4D1J | pdb_00004d1j

The structure of the GH35 beta-galactosidase Bgl35A from Cellvibrio japonicas in complex with 1-Deoxygalactonojirimycin

PDB DOI: https://doi.org/10.2210/pdb4D1J/pdb

Classification: HYDROLASE
Organism(s): Cellvibrio japonicus Ueda107
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-05-02 Released: 2014-05-28
Deposition Author(s): Larsbrink, J., Thompson, A.J., Lundqvist, M., Gardner, J.G., Davies, G.J., Brumer, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.195 (Depositor), 0.203 (DCC)
R-Value Work:
0.172 (Depositor), 0.181 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

A Complex Gene Locus Enables Xyloglucan Utilization in the Model Saprophyte Cellvibrio Japonicus.

Larsbrink, J., Thompson, A.J., Lundqvist, M., Gardner, J.G., Davies, G.J., Brumer, H.

(2014) Mol Microbiol 94: 418

PubMed: 25171165 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1111/mmi.12776
Primary Citation Related Structures:
4D1I, 4D1J

PubMed Abstract:
The degradation of plant biomass by saprophytes is an ecologically important part of the global carbon cycle, which has also inspired a vast diversity of industrial enzyme applications. The xyloglucans (XyGs) constitute a family of ubiquitous and abundant plant cell wall polysaccharides, yet the enzymology of XyG saccharification is poorly studied. Here, we present the identification and molecular characterization of a complex genetic locus that is required for xyloglucan utilization by the model saprophyte Cellvibrio japonicus. In harness, transcriptomics, reverse genetics, enzyme kinetics, and structural biology indicate that the encoded cohort of an α-xylosidase, a β-galactosidase, and an α-l-fucosidase is specifically adapted for efficient, concerted saccharification of dicot (fucogalacto)xyloglucan oligosaccharides following import into the periplasm via an associated TonB-dependent receptor. The data support a biological model of xyloglucan degradation by C. japonicus with striking similarities - and notable differences - to the complex polysaccharide utilization loci of the Bacteroidetes.

Organizational Affiliation

Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91, Stockholm, Sweden.

Macromolecule Content

Total Structure Weight: 489.62 kDa
Atom Count: 37,796
Modeled Residue Count: 4,314
Deposited Residue Count: 4,320
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GALACTOSIDASE, PUTATIVE, BGL35A	A, B, C, D, E A, B, C, D, E, F, G, H	540	Cellvibrio japonicus Ueda107	Mutation(s): 0 EC: 3.2.1.23
UniProt
Find proteins for B3PBE0 (Cellvibrio japonicus (strain Ueda107)) Explore B3PBE0 Go to UniProtKB: B3PBE0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3PBE0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGJ Query on DGJ Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain QA [auth H] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain LA [auth G] SDF format, chain I [auth A] SDF format, chain FA [auth F] SDF format, chain AA [auth E] MOL2 format, chain T [auth D] MOL2 format, chain QA [auth H] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain LA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain FA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain T [auth D] mmCIF format, chain QA [auth H] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain LA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain FA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] FA [auth F] I [auth A] LA [auth G] N [auth B] AA [auth E], FA [auth F], I [auth A], LA [auth G], N [auth B], Q [auth C], QA [auth H], T [auth D]	(2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol C₆ H₁₃ N O₄ LXBIFEVIBLOUGU-DPYQTVNSSA-N		Interactions Focus chain AA [auth E] Focus chain FA [auth F] Focus chain I [auth A] Focus chain LA [auth G] Focus chain N [auth B] Focus chain Q [auth C] Focus chain QA [auth H] Focus chain T [auth D] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth F] Focus chain I [auth A] Focus chain LA [auth G] Focus chain N [auth B] Focus chain Q [auth C] Focus chain QA [auth H] Focus chain T [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain KA [auth F] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain KA [auth F] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain KA [auth F]	KA [auth F], R [auth C], S [auth C], Y [auth D], Z [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain KA [auth F] Focus chain R [auth C] Focus chain S [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain KA [auth F] Focus chain R [auth C] Focus chain S [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain RA [auth H] SDF format, chain PA [auth G] SDF format, chain P [auth B] SDF format, chain OA [auth G] SDF format, chain O [auth B] SDF format, chain NA [auth G] SDF format, chain MA [auth G] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain JA [auth F] SDF format, chain J [auth A] SDF format, chain IA [auth F] SDF format, chain HA [auth F] SDF format, chain GA [auth F] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain CA [auth E] SDF format, chain BA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain RA [auth H] MOL2 format, chain PA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth G] MOL2 format, chain MA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain RA [auth H] mmCIF format, chain PA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth G] mmCIF format, chain MA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E]	BA [auth E] CA [auth E] DA [auth E] EA [auth E] GA [auth F] BA [auth E], CA [auth E], DA [auth E], EA [auth E], GA [auth F], HA [auth F], IA [auth F], J [auth A], JA [auth F], K [auth A], L [auth A], M [auth A], MA [auth G], NA [auth G], O [auth B], OA [auth G], P [auth B], PA [auth G], RA [auth H], U [auth D], V [auth D], W [auth D], X [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain O [auth B] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain RA [auth H] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain O [auth B] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain RA [auth H] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.195 (Depositor), 0.203 (DCC)
R-Value Work: 0.172 (Depositor), 0.181 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.257	α = 90
b = 116.095	β = 90.05
c = 116.113	γ = 90.04

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-05-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-28
Type: Initial release
Version 1.1: 2014-10-22
Changes: Database references
Version 1.2: 2020-03-11
Changes: Derived calculations, Other
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description