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PDBsum entry 1dli

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Oxidoreductase PDB id
1dli
Jmol
Contents
Protein chain
402 a.a. *
Ligands
SO4 ×3
NAD
UDX
GOL ×3
Waters ×280
* Residue conservation analysis
PDB id:
1dli
Name: Oxidoreductase
Title: The first structure of udp-glucose dehydrogenase (udpgdh) re catalytic residues necessary for the two-fold oxidation
Structure: Udp-glucose dehydrogenase. Chain: a. Engineered: yes
Source: Streptococcus pyogenes. Organism_taxid: 1314. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.31Å     R-factor:   0.186     R-free:   0.259
Authors: R.E.Campbell,S.C.Mosimann,I.Van De Rijn,M.E.Tanner,N.C.J.Str
Key ref:
R.E.Campbell et al. (2000). The first structure of UDP-glucose dehydrogenase reveals the catalytic residues necessary for the two-fold oxidation. Biochemistry, 39, 7012-7023. PubMed id: 10841783 DOI: 10.1021/bi000181h
Date:
09-Dec-99     Release date:   31-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0C0F4  (UDG_STRPY) -  UDP-glucose 6-dehydrogenase
Seq:
Struc:
402 a.a.
402 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.22  - UDP-glucose 6-dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
UDP-glucose, UDP-galactose and UDP-glucuronate Biosynthesis
      Reaction: UDP-glucose + 2 NAD+ + H2O = UDP-glucuronate + 2 NADH
UDP-glucose
Bound ligand (Het Group name = UDX)
matches with 94.44% similarity
+
2 × NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly
+ H(2)O
= UDP-glucuronate
+ 2 × NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi000181h Biochemistry 39:7012-7023 (2000)
PubMed id: 10841783  
 
 
The first structure of UDP-glucose dehydrogenase reveals the catalytic residues necessary for the two-fold oxidation.
R.E.Campbell, S.C.Mosimann, I.van De Rijn, M.E.Tanner, N.C.Strynadka.
 
  ABSTRACT  
 
Bacterial UDP-glucose dehydrogenase (UDPGlcDH) is essential for formation of the antiphagocytic capsule that protects many virulent bacteria such as Streptococcus pyogenes andStreptococcus pneumoniae type 3 from the host's immune system. We have determined the X-ray structures of both native and Cys260Ser UDPGlcDH from S. pyogenes (74% similarity to S. pneumoniae) in ternary complexes with UDP-xylose/NAD(+) and UDP-glucuronic acid/NAD(H), respectively. The 402 residue homodimeric UDPGlcDH is composed of an N-terminal NAD(+) dinucleotide binding domain and a C-terminal UDP-sugar binding domain connected by a long (48 A) central alpha-helix. The first 290 residues of UDPGlcDH share structural homology with 6-phosphogluconate dehydrogenase, including conservation of an active site lysine and asparagine that are implicated in the enzyme mechanism. Also proposed to participate in the catalytic mechanism are a threonine and a glutamate that hydrogen bond to a conserved active site water molecule suitably positioned for general acid/base catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21478878 Y.C.Liu, Y.S.Li, S.Y.Lyu, L.J.Hsu, Y.H.Chen, Y.T.Huang, H.C.Chan, C.J.Huang, G.H.Chen, C.C.Chou, M.D.Tsai, and T.L.Li (2011).
Interception of teicoplanin oxidation intermediates yields new antimicrobial scaffolds.
  Nat Chem Biol, 7, 304-309.
PDB codes: 2wdw 2wdx 4k3t
20067617 B.Manavalan, S.K.Murugapiran, G.Lee, and S.Choi (2010).
Molecular modeling of the reductase domain to elucidate the reaction mechanism of reduction of peptidyl thioester into its corresponding alcohol in non-ribosomal peptide synthetases.
  BMC Struct Biol, 10, 1.  
20876192 S.Mondal, C.Nagao, and K.Mizuguchi (2010).
Detecting subtle functional differences in ketopantoate reductase and related enzymes using a rule-based approach with sequence-structure homology recognition scores.
  Protein Eng Des Sel, 23, 859-869.  
19290519 D.Simkhada, T.J.Oh, B.B.Pageni, H.C.Lee, K.Liou, and J.K.Sohng (2009).
Characterization of CalS9 in the biosynthesis of UDP-xylose and the production of xylosyl-attached hybrid compound.
  Appl Microbiol Biotechnol, 83, 885-895.  
19500970 M.J.Sippl (2009).
Fold space unlimited.
  Curr Opin Struct Biol, 19, 312-320.  
19383677 S.A.Loutet, S.J.Bartholdson, J.R.Govan, D.J.Campopiano, and M.A.Valvano (2009).
Contributions of two UDP-glucose dehydrogenases to viability and polymyxin B resistance of Burkholderia cenocepacia.
  Microbiology, 155, 2029-2039.  
  19058170 C.J.Thibodeaux, C.E.Melançon, and H.W.Liu (2008).
Natural-product sugar biosynthesis and enzymatic glycodiversification.
  Angew Chem Int Ed Engl, 47, 9814-9859.  
19016847 R.Kluger, and S.Rathgeber (2008).
Catalyzing separation of carbon dioxide in thiamin diphosphate-promoted decarboxylation.
  FEBS J, 275, 6089-6100.  
17668199 A.T.Granja, A.Popescu, A.R.Marques, I.Sá-Correia, and A.M.Fialho (2007).
Biochemical characterization and phylogenetic analysis of UDP-glucose dehydrogenase from the gellan gum producer Sphingomonas elodea ATCC 31461.
  Appl Microbiol Biotechnol, 76, 1319-1327.  
17672887 G.Mayr, F.S.Domingues, and P.Lackner (2007).
Comparative analysis of protein structure alignments.
  BMC Struct Biol, 7, 50.  
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.  
  17565184 N.K.Lokanath, K.J.Pampa, T.Kamiya, and N.Kunishima (2007).
Purification, crystallization and preliminary X-ray diffraction studies of a putative UDP-N-acetyl-D-mannosamine dehydrogenase from Pyrococcus horikoshii OT3.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 412-414.  
17442666 R.J.Hung, H.S.Chien, R.Z.Lin, C.T.Lin, J.Vatsyayan, H.L.Peng, and H.Y.Chang (2007).
Comparative analysis of two UDP-glucose dehydrogenases in Pseudomonas aeruginosa PAO1.
  J Biol Chem, 282, 17738-17748.  
16650981 A.Andreeva, and A.G.Murzin (2006).
Evolution of protein fold in the presence of functional constraints.
  Curr Opin Struct Biol, 16, 399-408.  
16780566 C.L.Ventura, R.T.Cartee, W.T.Forsee, and J.Yother (2006).
Control of capsular polysaccharide chain length by UDP-sugar substrate concentrations in Streptococcus pneumoniae.
  Mol Microbiol, 61, 723-733.  
16418163 D.Vigetti, M.Ori, M.Viola, A.Genasetti, E.Karousou, M.Rizzi, F.Pallotti, I.Nardi, V.C.Hascall, G.De Luca, and A.Passi (2006).
Molecular cloning and characterization of UDP-glucose dehydrogenase from the amphibian Xenopus laevis and its involvement in hyaluronan synthesis.
  J Biol Chem, 281, 8254-8263.  
16800641 H.Zhang, Y.Zhou, H.Bao, and H.W.Liu (2006).
Vi antigen biosynthesis in Salmonella typhi: characterization of UDP-N-acetylglucosamine C-6 dehydrogenase (TviB) and UDP-N-acetylglucosaminuronic acid C-4 epimerase (TviC).
  Biochemistry, 45, 8163-8173.  
16817893 T.Oka, and Y.Jigami (2006).
Reconstruction of de novo pathway for synthesis of UDP-glucuronic acid and UDP-xylose from intrinsic UDP-glucose in Saccharomyces cerevisiae.
  FEBS J, 273, 2645-2657.  
15821883 L.V.Bindschedler, E.Wheatley, E.Gay, J.Cole, A.Cottage, and G.P.Bolwell (2005).
Characterisation and expression of the pathway from UDP-glucose to UDP-xylose in differentiating tobacco tissue.
  Plant Mol Biol, 57, 285-301.  
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
15044486 B.J.Sommer, J.J.Barycki, and M.A.Simpson (2004).
Characterization of human UDP-glucose dehydrogenase. CYS-276 is required for the second of two successive oxidations.
  J Biol Chem, 279, 23590-23596.  
15383535 C.L.Griffith, J.S.Klutts, L.Zhang, S.B.Levery, and T.L.Doering (2004).
UDP-glucose dehydrogenase plays multiple roles in the biology of the pathogenic fungus Cryptococcus neoformans.
  J Biol Chem, 279, 51669-51676.  
15247292 J.W.Huh, H.Y.Yoon, H.J.Lee, W.B.Choi, S.J.Yang, and S.W.Cho (2004).
Importance of Gly-13 for the coenzyme binding of human UDP-glucose dehydrogenase.
  J Biol Chem, 279, 37491-37498.  
15375143 M.C.Laus, T.J.Logman, A.A.Van Brussel, R.W.Carlson, P.Azadi, M.Y.Gao, and J.W.Kijne (2004).
Involvement of exo5 in production of surface polysaccharides in Rhizobium leguminosarum and its role in nodulation of Vicia sativa subsp. nigra.
  J Bacteriol, 186, 6617-6625.  
14686915 X.Ge, L.C.Penney, I.van de Rijn, and M.E.Tanner (2004).
Active site residues and mechanism of UDP-glucose dehydrogenase.
  Eur J Biochem, 271, 14-22.  
14505572 M.J.García-García, and K.V.Anderson (2003).
Essential role of glycosaminoglycans in Fgf signaling during mouse gastrulation.
  Cell, 114, 727-737.  
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.  
11842181 J.A.Barbosa, J.Sivaraman, Y.Li, R.Larocque, A.Matte, J.D.Schrag, and M.Cygler (2002).
Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase.
  Proc Natl Acad Sci U S A, 99, 1859-1864.
PDB codes: 1k75 1kae 1kah 1kar
12196534 K.L.Kavanagh, M.Klimacek, B.Nidetzky, and D.K.Wilson (2002).
Crystal structure of Pseudomonas fluorescens mannitol 2-dehydrogenase binary and ternary complexes. Specificity and catalytic mechanism.
  J Biol Chem, 277, 43433-43442.
PDB codes: 1lj8 1m2w
11943783 P.E.Pummill, and P.L.DeAngelis (2002).
Evaluation of critical structural elements of UDP-sugar substrates and certain cysteine residues of a vertebrate hyaluronan synthase.
  J Biol Chem, 277, 21610-21616.  
11533493 E.C.Walsh, and D.Y.Stainier (2001).
UDP-glucose dehydrogenase required for cardiac valve formation in zebrafish.
  Science, 293, 1670-1673.  
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.