7UWW

Sas6 with alpha-cyclodextrin

PDB DOI: https://doi.org/10.2210/pdb7UWW/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: 1.61 Å
R-Value Free: 0.212
R-Value Work: 0.168
R-Value Observed: 0.170

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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41594-023-01166-6
Primary Citation of 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: 142.1 kDa
Atom Count: 11,425
Modelled Residue Count: 1,259
Deposited Residue Count: 1,270
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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
UniProt
Find proteins for A0A2N0UYM2 (Ruminococcus bromii) Explore A0A2N0UYM2 Go to UniProtKB: A0A2N0UYM2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2N0UYM2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
Cyclohexakis-(1-4)-(alpha-D-glucopyranose)	C [auth D], D [auth I]	6		N/A	Interactions Focus chain C [auth D] Focus chain D [auth I] Interactions & Density Focus chain C [auth D] Focus chain D [auth I]
Glycosylation Resources
GlyTouCan: G22307HL GlyCosmos: G22307HL

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 AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain KA [auth B] SDF format, chain MA [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] E [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], G [auth A], H [auth A], KA [auth B], MA [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain KA [auth B] Focus chain MA [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain KA [auth B] Focus chain MA [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A]	FA [auth B] GA [auth B] HA [auth B] I [auth A] IA [auth B] FA [auth B], GA [auth B], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], L [auth A], LA [auth B], M [auth A], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], Q [auth A], R [auth A], S [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A]	PA [auth B] QA [auth B] RA [auth B] SA [auth B] T [auth A] PA [auth B], QA [auth B], RA [auth B], SA [auth B], T [auth A], U [auth A], V [auth A], W [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]