.Sá-Correia, and C.Frazão (2007).
The complex of Sphingomonas elodea ATCC 31461 glucose-1-phosphate uridylyltransferase with glucose-1-phosphate reveals a novel quaternary structure, unique among nucleoside diphosphate-sugar pyrophosphorylase members.
  J Bacteriol, 189, 4520-4528.
PDB code: 2ux8
17392279 D.Maruyama, Y.Nishitani, T.Nonaka, A.Kita, T.A.Fukami, T.Mio, H.Yamada-Okabe, T.Yamada-Okabe, and K.Miki (2007).
Crystal structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans and catalytic reaction mechanism.
  J Biol Chem, 282, 17221-17230.
PDB codes: 2yqc 2yqh 2yqj 2yqs
18029420 I.Mochalkin, S.Lightle, Y.Zhu, J.F.Ohren, C.Spessard, N.Y.Chirgadze, C.Banotai, M.Melnick, and L.McDowell (2007).
Characterization of substrate binding and catalysis in the potential antibacterial target N-acetylglucosamine-1-phosphate uridyltransferase (GlmU).
  Protein Sci, 16, 2657-2666.
PDB codes: 2v0h 2v0i 2v0j 2v0k 2v0l
17322528 J.B.Thoden, and H.M.Holden (2007).
The molecular architecture of glucose-1-phosphate uridylyltransferase.
  Protein Sci, 16, 432-440.
PDB code: 2e3d
17567737 J.B.Thoden, and H.M.Holden (2007).
Active site geometry of glucose-1-phosphate uridylyltransferase.
  Protein Sci, 16, 1379-1388.
PDB code: 2pa4
17303565 T.Steiner, A.C.Lamerz, P.Hess, C.Breithaupt, S.Krapp, G.Bourenkov, R.Huber, R.Gerardy-Schahn, and U.Jacob (2007).
Open and closed structures of the UDP-glucose pyrophosphorylase from Leishmania major.
  J Biol Chem, 282, 13003-13010.
PDB codes: 2oef 2oeg
17079236 C.M.Bejar, X.Jin, M.A.Ballicora, and J.Preiss (2006).
Molecular architecture of the glucose 1-phosphate site in ADP-glucose pyrophosphorylases.
  J Biol Chem, 281, 40473-40484.  
  16946483 D.Aragão, A.R.Marques, C.Frazão, F.J.Enguita, M.A.Carrondo, A.M.Fialho, I.Sá-Correia, and E.P.Mitchell (2006).
Cloning, expression, purification, crystallization and preliminary structure determination of glucose-1-phosphate uridylyltransferase (UgpG) from Sphingomonas elodea ATCC 31461 bound to glucose-1-phosphate.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 930-934.  
16085866 E.Silva, A.R.Marques, A.M.Fialho, A.T.Granja, and I.Sá-Correia (2005).
Proteins encoded by Sphingomonas elodea ATCC 31461 rmlA and ugpG genes, involved in gellan gum biosynthesis, exhibit both dTDP- and UDP-glucose pyrophosphorylase activities.
  Appl Environ Microbiol, 71, 4703-4712.  
16113286 I.T.Kudva, R.W.Griffin, J.M.Garren, S.B.Calderwood, and M.John (2005).
Identification of a protein subset of the anthrax spore immunome in humans immunized with the anthrax vaccine adsorbed preparation.
  Infect Immun, 73, 5685-5696.  
16206230 J.Bae, K.H.Kim, D.Kim, Y.Choi, J.S.Kim, S.Koh, S.I.Hong, and D.S.Lee (2005).
A practical enzymatic synthesis of UDP sugars and NDP glucoses.
  Chembiochem, 6, 1963-1966.  
  16511013 J.R.Cupp-Vickery, R.Y.Igarashi, and C.R.Meyer (2005).
Preliminary crystallographic analysis of ADP-glucose pyrophosphorylase from Agrobacterium tumefaciens.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 266-268.  
16356270 K.Usui, S.Katayama, M.Kanamori-Katayama, C.Ogawa, C.Kai, M.Okada, J.Kawai, T.Arakawa, P.Carninci, M.Itoh, K.Takio, M.Miyano, S.Kidoaki, T.Matsuda, Y.Hayashizaki, and H.Suzuki (2005).
Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
  Genome Biol, 6, R98.  
15632142 M.A.Ballicora, J.R.Dubay, C.H.Devillers, and J.Preiss (2005).
Resurrecting the ancestral enzymatic role of a modulatory subunit.
  J Biol Chem, 280, 10189-10195.  
15981001 M.A.Perugini, M.D.Griffin, B.J.Smith, L.E.Webb, A.J.Davis, E.Handman, and J.A.Gerrard (2005).
Insight into the self-association of key enzymes from pathogenic species.
  Eur Biophys J, 34, 469-476.  
15692569 X.Jin, M.A.Ballicora, J.Preiss, and J.H.Geiger (2005).
Crystal structure of potato tuber ADP-glucose pyrophosphorylase.
  EMBO J, 24, 694-704.
PDB codes: 1yp2 1yp3 1yp4
15598657 Z.Zhang, M.Tsujimura, J.Akutsu, M.Sasaki, H.Tajima, and Y.Kawarabayasi (2005).
Identification of an extremely thermostable enzyme with dual sugar-1-phosphate nucleotidylyltransferase activities from an acidothermophilic archaeon, Sulfolobus tokodaii strain 7.
  J Biol Chem, 280, 9698-9705.  
14756787 C.Kent, P.Gee, S.Y.Lee, X.Bian, and J.C.Fenno (2004).
A CDP-choline pathway for phosphatidylcholine biosynthesis in Treponema denticola.
  Mol Microbiol, 51, 471-481.  
14695508 J.S.Thorson, W.A.Barton, D.Hoffmeister, C.Albermann, and D.B.Nikolov (2004).
Structure-based enzyme engineering and its impact on in vitro glycorandomization.
  Chembiochem, 5, 16-25.  
15292268 N.M.Koropatkin, and H.M.Holden (2004).
Molecular structure of alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi.
  J Biol Chem, 279, 44023-44029.
PDB code: 1tzf
12837772 A.Matte, J.Sivaraman, I.Ekiel, K.Gehring, Z.Jia, and M.Cygler (2003).
Contribution of structural genomics to understanding the biology of Escherichia coli.
  J Bacteriol, 185, 3994-4002.  
12954627 B.A.Wolucka, and M.Van Montagu (2003).
GDP-mannose 3',5'-epimerase forms GDP-L-gulose, a putative intermediate for the de novo biosynthesis of vitamin C in plants.
  J Biol Chem, 278, 47483-47490.  
12581308 J.B.Frueauf, M.A.Ballicora, and J.Preiss (2003).
ADP-glucose pyrophosphorylase from potato tuber: site-directed mutagenesis of homologous aspartic acid residues in the small and large subunits.
  Plant J, 33, 503-511.  
12824488 J.Liu, and A.Mushegian (2003).
Three monophyletic superfamilies account for the majority of the known glycosyltransferases.
  Protein Sci, 12, 1418-1431.  
12794190 M.A.Ballicora, A.A.Iglesias, and J.Preiss (2003).
ADP-glucose pyrophosphorylase, a regulatory enzyme for bacterial glycogen synthesis.
  Microbiol Mol Biol Rev, 67, 213.  
12748181 P.Crevillén, M.A.Ballicora, A.Mérida, J.Preiss, and J.M.Romero (2003).
The different large subunit isoforms of Arabidopsis thaliana ADP-glucose pyrophosphorylase confer distinct kinetic and regulatory properties to the heterotetrameric enzyme.
  J Biol Chem, 278, 28508-28515.  
12077451 A.B.Merkel, G.K.Temple, M.D.Burkart, H.C.Losey, K.Beis, C.T.Walsh, and J.H.Naismith (2002).
Purification, crystallization and preliminary structural studies of dTDP-4-keto-6-deoxy-glucose-5-epimerase (EvaD) from Amycolatopsis orientalis, the fourth enzyme in the dTDP-L-epivancosamine biosynthetic pathway.
  Acta Crystallogr D Biol Crystallogr, 58, 1226-1228.
PDB code: 1ofn
11706035 B.Y.Kwak, Y.M.Zhang, M.Yun, R.J.Heath, C.O.Rock, S.Jackowski, and H.W.Park (2002).
Structure and mechanism of CTP:phosphocholine cytidylyltransferase (LicC) from Streptococcus pneumoniae.
  J Biol Chem, 277, 4343-4350.
PDB codes: 1jyk 1jyl
12171937 J.Sivaraman, V.Sauvé, A.Matte, and M.Cygler (2002).
Crystal structure of Escherichia coli glucose-1-phosphate thymidylyltransferase (RffH) complexed with dTTP and Mg2+.
  J Biol Chem, 277, 44214-44219.
PDB code: 1mc3
12374866 W.A.Barton, J.B.Biggins, J.Jiang, J.S.Thorson, and D.B.Nikolov (2002).
Expanding pyrimidine diphosphosugar libraries via structure-based nucleotidylyltransferase engineering.
  Proc Natl Acad Sci U S A, 99, 13397-13402.
PDB codes: 1mp3 1mp4 1mp5
12045109 X.M.He, and H.W.Liu (2002).
Formation of unusual sugars: mechanistic studies and biosynthetic applications.
  Annu Rev Biochem, 71, 701-754.  
11466299 C.O.Rock, R.J.Heath, H.W.Park, and S.Jackowski (2001).
The licC gene of Streptococcus pneumoniae encodes a CTP:phosphocholine cytidylyltransferase.
  J Bacteriol, 183, 4927-4931.  
11707391 C.Peneff, P.Ferrari, V.Charrier, Y.Taburet, C.Monnier, V.Zamboni, J.Winter, M.Harnois, F.Fassy, and Y.Bourne (2001).
Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture.
  EMBO J, 20, 6191-6202.
PDB codes: 1jv1 1jv3 1jvd 1jvg
11567027 J.B.Frueauf, M.A.Ballicora, and J.Preiss (2001).
Aspartate residue 142 is important for catalysis by ADP-glucose pyrophosphorylase from Escherichia coli.
  J Biol Chem, 276, 46319-46325.  
11114506 M.F.Giraud, and J.H.Naismith (2000).
The rhamnose pathway.
  Curr Opin Struct Biol, 10, 687-696.  
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.