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PDBsum entry 2cho

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2cho
Jmol
Contents
Protein chains
641 a.a. *
13 a.a. *
Ligands
ACT ×2
GOL ×4
Metals
_CA ×2
Waters ×1189
* Residue conservation analysis
PDB id:
2cho
Name: Hydrolase
Title: Bacteroides thetaiotaomicron hexosaminidase with o- glcnacase activity
Structure: Glucosaminidase. Chain: a, b. Fragment: residues 22-737. Synonym: hexosaminiase. Engineered: yes. Glucosaminidase. Chain: c, d. Fragment: c terminus, residues 650-653,660-669. Synonym: hexosaminiase.
Source: Bacteroides thetaiotaomicron. Organism_taxid: 226186. Strain: vpi-5482. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Resolution:
1.85Å     R-factor:   0.182     R-free:   0.220
Authors: R.J.Dennis,E.J.Taylor,M.S.Macauley,K.A.Stubbs, J.P.Turkenburg,S.J.Hart,G.N.Black,D.J.Vocadlo,G.J.Davies
Key ref:
R.J.Dennis et al. (2006). Structure and mechanism of a bacterial beta-glucosaminidase having O-GlcNAcase activity. Nat Struct Mol Biol, 13, 365-371. PubMed id: 16565725 DOI: 10.1038/nsmb1079
Date:
16-Mar-06     Release date:   19-Jun-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q89ZI2  (OGA_BACTN) -  O-GlcNAcase BT_4395
Seq:
Struc:
 
Seq:
Struc:
737 a.a.
641 a.a.
Protein chains
No UniProt id for this chain
Struc: 13 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1038/nsmb1079 Nat Struct Mol Biol 13:365-371 (2006)
PubMed id: 16565725  
 
 
Structure and mechanism of a bacterial beta-glucosaminidase having O-GlcNAcase activity.
R.J.Dennis, E.J.Taylor, M.S.Macauley, K.A.Stubbs, J.P.Turkenburg, S.J.Hart, G.N.Black, D.J.Vocadlo, G.J.Davies.
 
  ABSTRACT  
 
O-GlcNAc is an abundant post-translational modification of serine and threonine residues of nucleocytoplasmic proteins. This modification, found only within higher eukaryotes, is a dynamic modification that is often reciprocal to phosphorylation. In a manner analogous to phosphatases, a glycoside hydrolase termed O-GlcNAcase cleaves O-GlcNAc from modified proteins. Enzymes with high sequence similarity to human O-GlcNAcase are also found in human pathogens and symbionts. We report the three-dimensional structure of O-GlcNAcase from the human gut symbiont Bacteroides thetaiotaomicron both in its native form and in complex with a mimic of the reaction intermediate. Mutagenesis and kinetics studies show that the bacterial enzyme, very similarly to its human counterpart, operates via an unusual 'substrate-assisted' catalytic mechanism, which will inform the rational design of enzyme inhibitors.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Schematic diagram of the O-GlcNAc modification. (a) Dynamic interplay of phosphorylation and O-GlcNAc modification of intracellular proteins.(b) Mechanism of action of O-GlcNAc hydrolases using substrate-assisted catalysis (residue numbers are for the the BtGH84 enzyme). (c) Transition state of the O-GlcNAcase–catalyzed hydrolysis of N-acetylglucosaminides. (d) Structure of the mechanism-derived inhibitor NAG-thiazoline, which mimics the intermediate of the substrate-assisted mechanism.
Figure 2.
Figure 2. Three-dimensional structure of B. thetaiotaomicron GH84. (a) Divergent (wall-eyed) stereo cartoon, color-ramped from, N-terminus (blue) to C-terminus (red), with NAG-thiazoline and the acid/base Asp243 in ball-and-stick representation. (b) Overlay of BtGH84 (green) with the human hexosaminidase B from family GH20 (yellow). (c) Electron density (F[obs] – F[calc], omit map at 3 ) for the NAG-thiazoline inhibitor and its environment; kinetic parameters of mutants of these residues are given in Table 1. (d) Overlay of the experimentally determined BtGH84 (green) with a homology model of the human enzyme (gray) showing only a single Trp-Phe change near the active center. (e) Overlay of the acetamide pocket of BtGH84 (green) with human GH20 hexosaminidase B (yellow, black labels), revealing a smaller pocket in the latter by virtue of the steric blockage of Trp405. This difference in pocket volume has been exploited in the design of GH84-specific inhibitors, such as the N-butyl compounds used here. These figures were drawn with MolScript^45 and BobScript^46.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 365-371) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21487632 A.Bottoni, G.Pietro Miscione, and M.Calvaresi (2011).
Computational evidence for the substrate-assisted catalytic mechanism of O-GlcNAcase. A DFT investigation.
  Phys Chem Chem Phys, 13, 9568-9577.  
20640461 H.C.Dorfmueller, V.S.Borodkin, D.E.Blair, S.Pathak, I.Navratilova, and D.M.van Aalten (2011).
Substrate and product analogues as human O-GlcNAc transferase inhibitors.
  Amino Acids, 40, 781-792.
PDB codes: 2xgm 2xgo 2xgs
21300897 M.Boyce, I.S.Carrico, A.S.Ganguli, S.H.Yu, M.J.Hangauer, S.C.Hubbard, J.J.Kohler, and C.R.Bertozzi (2011).
Metabolic cross-talk allows labeling of O-linked {beta}-N-acetylglucosamine-modified proteins via the N-acetylgalactosamine salvage pathway.
  Proc Natl Acad Sci U S A, 108, 3141-3146.  
20706749 S.A.Yuzwa, A.K.Yadav, Y.Skorobogatko, T.Clark, K.Vosseller, and D.J.Vocadlo (2011).
Mapping O-GlcNAc modification sites on tau and generation of a site-specific O-GlcNAc tau antibody.
  Amino Acids, 40, 857-868.  
21258330 T.M.Gloster, W.F.Zandberg, J.E.Heinonen, D.L.Shen, L.Deng, and D.J.Vocadlo (2011).
Hijacking a biosynthetic pathway yields a glycosyltransferase inhibitor within cells.
  Nat Chem Biol, 7, 174-181.  
20689974 Y.He, A.K.Bubb, K.A.Stubbs, T.M.Gloster, and G.J.Davies (2011).
Inhibition of a bacterial O-GlcNAcase homologue by lactone and lactam derivatives: structural, kinetic and thermodynamic analyses.
  Amino Acids, 40, 829-839.
PDB codes: 2xm1 2xm2
19647786 C.Butkinaree, K.Park, and G.W.Hart (2010).
O-linked beta-N-acetylglucosamine (O-GlcNAc): Extensive crosstalk with phosphorylation to regulate signaling and transcription in response to nutrients and stress.
  Biochim Biophys Acta, 1800, 96.  
20026047 H.C.Dorfmueller, and D.M.van Aalten (2010).
Screening-based discovery of drug-like O-GlcNAcase inhibitor scaffolds.
  FEBS Lett, 584, 694-700.
PDB code: 2x0y
19647043 J.A.Hanover, M.W.Krause, and D.C.Love (2010).
The hexosamine signaling pathway: O-GlcNAc cycling in feast or famine.
  Biochim Biophys Acta, 1800, 80-95.  
20851343 M.S.Macauley, Y.He, T.M.Gloster, K.A.Stubbs, G.J.Davies, and D.J.Vocadlo (2010).
Inhibition of O-GlcNAcase using a potent and cell-permeable inhibitor does not induce insulin resistance in 3T3-L1 adipocytes.
  Chem Biol, 17, 937-948.
PDB code: 2xj7
20863279 M.Schimpl, A.W.Schüttelkopf, V.S.Borodkin, and D.M.van Aalten (2010).
Human OGA binds substrates in a conserved peptide recognition groove.
  Biochem J, 432, 1-7.
PDB codes: 2xsa 2xsb
20396401 T.M.Gloster, and D.J.Vocadlo (2010).
Mechanism, Structure, and Inhibition of O-GlcNAc Processing Enzymes.
  Curr Signal Transduct Ther, 5, 74-91.  
20552664 T.V.Vuong, and D.B.Wilson (2010).
Glycoside hydrolases: catalytic base/nucleophile diversity.
  Biotechnol Bioeng, 107, 195-205.  
19782947 B.D.Lazarus, D.C.Love, and J.A.Hanover (2009).
O-GlcNAc cycling: implications for neurodegenerative disorders.
  Int J Biochem Cell Biol, 41, 2134-2146.  
19181667 D.W.Abbott, M.S.Macauley, D.J.Vocadlo, and A.B.Boraston (2009).
Streptococcus pneumoniae Endohexosaminidase D, Structural and Mechanistic Insight into Substrate-assisted Catalysis in Family 85 Glycoside Hydrolases.
  J Biol Chem, 284, 11676-11689.
PDB codes: 2w91 2w92
19422833 E.Ficko-Blean, and A.B.Boraston (2009).
N-acetylglucosamine recognition by a family 32 carbohydrate-binding module from Clostridium perfringens NagH.
  J Mol Biol, 390, 208-220.
PDB codes: 2w1q 2w1s 2w1u 2wdb
19193644 E.Ficko-Blean, K.J.Gregg, J.J.Adams, J.H.Hehemann, M.Czjzek, S.P.Smith, and A.B.Boraston (2009).
Portrait of an enzyme, a complete structural analysis of a multimodular {beta}-N-acetylglucosaminidase from Clostridium perfringens.
  J Biol Chem, 284, 9876-9884.
PDB codes: 2v5c 2v5d 2w1n
19275764 H.C.Dorfmueller, V.S.Borodkin, M.Schimpl, and D.M.van Aalten (2009).
GlcNAcstatins are nanomolar inhibitors of human O-GlcNAcase inducing cellular hyper-O-GlcNAcylation.
  Biochem J, 420, 221-227.
PDB code: 2wb5
19499593 M.D.Balcewich, K.A.Stubbs, Y.He, T.W.James, G.J.Davies, D.J.Vocadlo, and B.L.Mark (2009).
Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: structural basis for selective inhibition of the glycoside hydrolase NagZ.
  Protein Sci, 18, 1541-1551.
PDB codes: 2wca 3gs6 3gsm
18822375 B.Henrissat, G.Sulzenbacher, and Y.Bourne (2008).
Glycosyltransferases, glycoside hydrolases: surprise, surprise!
  Curr Opin Struct Biol, 18, 527-533.  
18558099 D.J.Vocadlo, and G.J.Davies (2008).
Mechanistic insights into glycosidase chemistry.
  Curr Opin Chem Biol, 12, 539-555.  
18842583 M.S.Macauley, A.K.Bubb, C.Martinez-Fleites, G.J.Davies, and D.J.Vocadlo (2008).
Elevation of Global O-GlcNAc Levels in 3T3-L1 Adipocytes by Selective Inhibition of O-GlcNAcase Does Not Induce Insulin Resistance.
  J Biol Chem, 283, 34687-34695.
PDB code: 2vvs
18641620 P.M.Fischer (2008).
Turning down tau phosphorylation.
  Nat Chem Biol, 4, 448-449.  
18822376 R.Hurtado-Guerrero, H.C.Dorfmueller, and D.M.van Aalten (2008).
Molecular mechanisms of O-GlcNAcylation.
  Curr Opin Struct Biol, 18, 551-557.  
18587388 S.A.Yuzwa, M.S.Macauley, J.E.Heinonen, X.Shan, R.J.Dennis, Y.He, G.E.Whitworth, K.A.Stubbs, E.J.McEachern, G.J.Davies, and D.J.Vocadlo (2008).
A potent mechanism-inspired O-GlcNAcase inhibitor that blocks phosphorylation of tau in vivo.
  Nat Chem Biol, 4, 483-490.
PDB code: 2vvn
17728868 A.Scaffidi, K.A.Stubbs, R.J.Dennis, E.J.Taylor, G.J.Davies, D.J.Vocadlo, and R.V.Stick (2007).
A 1-acetamido derivative of 6-epi-valienamine: an inhibitor of a diverse group of beta-N-acetylglucosaminidases.
  Org Biomol Chem, 5, 3013-3019.
PDB code: 2jiw
17951578 B.C.Smith, and J.M.Denu (2007).
Acetyl-lysine Analog Peptides as Mechanistic Probes of Protein Deacetylases.
  J Biol Chem, 282, 37256-37265.  
17439123 B.C.Smith, and J.M.Denu (2007).
Sir2 deacetylases exhibit nucleophilic participation of acetyl-lysine in NAD+ cleavage.
  J Am Chem Soc, 129, 5802-5803.  
17851615 I.R.Greig, and I.H.Williams (2007).
Glycosidase inhibitors as conformational transition state analogues.
  Chem Commun (Camb), (), 3747-3749.  
17439950 K.A.Stubbs, M.Balcewich, B.L.Mark, and D.J.Vocadlo (2007).
Small molecule inhibitors of a glycoside hydrolase attenuate inducible AmpC-mediated beta-lactam resistance.
  J Biol Chem, 282, 21382-21391.
PDB code: 2oxn
17057847 B.Shanmugasundaram, A.W.Debowski, R.J.Dennis, G.J.Davies, D.J.Vocadlo, and A.Vasella (2006).
Inhibition of O-GlcNAcase by a gluco-configured nagstatin and a PUGNAc-imidazole hybrid inhibitor.
  Chem Commun (Camb), (), 4372-4374.
PDB code: 2j47
16990278 E.Ficko-Blean, and A.B.Boraston (2006).
The interaction of a carbohydrate-binding module from a Clostridium perfringens N-acetyl-beta-hexosaminidase with its carbohydrate receptor.
  J Biol Chem, 281, 37748-37757.
PDB codes: 2j1a 2j1e 2j1f 2j7m
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.