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Hydrolase PDB id
1hp4
Jmol
Contents
Protein chain
499 a.a. *
Ligands
SO4
GOL ×3
Metals
_CL ×4
Waters ×382
* Residue conservation analysis
PDB id:
1hp4
Name: Hydrolase
Title: Crystal structure of streptomyces plicatus beta-n-acetylhexo
Structure: Beta-n-acetylhexosaminidase. Chain: a. Engineered: yes
Source: Streptomyces plicatus. Organism_taxid: 1922. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.181     R-free:   0.209
Authors: B.L.Mark
Key ref:
B.L.Mark et al. (2001). Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosaminidase. J Biol Chem, 276, 10330-10337. PubMed id: 11124970 DOI: 10.1074/jbc.M011067200
Date:
12-Dec-00     Release date:   04-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O85361  (O85361_STRPL) -  B-N-acetylhexosaminidase
Seq:
Struc: 		506 a.a.
499 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
DOI no: 10.1074/jbc.M011067200 J Biol Chem 276:10330-10337 (2001)
PubMed id: 11124970  
 
 
Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosaminidase.
B.L.Mark, D.J.Vocadlo, S.Knapp, B.L.Triggs-Raine, S.G.Withers, M.N.James.
 
  ABSTRACT  
 
beta-Hexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of beta-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. Heritable deficiency of this enzyme results in various forms of GalNAc-beta(1,4)-[N-acetylneuraminic acid (2,3)]-Gal-beta(1,4)-Glc-ceramide gangliosidosis, including Tay-Sachs disease. We have determined the x-ray crystal structure of a beta-hexosaminidase from Streptomyces plicatus to 2.2 A resolution (Protein Data Bank code ). beta-Hexosaminidases are believed to use a substrate-assisted catalytic mechanism that generates a cyclic oxazolinium ion intermediate. We have solved and refined a complex between the cyclic intermediate analogue N-acetylglucosamine-thiazoline and beta-hexosaminidase from S. plicatus to 2.1 A resolution (Protein Data Bank code ). Difference Fourier analysis revealed the pyranose ring of N-acetylglucosamine-thiazoline bound in the enzyme active site with a conformation close to that of a (4)C(1) chair. A tryptophan-lined hydrophobic pocket envelopes the thiazoline ring, protecting it from solvolysis at the iminium ion carbon. Within this pocket, Tyr(393) and Asp(313) appear important for positioning the 2-acetamido group of the substrate for nucleophilic attack at the anomeric center and for dispersing the positive charge distributed into the oxazolinium ring upon cyclization. This complex provides decisive structural evidence for substrate-assisted catalysis and the formation of a covalent, cyclic intermediate in family 20 beta-hexosaminidases.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Proposed catalytic mechanism for -hexosaminidase. A, detailed SpHEX catalytic mechanism. The general acid/base (Glu314) and the residue (Asp313) primarily responsible for stabilizing positive charge on the oxazolinium ion intermediate are shown, although no attempt is made to indicate their true locations. Hydroxyl groups and C6 have been removed from the pyranose ring for clarity. B, chemical structure of the cyclic intermediate analogue NAG-thiazoline. 		Figure 8.
Fig. 8. NAG-thiazoline (NGT) and glycerol (Gol) bound to sugar binding subsites 1 and +1 of SpHEX, respectively. Semi-transparent surfaces have been drawn around hydrophobic residues using GRASP (50). The catalytic triad (Glu314, His250, and Asp191) has been drawn along with its hydrogen-bonding network. The glycerol hydroxyl group hydrogen bonding to the carboxylate of Glu314 is believed to occupy the position that an incoming water molecule would take to nucleophilically attack C-1. WAT indicates the conserved incoming water molecule proposed by Ref. 10.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 10330-10337) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21373681 H.Usuki, Y.Yamamoto, Y.Kumagai, T.Nitoda, H.Kanzaki, and T.Hatanaka (2011).
MS/MS fragmentation-guided search of TMG-chitooligomycins and their structure-activity relationship in specific β-N-acetylglucosaminidase inhibition.
  Org Biomol Chem, 9, 2943-2951.  
21290547 Y.Yang, T.Liu, Y.Yang, Q.Wu, Q.Yang, and B.Yu (2011).
Synthesis, Evaluation, and Mechanism of N,N,N-Trimethyl-D-glucosamine-(1→4)-chitooligosaccharides as Selective Inhibitors of Glycosyl Hydrolase Family 20 β-N-Acetyl-D-hexosaminidases.
  Chembiochem, 12, 457-467.  
20400549 S.Litzinger, A.Duckworth, K.Nitzsche, C.Risinger, V.Wittmann, and C.Mayer (2010).
Muropeptide rescue in Bacillus subtilis involves sequential hydrolysis by beta-N-acetylglucosaminidase and N-acetylmuramyl-L-alanine amidase.
  J Bacteriol, 192, 3132-3143.  
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.  
19691080 C.Goedl, and B.Nidetzky (2009).
Sucrose phosphorylase harbouring a redesigned, glycosyltransferase-like active site exhibits retaining glucosyl transfer in the absence of a covalent intermediate.
  Chembiochem, 10, 2333-2337.  
19295526 J.R.Rich, and S.G.Withers (2009).
Emerging methods for the production of homogeneous human glycoproteins.
  Nat Chem Biol, 5, 206-215.  
19156788 K.J.Loft, P.Bojarová, K.Slámová, V.Kren, and S.J.Williams (2009).
Synthesis of sulfated glucosaminides for profiling substrate specificities of sulfatases and fungal beta-N-acetylhexosaminidases.
  Chembiochem, 10, 565-576.  
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
18304822 B.Li, K.Takegawa, T.Suzuki, K.Yamamoto, and L.X.Wang (2008).
Synthesis and inhibitory activity of oligosaccharide thiazolines as a class of mechanism-based inhibitors for endo-beta-N-acetylglucosaminidases.
  Bioorg Med Chem, 16, 4670-4675.  
  19133500 J.E.Kerrigan, C.Ragunath, L.Kandra, G.Gyémánt, A.Lipták, L.Jánossy, J.B.Kaplan, and N.Ramasubbu (2008).
Modeling and biochemical analysis of the activity of antibiofilm agent Dispersin B.
  Acta Biol Hung, 59, 439-451.  
18405887 L.X.Wang (2008).
Chemoenzymatic synthesis of glycopeptides and glycoproteins through endoglycosidase-catalyzed transglycosylation.
  Carbohydr Res, 343, 1509-1522.  
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
17594485 J.D.Funkhouser, and N.N.Aronson (2007).
Chitinase family GH18: evolutionary insights from the genomic history of a diverse protein family.
  BMC Evol Biol, 7, 96.  
17317569 M.B.Tropak, J.E.Blanchard, S.G.Withers, E.D.Brown, and D.Mahuran (2007).
High-throughput screening for human lysosomal beta-N-Acetyl hexosaminidase inhibitors acting as pharmacological chaperones.
  Chem Biol, 14, 153-164.  
17636254 M.Gutternigg, D.Kretschmer-Lubich, K.Paschinger, D.Rendić, J.Hader, P.Geier, R.Ranftl, V.Jantsch, G.Lochnit, and I.B.Wilson (2007).
Biosynthesis of truncated N-linked oligosaccharides results from non-orthologous hexosaminidase-mediated mechanisms in nematodes, plants, and insects.
  J Biol Chem, 282, 27825-27840.  
17509134 R.Ettrich, V.Kopecký, K.Hofbauerová, V.Baumruk, P.Novák, P.Pompach, P.Man, O.Plíhal, M.Kutý, N.Kulik, J.Sklenár, H.Ryslavá, V.Kren, and K.Bezouska (2007).
Structure of the dimeric N-glycosylated form of fungal beta-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies.
  BMC Struct Biol, 7, 32.  
17949435 S.G.Manuel, C.Ragunath, H.B.Sait, E.A.Izano, J.B.Kaplan, and N.Ramasubbu (2007).
Role of active-site residues of dispersin B, a biofilm-releasing beta-hexosaminidase from a periodontal pathogen, in substrate hydrolysis.
  FEBS J, 274, 5987-5999.  
16762038 C.Mayer, D.J.Vocadlo, M.Mah, K.Rupitz, D.Stoll, R.A.Warren, and S.G.Withers (2006).
Characterization of a beta-N-acetylhexosaminidase and a beta-N-acetylglucosaminidase/beta-glucosidase from Cellulomonas fimi.
  FEBS J, 273, 2929-2941.  
16493467 K.A.Stubbs, N.Zhang, and D.J.Vocadlo (2006).
A divergent synthesis of 2-acyl derivatives of PUGNAc yields selective inhibitors of O-GlcNAcase.
  Org Biomol Chem, 4, 839-845.  
16641107 M.Wacker, M.F.Feldman, N.Callewaert, M.Kowarik, B.R.Clarke, N.L.Pohl, M.Hernandez, E.D.Vines, M.A.Valvano, C.Whitfield, and M.Aebi (2006).
Substrate specificity of bacterial oligosaccharyltransferase suggests a common transfer mechanism for the bacterial and eukaryotic systems.
  Proc Natl Acad Sci U S A, 103, 7088-7093.  
16565725 R.J.Dennis, E.J.Taylor, M.S.Macauley, K.A.Stubbs, J.P.Turkenburg, S.J.Hart, G.N.Black, D.J.Vocadlo, and G.J.Davies (2006).
Structure and mechanism of a bacterial beta-glucosaminidase having O-GlcNAcase activity.
  Nat Struct Mol Biol, 13, 365-371.
PDB codes: 2chn 2cho
16470771 Y.Zeng, J.Wang, B.Li, S.Hauser, H.Li, and L.X.Wang (2006).
Glycopeptide synthesis through endo-glycosidase-catalyzed oligosaccharide transfer of sugar oxazolines: probing substrate structural requirement.
  Chemistry, 12, 3355-3364.  
15654891 A.Sørbotten, S.J.Horn, V.G.Eijsink, and K.M.Vårum (2005).
Degradation of chitosans with chitinase B from Serratia marcescens. Production of chito-oligosaccharides and insight into enzyme processivity.
  FEBS J, 272, 538-549.  
14717693 B.Synstad, S.Gåseidnes, D.M.Van Aalten, G.Vriend, J.E.Nielsen, and V.G.Eijsink (2004).
Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase.
  Eur J Biochem, 271, 253-262.  
15135542 C.W.Reid, N.T.Blackburn, and A.J.Clarke (2004).
The effect of NAG-thiazoline on morphology and surface hydrophobicity of Escherichia coli.
  FEMS Microbiol Lett, 234, 343-348.  
15130470 M.F.Amaya, A.G.Watts, I.Damager, A.Wehenkel, T.Nguyen, A.Buschiazzo, G.Paris, A.C.Frasch, S.G.Withers, and P.M.Alzari (2004).
Structural insights into the catalytic mechanism of Trypanosoma cruzi trans-sialidase.
  Structure, 12, 775-784.
PDB codes: 1s0i 1s0j 1s0k 2ah2
12662933 B.L.Mark, D.J.Mahuran, M.M.Cherney, D.Zhao, S.Knapp, and M.N.James (2003).
Crystal structure of human beta-hexosaminidase B: understanding the molecular basis of Sandhoff and Tay-Sachs disease.
  J Mol Biol, 327, 1093-1109.
PDB codes: 1nou 1now 1np0
12792654 H.Dvir, M.Harel, A.A.McCarthy, L.Toker, I.Silman, A.H.Futerman, and J.L.Sussman (2003).
X-ray structure of human acid-beta-glucosidase, the defective enzyme in Gaucher disease.
  EMBO Rep, 4, 704-709.
PDB code: 1ogs
12896987 J.B.Kaplan, C.Ragunath, N.Ramasubbu, and D.H.Fine (2003).
Detachment of Actinobacillus actinomycetemcomitans biofilm cells by an endogenous beta-hexosaminidase activity.
  J Bacteriol, 185, 4693-4698.  
  12413546 A.Vasella, G.J.Davies, and M.Böhm (2002).
Glycosidase mechanisms.
  Curr Opin Chem Biol, 6, 619-629.  
11785761 Y.Bourne, and B.Henrissat (2001).
Glycoside hydrolases and glycosyltransferases: families and functional modules.
  Curr Opin Struct Biol, 11, 593-600.  
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.