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Hydrolase PDB id
3c2u
Jmol
Contents
Protein chains
538 a.a. *
Ligands
B3P ×4
Waters ×2050
* Residue conservation analysis
PDB id:
3c2u
Name: Hydrolase
Title: Structure of the two subsite d-xylosidase from selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl) methylamino]propane
Structure: Xylosidase/arabinosidase. Chain: a, b, c, d. Engineered: yes
Source: Selenomonas ruminantium. Organism_taxid: 971. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.30Å     R-factor:   0.136     R-free:   0.163
Authors: J.S.Brunzelle,D.B.Jordan,D.R.Mccaslin,A.Olczak,A.Wawrzak
Key ref: J.S.Brunzelle et al. (2008). Structure of the two-subsite beta-d-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane. Arch Biochem Biophys, 474, 157-166. PubMed id: 18374656 DOI: 10.1016/j.abb.2008.03.007
Date:
25-Jan-08     Release date:   22-Apr-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O52575  (O52575_SELRU) -  Xylosidase/arabinosidase
Seq:
Struc:
 
Seq:
Struc:
538 a.a.
538 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     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  

 

 
DOI no: 10.1016/j.abb.2008.03.007 Arch Biochem Biophys 474:157-166 (2008)
PubMed id: 18374656  
 
 
Structure of the two-subsite beta-d-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane.
J.S.Brunzelle, D.B.Jordan, D.R.McCaslin, A.Olczak, Z.Wawrzak.
 
  ABSTRACT  
 
The three-dimensional structure of the catalytically efficient beta-xylosidase from Selenomonas ruminantium in complex with competitive inhibitor 1,3-bis[tris(hydroxymethyl)methylamino]propane (BTP) was determined by using X-ray crystallography (1.3A resolution). Most H bonds between inhibitor and protein occur within subsite -1, including one between the carboxyl group of E186 and an N group of BTP. The other N of BTP occupies subsite +1 near K99. E186 (pK(a) 7.2) serves as catalytic acid. The pH (6-10) profile for 1/K(i)((BTP)) is bell-shaped with pK(a)'s 6.8 and 7.8 on the acidic limb assigned to E186 and inhibitor groups and 9.9 on the basic limb assigned to inhibitor. Mutation K99A eliminates pK(a) 7.8, strongly suggesting that the BTP monocation binds to the dianionic enzyme D14(-)E186(-). A sedimentation equilibrium experiment estimates a K(d) ([dimer](2)/[tetramer]) of 7 x 10(-9)M. Similar k(cat) and k(cat)/K(m) values were determined when the tetramer/dimer ratio changes from 0.0028 to 26 suggesting that dimers and tetramers are equally active forms.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20127424 D.B.Jordan, and J.D.Braker (2010).
beta-D-Xylosidase from Selenomonas ruminantium: role of glutamate 186 in catalysis revealed by site-directed mutagenesis, alternate substrates, and active-site inhibitor.
  Appl Biochem Biotechnol, 161, 395-410.  
20352422 D.B.Jordan, and K.Wagschal (2010).
Properties and applications of microbial beta-D-xylosidases featuring the catalytically efficient enzyme from Selenomonas ruminantium.
  Appl Microbiol Biotechnol, 86, 1647-1658.  
19921178 Z.Fan, L.Yuan, D.B.Jordan, K.Wagschal, C.Heng, and J.D.Braker (2010).
Engineering lower inhibitor affinities in beta-D-xylosidase.
  Appl Microbiol Biotechnol, 86, 1099-1113.  
19361432 A.D.Nesbit, J.L.Giel, J.C.Rose, and P.J.Kiley (2009).
Sequence-specific binding to a subset of IscR-regulated promoters does not require IscR Fe-S cluster ligation.
  J Mol Biol, 387, 28-41.  
18953511 D.B.Jordan, and J.D.Braker (2009).
Beta-D-xylosidase from Selenomonas ruminantium: thermodynamics of enzyme-catalyzed and noncatalyzed reactions.
  Appl Biochem Biotechnol, 155, 330-346.  
  20431716 D.Dodd, and I.K.Cann (2009).
Enzymatic deconstruction of xylan for biofuel production.
  Glob Change Biol Bioenergy, 1, 2.  
19269961 R.Carapito, A.Imberty, J.M.Jeltsch, S.C.Byrns, P.H.Tam, T.L.Lowary, A.Varrot, and V.Phalip (2009).
Molecular Basis of Arabinobio-hydrolase Activity in Phytopathogenic Fungi: CRYSTAL STRUCTURE AND CATALYTIC MECHANISM OF FUSARIUM GRAMINEARUM GH93 EXO-{alpha}-L-ARABINANASE.
  J Biol Chem, 284, 12285-12296.
PDB codes: 2w5n 2w5o
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.