7OYV | pdb_00007oyv

E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D F88A S247D in complex with spermidine

PDB DOI: https://doi.org/10.2210/pdb7OYV/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-06-25 Released: 2021-12-01
Deposition Author(s): Shanmugaratnam, S., Kroeger, P., Hocker, B.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.276 (Depositor), 0.273 (DCC)
R-Value Work:
0.227 (Depositor), 0.227 (DCC)
R-Value Observed:
0.229 (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

Fine-tuning spermidine binding modes in the putrescine binding protein PotF.

Kroger, P., Shanmugaratnam, S., Scheib, U., Hocker, B.

(2021) J Biological Chem 297: 101419-101419

PubMed: 34801550 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2021.101419
Primary Citation Related Structures:
7OYS, 7OYT, 7OYU, 7OYV, 7OYW, 7OYX, 7OYY, 7OYZ

PubMed Abstract:
A profound understanding of the molecular interactions between receptors and ligands is important throughout diverse research, such as protein design, drug discovery, or neuroscience. What determines specificity and how do proteins discriminate against similar ligands? In this study, we analyzed factors that determine binding in two homologs belonging to the well-known superfamily of periplasmic binding proteins, PotF and PotD. Building on a previously designed construct, modes of polyamine binding were swapped. This change of specificity was approached by analyzing local differences in the binding pocket as well as overall conformational changes in the protein. Throughout the study, protein variants were generated and characterized structurally and thermodynamically, leading to a specificity swap and improvement in affinity. This dataset not only enriches our knowledge applicable to rational protein design but also our results can further lay groundwork for engineering of specific biosensors as well as help to explain the adaptability of pathogenic bacteria.

Organizational Affiliation

Department for Biochemistry, University of Bayreuth, Bayreuth, Germany.

Macromolecule Content

Total Structure Weight: 80.29 kDa
Atom Count: 5,749
Modeled Residue Count: 682
Deposited Residue Count: 704
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putrescine-binding periplasmic protein	A, B	352	Escherichia coli	Mutation(s): 6 Gene Names: potF, HPE39_07830, WP7S17E04_28980
UniProt
Find proteins for P31133 (Escherichia coli (strain K12)) Explore P31133 Go to UniProtKB: P31133
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31133
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3IZ Query on 3IZ Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2~{R})-1-[(2~{R})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-yl]oxypropan-2-amine C₁₂ H₂₇ N O₄ JAVLCTSZYWYEEE-IJLUTSLNSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SPD (Subject of Investigation/LOI) Query on SPD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	SPERMIDINE C₇ H₁₉ N₃ ATHGHQPFGPMSJY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
3IE Query on 3IE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	G [auth A], H [auth A], N [auth B]	(2~{S})-1-methoxypropan-2-amine C₄ H₁₁ N O NXMXETCTWNXSFG-BYPYZUCNSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B]
JFN Query on JFN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	D [auth A], E [auth A], J [auth B], K [auth B], L [auth B]	(2R)-1-methoxypropan-2-amine C₄ H₁₁ N O NXMXETCTWNXSFG-SCSAIBSYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B]	I [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain O [auth B]