PDBsum entry 1qw9

Hydrolase

PDB id

1qw9

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Contents

			Protein chains

					497 a.a. *

			Ligands

					KHP ×2

			Waters ×1588

* Residue conservation analysis

PDB id:

1qw9

Links

Name:

Hydrolase

Title:

Crystal structure of a family 51 alpha-l-arabinofuranosidase in complex with 4-nitrophenyl-ara

Structure:

Alpha-l-arabinofuranosidase. Chain: a, b. Synonym: arabinosidase. Engineered: yes. Mutation: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: abfa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Hexamer (from PDB file)

Resolution:

1.20Å

R-factor:

0.173

R-free:

0.179

Authors:

K.Hoevel,D.Shallom,K.Niefind,V.Belakhov,G.Shoham,T.Bassov,Y.Shoham, D.Schomburg

Key ref:

K.Hövel et al. (2003). Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase. Embo J, 22, 4922-4932. PubMed id: 14517232

Date:

01-Sep-03

Release date:

07-Oct-03

PROCHECK

	Headers

	References

Protein chains

Q9XBQ3 (IABF_GEOSE) - Intracellular exo-alpha-(1->5)-L-arabinofuranosidase from Geobacillus stearothermophilus

Seq: Struc:					502 a.a. 497 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)



		Enzyme reactions

Enzyme class:

E.C.3.2.1.55 - non-reducing end alpha-L-arabinofuranosidase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.

	Embo J 22:4922-4932 (2003)
PubMed id: 14517232

Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase.
K.Hövel, D.Shallom, K.Niefind, V.Belakhov, G.Shoham, T.Baasov, Y.Shoham, D.Schomburg.

ABSTRACT

High-resolution crystal structures of alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycosidase, are described. The enzyme is a hexamer, and each monomer is organized into two domains: a (beta/alpha)8-barrel and a 12-stranded beta sandwich with jelly-roll topology. The structures of the Michaelis complexes with natural and synthetic substrates, and of the transient covalent arabinofuranosyl-enzyme intermediate represent two stable states in the double displacement mechanism, and allow thorough examination of the catalytic mechanism. The arabinofuranose sugar is tightly bound and distorted by an extensive network of hydrogen bonds. The two catalytic residues are 4.7 A apart, and together with other conserved residues contribute to the stabilization of the oxocarbenium ion-like transition state via charge delocalization and specific protein-substrate interactions. The enzyme is an anti-protonator, and a 1.7 A electrophilic migration of the anomeric carbon takes place during the hydrolysis.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21445259

G.Agarwal, S.Mahajan, N.Srinivasan, and A.G.de Brevern (2011).
Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks.

PLoS One, 6, e17826.

20376631

C.S.Park, M.H.Yoo, K.H.Noh, and D.K.Oh (2010).
Biotransformation of ginsenosides by hydrolyzing the sugar moieties of ginsenosides using microbial glycosidases.

Appl Microbiol Biotechnol, 87, 9.

20560210

S.B.Daly, J.E.Urquhart, E.Hilton, E.A.McKenzie, R.A.Kammerer, M.Lewis, B.Kerr, H.Stuart, D.Donnai, D.A.Long, B.Burgu, O.Aydogdu, M.Derbent, S.Garcia-Minaur, W.Reardon, B.Gener, S.Shalev, R.Smith, A.S.Woolf, G.C.Black, and W.G.Newman (2010).
Mutations in HPSE2 cause urofacial syndrome.

Am J Hum Genet, 86, 963-969.

20477891

Y.R.Lim, R.Y.Yoon, E.S.Seo, Y.S.Kim, C.S.Park, and D.K.Oh (2010).
Hydrolytic properties of a thermostable α-L-arabinofuranosidase from Caldicellulosiruptor saccharolyticus.

J Appl Microbiol, 109, 1188-1197.

19244131

L.Fux, N.Feibish, V.Cohen-Kaplan, S.Gingis-Velitski, S.Feld, C.Geffen, I.Vlodavsky, and N.Ilan (2009).
Structure-function approach identifies a COOH-terminal domain that mediates heparanase signaling.

Cancer Res, 69, 1758-1767.

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

19279191

R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, and A.Kuno (2009).
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.

J Biochem, 146, 61-70.

PDB codes:

2d1z 2d20 2d22 2d23 2d24

18665359

H.Ichinose, M.Yoshida, Z.Fujimoto, and S.Kaneko (2008).
Characterization of a modular enzyme of exo-1,5-alpha-L: -arabinofuranosidase and arabinan binding module from Streptomyces avermitilis NBRC14893.

Appl Microbiol Biotechnol, 80, 399-408.

18679678

S.Canakci, M.Kacagan, K.Inan, A.O.Belduz, and B.C.Saha (2008).
Cloning, purification, and characterization of a thermostable alpha-L-arabinofuranosidase from Anoxybacillus kestanbolensis AC26Sari.

Appl Microbiol Biotechnol, 81, 61-68.

17955483

A.Ben-David, T.Bravman, Y.S.Balazs, M.Czjzek, D.Schomburg, G.Shoham, and Y.Shoham (2007).
Glycosynthase activity of Geobacillus stearothermophilus GH52 beta-xylosidase: efficient synthesis of xylooligosaccharides from alpha-D-xylopyranosyl fluoride through a conjugated reaction.

Chembiochem, 8, 2145-2151.

17142383

S.Shulami, G.Zaide, G.Zolotnitsky, Y.Langut, G.Feld, A.L.Sonenshein, and Y.Shoham (2007).
A two-component system regulates the expression of an ABC transporter for xylo-oligosaccharides in Geobacillus stearothermophilus.

Appl Environ Microbiol, 73, 874-884.

17905739

Y.Kitago, S.Karita, N.Watanabe, M.Kamiya, T.Aizawa, K.Sakka, and I.Tanaka (2007).
Crystal structure of Cel44A, a glycoside hydrolase family 44 endoglucanase from Clostridium thermocellum.

J Biol Chem, 282, 35703-35711.

PDB codes:

2e0p 2e4t 2eex 2ej1 2eo7 2eqd

16385399

M.T.Numan, and N.B.Bhosle (2006).
Alpha-L-arabinofuranosidases: the potential applications in biotechnology.

J Ind Microbiol Biotechnol, 33, 247-260.

15501829

A.L.Lovering, S.S.Lee, Y.W.Kim, S.G.Withers, and N.C.Strynadka (2005).
Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate.

J Biol Chem, 280, 2105-2115.

PDB codes:

1xsi 1xsj 1xsk

15965714

K.Miyazaki (2005).
Hyperthermophilic alpha-L: -arabinofuranosidase from Thermotoga maritima MSB8: molecular cloning, gene expression, and characterization of the recombinant protein.

Extremophiles, 9, 399-406.

15708971

M.R.Proctor, E.J.Taylor, D.Nurizzo, J.P.Turkenburg, R.M.Lloyd, M.Vardakou, G.J.Davies, and H.J.Gilbert (2005).
Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A.

Proc Natl Acad Sci U S A, 102, 2697-2702.

PDB code:

1uv4

15213394

A.Miyanaga, T.Koseki, H.Matsuzawa, T.Wakagi, H.Shoun, and S.Fushinobu (2004).
Expression, purification, crystallization and preliminary X-ray analysis of alpha-L-arabinofuranosidase B from Aspergillus kawachii.

Acta Crystallogr D Biol Crystallogr, 60, 1286-1288.

15292273

A.Miyanaga, T.Koseki, H.Matsuzawa, T.Wakagi, H.Shoun, and S.Fushinobu (2004).
Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose.

J Biol Chem, 279, 44907-44914.

PDB codes:

1wd3 1wd4

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.