6HOS | pdb_00006hos

Structure of the KpFlo2 adhesin domain in complex with glycerol

PDB DOI: https://doi.org/10.2210/pdb6HOS/pdb

Classification: CELL ADHESION
Organism(s): Komagataella pastoris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-09-18 Released: 2018-10-24
Deposition Author(s): Essen, L.-O., Kock, M., Veelders, M.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.199 (Depositor), 0.199 (DCC)
R-Value Work:
0.172 (Depositor), 0.174 (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

Structural and Functional Characterization of PA14/Flo5-Like Adhesins FromKomagataella pastoris.

Kock, M., Bruckner, S., Wozniak, N., Maestre-Reyna, M., Veelders, M., Schlereth, J., Mosch, H.U., Essen, L.O.

(2018) Front Microbiol 9: 2581-2581

PubMed: 30425696 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3389/fmicb.2018.02581
Primary Citation Related Structures:
6HOS

PubMed Abstract:
Cell-cell and cell-substrate based adhesion of yeasts are major determinants of their adoption of different life styles. Genome-mining of ascomycetous GPI-anchored cell wall proteins with lectin-like PA14 domains identified a unique class of putative adhesins in the clade of methylotrophic Komagataella yeasts, many of which are known to colonize plants and insects involving yet unknown adhesion mechanisms. Here, we report the functional and structural analysis of two of its members: Kp Flo1 (=Cea1), that is highly specific for terminal N -acetylglucosamine moieties, and Kp Flo2, which represents an orphan lectin with intact binding site but unknown specificity. Crystal structures of the Cea1 adhesion domain complexed to N -acetylglucosamine and N , N '-diacetylchitobiose reveal a Ca ²⁺-dependent binding mode that differs from other members of the PA14/Flo5 adhesin family. Heterologous expression of Cea1A in Saccharomyces cerevisiae promotes cellular adhesion to non-reducing ends of non-crystalline chitin. Overall, our data suggest that high-affinity recognition of β-GlcNAc-capped glycans by Cea1 enable Komagataella species to interact with surface cues present in fungi and insects.

Organizational Affiliation

Department of Biochemistry, Faculty of Chemistry, Philipps University of Marburg, Marburg, Germany.

Macromolecule Content

Total Structure Weight: 58.01 kDa
Atom Count: 3,899
Modeled Residue Count: 435
Deposited Residue Count: 495
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BA75_04148T0	A, B	242	Komagataella pastoris	Mutation(s): 0 Gene Names: ATY40_BA7504148
UniProt
Find proteins for A0A1B2JGH2 (Komagataella pastoris) Explore A0A1B2JGH2 Go to UniProtKB: A0A1B2JGH2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1B2JGH2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Expression tag from chain B, or symmetry related chain	C	11	Komagataella pastoris	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P33 Query on P33 Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], S [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth B] 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 H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain R [auth B] 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 H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain R [auth B] 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 H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] N [auth B] E [auth A], F [auth A], G [auth A], H [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain D [auth A]	D [auth A], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain M [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], T [auth B], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.199 (Depositor), 0.199 (DCC)
R-Value Work: 0.172 (Depositor), 0.174 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.943	α = 90
b = 103.186	β = 113.51
c = 72.099	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-10-24

Deposition Author(s):

Essen, L.-O.

Kock, M.

Veelders, M.

Funding Organization	Location	Grant Number
German Research Foundation	Germany	ES152/10

Revision History (Full details and data files)

Version 1.0: 2018-10-24
Type: Initial release
Version 1.1: 2018-11-28
Changes: Data collection, Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.3: 2024-11-13
Changes: Structure summary