PDBsum entry: 1fh7

Hydrolase

PDB-id: 1fh7

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

312 a.a. *

Ligands

XYP-XDN

Waters ×268

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1fh7

Name:

Hydrolase

Title:

Crystal structure of the xylanase cex with xylobiose- derived inhibitor deoxynojirimycin

Structure:

Beta-1,4-xylanase. Chain: a. Fragment: catalytic domain. Synonym: cex. Engineered: yes

Source:

Cellulomonas fimi. Organism_taxid: 1708. Expressed in: escherichia coli. Expression_system_taxid: 562

UniProt:

P07986 (GUX_CELFI)

Seq:

Struc:

Seq:

484 a.a.

Struc:

312 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme class:

E.C.3.2.1.8   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.

Resolution:

1.82Å

R-factor:

0.210

R-free:

0.234

Authors:

V.Notenboom,S.J.Williams,R.Hoos,S.G.Withers,D.R.Rose

Key ref:

V.Notenboom et al. (2000). Detailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars.. Biochemistry, 39, 11553-11563. [PubMed id: 10995222] [DOI: 10.1021/bi0010625]

Date:

31-Jul-00

Release date:

23-Aug-00

Related entries:

1exp
cex xylanase 2-f-cellobiose complex
2exo
cex xylanase
1xyl
cex xylanase 2-f-xylobiose complex
2xyl
cex 2-fluoro xylobiose
1fh8
cex xylanase with xylobiose-derived isofagomine inhibitor
... plus others (see Header records)

Quick_links

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Clefts

Surface

Key reference

DOI no: 10.1021/bi0010625

Biochemistry 39:11553-11563 (2000)

PubMed id: 10995222

Detailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars.

V.Notenboom, S.J.Williams, R.Hoos, S.G.Withers, D.R.Rose.

ABSTRACT

Detailed insights into the mode of binding of a series of tight-binding aza-sugar glycosidase inhibitors of two fundamentally different classes are described through X-ray crystallographic studies of complexes with the retaining family 10 xylanase Cex from Cellulomonas fimi. Complexes with xylobiose-derived aza-sugar inhibitors of the substituted "amidine" class (xylobio-imidazole, K(i) = 150 nM; xylobio-lactam oxime, K(i) = 370 nM) reveal lateral interaction of the "glycosidic" nitrogen with the acid/base catalyst (Glu127) and hydrogen bonding of the sugar 2-hydroxyl with the catalytic nucleophile (Glu233), as expected. Tight binding of xylobio-isofagomine (K(i) = 130 nM) appears to be a consequence of strong interactions of the ring nitrogen with the catalytic nucleophile while, surprisingly, no direct protein contacts are made with the ring nitrogen of the xylobio-deoxynojirimycin analogue (K(i) = 5800 nM). Instead the nitrogen interacts with two ordered water molecules, thereby accounting for its relatively weaker binding, though it still binds some 1200-fold more tightly than does xylobiose, presumably as a consequence of electrostatic interactions at the active site. Dramatically weaker binding of these same inhibitors to the family 11 xylanase Bcx from Bacillus circulans (K(i) from 0.5 to 1.5 mM) is rationalized for the substituted amidines on the basis that this enzyme utilizes a syn protonation trajectory and likely hydrolyzes via a (2,5)B boat transition state. Weaker binding of the deoxynojirimycin and isofagomine analogues likely reflects the energetic penalty for distortion of these analogues to a (2,5)B conformation, possibly coupled with destabilizing interactions with Tyr69, a conserved, catalytically essential active site residue.