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Nucleotidyltransferase PDB id
1hxq
Jmol
Contents
Protein chains
340 a.a. *
Ligands
U5P ×2
Metals
_ZN ×2
_FE ×2
Waters ×730
* Residue conservation analysis
PDB id:
1hxq
Name: Nucleotidyltransferase
Title: The structure of nucleotidylated galactose-1-phosphate uridylyltransferase from escherichia coli at 1.86 angstroms resolution
Structure: Hexose-1-phosphate uridylyltransferase. Chain: a, b. Synonym: alpha-d-galactose-1-phosphate uridylyltransferase, galactose-1-phosphate uridylyltransferase-uridylylated his 166. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Cell_line: bl21. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.86Å     R-factor:   0.196    
Authors: J.E.Wedekind,P.A.Frey,I.Rayment
Key ref:
J.E.Wedekind et al. (1996). The structure of nucleotidylated histidine-166 of galactose-1-phosphate uridylyltransferase provides insight into phosphoryl group transfer. Biochemistry, 35, 11560-11569. PubMed id: 8794735 DOI: 10.1021/bi9612677
Date:
16-Jun-96     Release date:   22-Oct-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P09148  (GAL7_ECOLI) -  Galactose-1-phosphate uridylyltransferase
Seq:
Struc: 		348 a.a.
340 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.12  - UDP-glucose--hexose-1-phosphate uridylyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		UDP-glucose, UDP-galactose and UDP-glucuronate Biosynthesis
      Reaction: UDP-glucose + alpha-D-galactose 1-phosphate = alpha-D-glucose 1-phosphate + UDP-galactose
UDP-glucose
Bound ligand (Het Group name = U5P)
matches with 55.00% similarity 		+ alpha-D-galactose 1-phosphate
 = alpha-D-glucose 1-phosphate
 + UDP-galactose
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   3 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi9612677 Biochemistry 35:11560-11569 (1996)
PubMed id: 8794735  
 
 
The structure of nucleotidylated histidine-166 of galactose-1-phosphate uridylyltransferase provides insight into phosphoryl group transfer.
J.E.Wedekind, P.A.Frey, I.Rayment.
 
  ABSTRACT  
 
Galactose-1-phosphate uridylyltransferase catalyzes the reaction of UDP-glucose with galactose 1-phosphate to form UDP-galactose and glucose 1-phosphate during normal cellular metabolism. The reaction proceeds through a double displacement mechanism characterized by the formation of a stable nucleotidylated histidine intermediate. This paper describes the preparation of the uridylyl-enzyme complex on the crystalline enzyme from Escherichia coli and its subsequent structure determination by X-ray crystallography. The refined structure has an R-factor of 19.6% (data between 65 and 1.86 A resolution) and reveals modest conformational changes at the active site compared to the inactive UMP/UDP-enzyme complex reported previously [Wedekind, J.E., Frey, P.A., & Rayment, I. (1995) Biochemistry 34, 11049-11061]. In particular, positions of the respective UMP alpha-phosphoryl groups differ by approximately 4 A. Well-defined electron density for the nucleotidylated imidazole supports the existence of a covalent bond between N epsilon 2 of the nucleophile and the alpha-phosphorus of UMP. A hydrogen bond that is conserved in both complexes between His 166 N delta 1 and the carbonyl O of His 164 serves to properly orient the nucleophile and electrostatically stabilize the positively charged imidazolium that results from nucleotidylation. Hydrogen bonds from side-chain Gln 168 to the nonbridging phosphoryl oxygens of the nucleotidyl intermediate appear crucial for the formation and reaction of the uridylyl-enzyme complex as well. The significance of the latter interaction is underscored by the fact that the predominant cause of the metabolic disease galactosemia is the mutation of the corresponding Gln (Gln 188 in humans) to Arg. A comparison to other phosphohistidyl enzymes is described, as well as a revised model for the mechanism of the uridylyltransferase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20008339 A.Facchiano, and A.Marabotti (2010).
Analysis of galactosemia-linked mutations of GALT enzyme using a computational biology approach.
  Protein Eng Des Sel, 23, 103-113.  
20399182 N.Tanaka, P.Smith, and S.Shuman (2010).
Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer.
  Structure, 18, 449-457.
PDB code: 3kgd
19559088 R.C.Spitale, and J.E.Wedekind (2009).
Exploring ribozyme conformational changes with X-ray crystallography.
  Methods, 49, 87.  
18723650 M.Nakajima, and M.Kitaoka (2008).
Identification of lacto-N-Biose I phosphorylase from Vibrio vulnificus CMCP6.
  Appl Environ Microbiol, 74, 6333-6337.  
17337452 T.F.Chou, I.B.Tikh, B.A.Horta, B.Ghosh, R.B.De Alencastro, and C.R.Wagner (2007).
Engineered monomeric human histidine triad nucleotide-binding protein 1 hydrolyzes fluorogenic acyl-adenylate and lysyl-tRNA synthetase-generated lysyl-adenylate.
  J Biol Chem, 282, 15137-15147.  
16519510 J.G.McCoy, A.Arabshahi, E.Bitto, C.A.Bingman, F.J.Ruzicka, P.A.Frey, and G.N.Phillips (2006).
Structure and mechanism of an ADP-glucose phosphorylase from Arabidopsis thaliana.
  Biochemistry, 45, 3154-3162.
PDB codes: 1z84 1zwj
16257985 K.L.Jensen, M.P.Styczynski, I.Rigoutsos, and G.N.Stephanopoulos (2006).
A generic motif discovery algorithm for sequential data.
  Bioinformatics, 22, 21-28.  
16840321 O.C.Richards, J.F.Spagnolo, J.M.Lyle, S.E.Vleck, R.D.Kuchta, and K.Kirkegaard (2006).
Intramolecular and intermolecular uridylylation by poliovirus RNA-dependent RNA polymerase.
  J Virol, 80, 7405-7415.  
15795221 J.B.Thoden, and H.M.Holden (2005).
The molecular architecture of galactose mutarotase/UDP-galactose 4-epimerase from Saccharomyces cerevisiae.
  J Biol Chem, 280, 21900-21907.
PDB code: 1z45
12574506 F.Trapasso, A.Krakowiak, R.Cesari, J.Arkles, S.Yendamuri, H.Ishii, A.Vecchione, T.Kuroki, P.Bieganowski, H.C.Pace, K.Huebner, C.M.Croce, and C.Brenner (2003).
Designed FHIT alleles establish that Fhit-induced apoptosis in cancer cells is limited by substrate binding.
  Proc Natl Acad Sci U S A, 100, 1592-1597.  
12923184 H.M.Holden, I.Rayment, and J.B.Thoden (2003).
Structure and function of enzymes of the Leloir pathway for galactose metabolism.
  J Biol Chem, 278, 43885-43888.  
12119013 C.Brenner (2002).
Hint, Fhit, and GalT: function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases.
  Biochemistry, 41, 9003-9014.  
11805111 P.Bieganowski, P.N.Garrison, S.C.Hodawadekar, G.Faye, L.D.Barnes, and C.Brenner (2002).
Adenosine monophosphoramidase activity of Hint and Hnt1 supports function of Kin28, Ccl1, and Tfb3.
  J Biol Chem, 277, 10852-10860.  
  10673421 G.J.Palm, E.Billy, W.Filipowicz, and A.Wlodawer (2000).
Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology.
  Structure, 8, 13-23.
PDB codes: 1qmh 1qmi
10820011 S.Geeganage, V.W.Ling, and P.A.Frey (2000).
Roles of two conserved amino acid residues in the active site of galactose-1-phosphate uridylyltransferase: an essential serine and a nonessential cysteine.
  Biochemistry, 39, 5397-5404.  
10636864 T.Brüser, T.Selmer, and C.Dahl (2000).
"ADP sulfurylase" from Thiobacillus denitrificans is an adenylylsulfate:phosphate adenylyltransferase and belongs to a new family of nucleotidyltransferases.
  J Biol Chem, 275, 1691-1698.  
10090754 A.Abend, P.N.Garrison, L.D.Barnes, and P.A.Frey (1999).
Stereochemical retention of the configuration in the action of Fhit on phosphorus-chiral substrates.
  Biochemistry, 38, 3668-3676.  
10574971 E.Billy, D.Hess, J.Hofsteenge, and W.Filipowicz (1999).
Characterization of the adenylation site in the RNA 3'-terminal phosphate cyclase from Escherichia coli.
  J Biol Chem, 274, 34955-34960.  
10037750 K.Lai, A.C.Willis, and L.J.Elsas (1999).
The biochemical role of glutamine 188 in human galactose-1-phosphate uridyltransferase.
  J Biol Chem, 274, 6559-6566.  
9698386 F.J.Ruzicka, S.Geeganage, and P.A.Frey (1998).
Kinetic mechanism of UDP-hexose synthase, a point variant of hexose-1-phosphate uridylyltransferase from Escherichia coli.
  Biochemistry, 37, 11385-11392.  
9421505 J.Wittschieben, B.O.Petersen, and S.Shuman (1998).
Replacement of the active site tyrosine of vaccinia DNA topoisomerase by glutamate, cysteine or histidine converts the enzyme into a site-specific endonuclease.
  Nucleic Acids Res, 26, 490-496.  
9928473 K.Huebner, P.N.Garrison, L.D.Barnes, and C.M.Croce (1998).
The role of the FHIT/FRA3B locus in cancer.
  Annu Rev Genet, 32, 7.  
9772178 S.Geeganage, and P.A.Frey (1998).
Transient kinetics of formation and reaction of the uridylyl-enzyme form of galactose-1-P uridylyltransferase and its Q168R-variant: insight into the molecular basis of galactosemia.
  Biochemistry, 37, 14500-14507.  
9164465 C.Brenner, P.Garrison, J.Gilmour, D.Peisach, D.Ringe, G.A.Petsko, and J.M.Lowenstein (1997).
Crystal structures of HINT demonstrate that histidine triad proteins are GalT-related nucleotide-binding proteins.
  Nat Struct Biol, 4, 231-238.
PDB codes: 3rhn 4rhn 5rhn 6rhn
  9261067 C.D.Lima, K.L.D'Amico, I.Naday, G.Rosenbaum, E.M.Westbrook, and W.A.Hendrickson (1997).
MAD analysis of FHIT, a putative human tumor suppressor from the HIT protein family.
  Structure, 5, 763-774.
PDB codes: 1fit 2fit 3fit
9063869 J.B.Thoden, F.J.Ruzicka, P.A.Frey, I.Rayment, and H.M.Holden (1997).
Structural analysis of the H166G site-directed mutant of galactose-1-phosphate uridylyltransferase complexed with either UDP-glucose or UDP-galactose: detailed description of the nucleotide sugar binding site.
  Biochemistry, 36, 1212-1222.
PDB codes: 1gup 1guq
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.