PDBsum entry 2e9m

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Hydrolase PDB id
Protein chain
466 a.a. *
Waters ×380
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of human cytosolic neutral beta- glycosylceramidase (klotho-related prote:klrp) complex with galactose and fatty acids
Structure: Cytosolic beta-glucosidase. Chain: a. Synonym: cytosolic neutral beta-glycosylceramidase, klotho- related protein, klrp, cytosolic beta-glucosidase- like protein 1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.80Å     R-factor:   0.203     R-free:   0.236
Authors: Y.Kakuta,Y.Hayashi,N.Okino,M.Ito
Key ref:
Y.Hayashi et al. (2007). Klotho-related protein is a novel cytosolic neutral beta-glycosylceramidase. J Biol Chem, 282, 30889-30900. PubMed id: 17595169 DOI: 10.1074/jbc.M700832200
25-Jan-07     Release date:   11-Sep-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9H227  (GBA3_HUMAN) -  Cytosolic beta-glucosidase
469 a.a.
466 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Beta-glucosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     metabolic process   7 terms 
  Biochemical function     hydrolase activity     6 terms  


DOI no: 10.1074/jbc.M700832200 J Biol Chem 282:30889-30900 (2007)
PubMed id: 17595169  
Klotho-related protein is a novel cytosolic neutral beta-glycosylceramidase.
Y.Hayashi, N.Okino, Y.Kakuta, T.Shikanai, M.Tani, H.Narimatsu, M.Ito.
Using C6-NBD-glucosylceramide (GlcCer) as a substrate, we detected the activity of a conduritol B epoxide-insensitive neutral glycosylceramidase in cytosolic fractions of zebrafish embryos, mouse and rat brains, and human fibroblasts. The candidates for the enzyme were assigned to the Klotho (KL), whose family members share a beta-glucosidase-like domain but whose natural substrates are unknown. Among this family, only the KL-related protein (KLrP) is capable of degrading C6-NBD-GlcCer when expressed in CHOP cells, in which Myc-tagged KLrP was exclusively distributed in the cytosol. In addition, knockdown of the endogenous KLrP by small interfering RNA increased the cellular level of GlcCer. The purified recombinant KLrP hydrolyzed 4-methylumbelliferyl-glucose, C6-NBD-GlcCer, and authentic GlcCer at pH 6.0. The enzyme also hydrolyzed the corresponding galactosyl derivatives, but each k(cat)/Km was much lower than that for glucosyl derivatives. The x-ray structure of KLrP at 1.6A resolution revealed that KLrP is a (beta/alpha)8 TIM barrel, in which Glu(165) and Glu(373) at the carboxyl termini of beta-strands 4 and 7 could function as an acid/base catalyst and nucleophile, respectively. The substrate-binding cleft of the enzyme was occupied with palmitic acid and oleic acid when the recombinant protein was crystallized in a complex with glucose. GlcCer was found to fit well the cleft of the crystal structure of KLrP. Collectively, KLrP was identified as a cytosolic neutral glycosylceramidase that could be involved in a novel nonlysosomal catabolic pathway of GlcCer.
  Selected figure(s)  
Figure 9.
FIGURE 9. Close-up view of the substrate-binding cleft of KLrP·Glc and residues interacting with Glc and fatty acids. A, molecular surface gray model of KLrP·Glc with fatty acids. Green, Glc; blue, palmitic acid; yellow, oleic acid. B, schematic expression of amino acid residues interacting with Glc and fatty acids.
Figure 10.
FIGURE 10. Comparison of the active sites of KLrP·Glc and KLrP·Gal. A, KLrP·Glc. Palmitic acid is likely to be located at two different positions, form I (blue) and form II (light blue) at one position. The distance between the C1 of Glc and the carboxyl residue of palmitic acid is 3.9 Å for form I and 5.6 Å for form II of the fatty acid. B, KLrP·Gal. Light blue, palmitic acid. The distance between the C1 of Gal and carboxyl residue of the palmitic acid is 9.8 Å. Glu^165 and Glu^424 are an acid/base catalyst and nucleophile of KLrP, respectively.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 30889-30900) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20590845 H.Manya, K.Akasaka-Manya, and T.Endo (2010).
Klotho protein deficiency and aging.
  Geriatr Gerontol Int, 10, S80-S87.  
20490603 J.R.Ketudat Cairns, and A.Esen (2010).
  Cell Mol Life Sci, 67, 3389-3405.  
19955176 M.Behrendt, J.Polaina, and H.Y.Naim (2010).
Structural hierarchy of regulatory elements in the folding and transport of an intestinal multidomain protein.
  J Biol Chem, 285, 4143-4152.  
19279008 K.Kitatani, K.Sheldon, V.Anelli, R.W.Jenkins, Y.Sun, G.A.Grabowski, L.M.Obeid, and Y.A.Hannun (2009).
Acid beta-glucosidase 1 counteracts p38delta-dependent induction of interleukin-6: possible role for ceramide as an anti-inflammatory lipid.
  J Biol Chem, 284, 12979-12988.  
19279011 K.Kitatani, K.Sheldon, V.Rajagopalan, V.Anelli, R.W.Jenkins, Y.Sun, G.A.Grabowski, L.M.Obeid, and Y.A.Hannun (2009).
Involvement of acid beta-glucosidase 1 in the salvage pathway of ceramide formation.
  J Biol Chem, 284, 12972-12978.  
19843320 M.Janot, A.Audfray, C.Loriol, A.Germot, A.Maftah, and F.Dupuy (2009).
Glycogenome expression dynamics during mouse C2C12 myoblast differentiation suggests a sequential reorganization of membrane glycoconjugates.
  BMC Genomics, 10, 483.  
18972510 M.B.Tropak, G.J.Kornhaber, B.A.Rigat, G.H.Maegawa, J.D.Buttner, J.E.Blanchard, C.Murphy, S.J.Tuske, S.J.Coales, Y.Hamuro, E.D.Brown, and D.J.Mahuran (2008).
Identification of pharmacological chaperones for Gaucher disease and characterization of their effects on beta-glucocerebrosidase by hydrogen/deuterium exchange mass spectrometry.
  Chembiochem, 9, 2650-2662.  
17923531 D.Halter, S.Neumann, S.M.van Dijk, J.Wolthoorn, Mazière, O.V.Vieira, P.Mattjus, J.Klumperman, G.van Meer, and H.Sprong (2007).
Pre- and post-Golgi translocation of glucosylceramide in glycosphingolipid synthesis.
  J Cell Biol, 179, 101-115.  
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.