PDBsum entry 5a8d

Hydrolase

PDB id: 5a8d

Contents

Protein chain

302 a.a.

Ligands

SO4 ×5

ACT ×2

GOL ×4

Waters ×232

PDB id:

5a8d

Name:

Hydrolase

Title:

The high resolution structure of a novel alpha-l-arabinofuranosidase (ctgh43) from clostridium thermocellum atcc 27405

Structure:

Carbohydrate binding family 6. Chain: a. Fragment: family 43 glycoside hydrolase, residues 30-330. Synonym: alpha-l-arabinofuranosidase. Engineered: yes

Source:

Clostridium thermocellum. Organism_taxid: 1515. Atcc: 27405. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: plyss.

Resolution:

1.65Å R-factor: 0.171 R-free: 0.193

Authors:

A.Goyal,S.Ahmed,K.Sharma,C.M.G.A.Fontes,S.Najmudin

Key ref:

A.Goyal et al. (2016). Molecular determinants of substrate specificity revealed by the structure of Clostridium thermocellum arabinofuranosidase 43A from glycosyl hydrolase family 43 subfamily 16. Acta Crystallogr D Struct Biol, 72, 1281-1289. PubMed id: 27917828 DOI: 10.1107/S205979831601737X

Date:

14-Jul-15 Release date: 27-Jul-16

Protein chain

A3DEX4  (A3DEX4_CLOTH) -  Carbohydrate binding family 6 from Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)

Seq: 679 a.a.

Struc: 302 a.a.*

* 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.
• Reaction: Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.

DOI no: 10.1107/S205979831601737X

Acta Crystallogr D Struct Biol 72:1281-1289 (2016)

PubMed id: 27917828

Molecular determinants of substrate specificity revealed by the structure of Clostridium thermocellum arabinofuranosidase 43A from glycosyl hydrolase family 43 subfamily 16.

A.Goyal, S.Ahmed, K.Sharma, V.Gupta, P.Bule, V.D.Alves, C.M.Fontes, S.Najmudin.

ABSTRACT

The recent division of the large glycoside hydrolase family 43 (GH43) into subfamilies offers a renewed opportunity to develop structure-function studies aimed at clarifying the molecular determinants of substrate specificity in carbohydrate-degrading enzymes. α-L-Arabinofuranosidases (EC 3.2.1.55) remove arabinose side chains from heteropolysaccharides such as xylan and arabinan. However, there is some evidence suggesting that arabinofuranosidases are substrate-specific, being unable to display a debranching activity on different polysaccharides. Here, the structure of Clostridium thermocellum arabinofuranosidase 43A (CtAbf43A), which has been shown to act in the removal of arabinose side chains from arabinoxylan but not from pectic arabinan, is reported. CtAbf43A belongs to GH43 subfamily 16, the members of which have a restricted capacity to attack xylans. The crystal structure of CtAbf43A comprises a five-bladed β-propeller fold typical of GH43 enzymes. CtAbf43A displays a highly compact architecture compatible with its high thermostability. Analysis of CtAbf43A along with the other member of GH43 subfamily 16 with known structure, the Bacillus subtilis arabinofuranosidase BsAXH-m2,3, suggests that the specificity of subfamily 16 for arabinoxylan is conferred by a long surface substrate-binding cleft that is complementary to the xylan backbone. The lack of a curved-shaped carbohydrate-interacting platform precludes GH43 subfamily 16 enzymes from interacting with the nonlinear arabinan scaffold and therefore from deconstructing this polysaccharide.