7UWU | pdb_00007uwu

Starch adherence system protein 6 (Sas6)

PDB DOI: https://doi.org/10.2210/pdb7UWU/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Ruminococcus bromii L2-63
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-04 Released: 2023-06-14
Deposition Author(s): Photenhauer, A.L., Koropatkin, N.M.
Funding Organization(s): National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.255 (Depositor), 0.240 (DCC)
R-Value Work:
0.186 (Depositor)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The Ruminococcus bromii amylosome protein Sas6 binds single and double helical alpha-glucan structures in starch.

Photenhauer, A.L., Villafuerte-Vega, R.C., Cerqueira, F.M., Armbruster, K.M., Marecek, F., Chen, T., Wawrzak, Z., Hopkins, J.B., Vander Kooi, C.W., Janecek, S., Ruotolo, B.T., Koropatkin, N.M.

(2024) Nat Struct Mol Biol 31: 255-265

PubMed: 38177679 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-023-01166-6
Primary Citation Related Structures:
7UWU, 7UWV, 7UWW

PubMed Abstract:
Resistant starch is a prebiotic accessed by gut bacteria with specialized amylases and starch-binding proteins. The human gut symbiont Ruminococcus bromii expresses Sas6 (Starch Adherence System member 6), which consists of two starch-specific carbohydrate-binding modules from family 26 (RbCBM26) and family 74 (RbCBM74). Here, we present the crystal structures of Sas6 and of RbCBM74 bound with a double helical dimer of maltodecaose. The RbCBM74 starch-binding groove complements the double helical α-glucan geometry of amylopectin, suggesting that this module selects this feature in starch granules. Isothermal titration calorimetry and native mass spectrometry demonstrate that RbCBM74 recognizes longer single and double helical α-glucans, while RbCBM26 binds short maltooligosaccharides. Bioinformatic analysis supports the conservation of the amylopectin-targeting platform in CBM74s from resistant-starch degrading bacteria. Our results suggest that RbCBM74 and RbCBM26 within Sas6 recognize discrete aspects of the starch granule, providing molecular insight into how this structure is accommodated by gut bacteria.

Organizational Affiliation

Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.

Macromolecule Content

Total Structure Weight: 138.56 kDa
Atom Count: 10,523
Modeled Residue Count: 1,246
Deposited Residue Count: 1,270
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Starch Adherence System protein 6 (Sas6)	A, B	635	Ruminococcus bromii L2-63	Mutation(s): 0 Gene Names: sas6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	C [auth A], G [auth A], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth A] Focus chain L [auth B]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A], M [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] N [auth B] H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]