1GYH | pdb_00001gyh

Structure of D158A Cellvibrio cellulosa alpha-L-arabinanase mutant

PDB DOI: https://doi.org/10.2210/pdb1GYH/pdb

Classification: HYDROLASE
Organism(s): Cellvibrio japonicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2002-04-23 Released: 2002-08-23
Deposition Author(s): Nurizzo, D., Turkenburg, J.P., Charnock, S.J., Roberts, S.M., Dodson, E.J., McKie, V.A., Taylor, E.J., Gilbert, H.J., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.203 (Depositor)
R-Value Work:
0.147 (Depositor), 0.226 (DCC)
R-Value Observed:
0.147 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Cellovibrio Cellulosa Alpha-L-Arabinanase 43A Has a Novel Five-Blade Beta-Propeller Fold

Nurizzo, D., Turkenburg, J.P., Charnock, S.J., Roberts, S.M., Dodson, E.J., Mckie, V.A., Taylor, E.J., Gilbert, H.J., Davies, G.J.

(2002) Nat Struct Biol 9: 665

PubMed: 12198486 Search on PubMed
DOI: https://doi.org/10.1038/nsb835
Primary Citation Related Structures:
1GYD, 1GYE, 1GYH

PubMed Abstract:
Cellvibrio japonicus arabinanase Arb43A hydrolyzes the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans. The three-dimensional structure of Arb43A, determined at 1.9 A resolution, reveals a five-bladed beta-propeller fold. Arb43A is the first enzyme known to display this topology. A long V-shaped surface groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. Three carboxylates deep in the active site groove provide the general acid and base components for glycosidic bond hydrolysis with inversion of anomeric configuration.

Organizational Affiliation

Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.

Macromolecule Content

Total Structure Weight: 217.09 kDa
Atom Count: 17,338
Modeled Residue Count: 1,903
Deposited Residue Count: 1,908
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A	A, B, C, D, E A, B, C, D, E, F	318	Cellvibrio japonicus	Mutation(s): 0 EC: 3.2.1.99 (PDB Primary Data), 3.2.1.55 (UniProt)
UniProt
Find proteins for P95470 (Cellvibrio japonicus (strain Ueda107)) Explore P95470 Go to UniProtKB: P95470
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P95470
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain K [auth E] SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth F] MOL2 format, chain K [auth E] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth F] mmCIF format, chain K [auth E] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.203 (Depositor)
R-Value Work: 0.147 (Depositor), 0.226 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.556	α = 88.83
b = 79.557	β = 89.58
c = 132.402	γ = 83.58

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2002-08-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-08-23
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-04-10
Changes: Data collection, Other, Source and taxonomy
Version 1.4: 2024-05-01
Changes: Data collection, Database references, Other, Refinement description
Version 1.5: 2024-11-20
Changes: Structure summary