8Q52 | pdb_00008q52

A PBP-like protein built from fragments of different folds

• PDB DOI: https://doi.org/10.2210/pdb8Q52/pdb
• Entry: 8Q52 supersedes: 4QWV

• Classification: DE NOVO PROTEIN
• Organism(s): Escherichia coli K-12, Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-08 Released: 2024-04-10 
• Deposition Author(s): Shanmugaratnam, S., Toledo-Patino, S., Goetz, S.K., Farias-Rico, J.A., Hocker, B.
• Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC), Volkswagen Foundation, Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT), Consejo Nacional de Ciencia y Tecnologia (CONACYT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.253 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Molecular handcraft of a well-folded protein chimera.

Toledo-Patino, S., Goetz, S.K., Shanmugaratnam, S., Hocker, B., Farias-Rico, J.A.

(2024) FEBS Lett 598: 1375-1386

• PubMed: 38508768 
• DOI: https://doi.org/10.1002/1873-3468.14856
• Primary Citation Related Structures: 
  8Q52


• PubMed Abstract: 
  

  Modular assembly is a compelling pathway to create new proteins, a concept supported by protein engineering and millennia of evolution. Natural evolution provided a repository of building blocks, known as domains, which trace back to even shorter segments that underwent numerous 'copy-paste' processes culminating in the scaffolds we see today. Utilizing the subdomain-database Fuzzle, we constructed a fold-chimera by integrating a flavodoxin-like fragment into a periplasmic binding protein. This chimera is well-folded and a crystal structure reveals stable interfaces between the fragments. These findings demonstrate the adaptability of α/β-proteins and offer a stepping stone for optimization. By emphasizing the practicality of fragment databases, our work pioneers new pathways in protein engineering. Ultimately, the results substantiate the conjecture that periplasmic binding proteins originated from a flavodoxin-like ancestor.

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Organizational Affiliation: 
• Max Planck Institute for Developmental Biology, Tübingen, Germany.
Okinawa Institute of Science and Technology Graduate University, Japan.
Department of Biochemistry, University of Bayreuth, Germany.
Synthetic Biology Program, Center for Genome Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.84 kDa 
• Atom Count: 2,599 
• Modeled Residue Count: 320 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-specific-binding protein,Chemotaxis protein CheY	A	321	Escherichia coli K-12, Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: livK, b3458, JW3423, cheY, TM_0700
UniProt
Find proteins for P04816 (Escherichia coli (strain K12)) Explore P04816  Go to UniProtKB:  P04816
Find proteins for Q56312 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q56312  Go to UniProtKB:  Q56312
UniProt Groups	Q56312P04816

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.253 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.56	α = 90
b = 129.56	β = 90
c = 43.64	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Shanmugaratnam, S., Toledo-Patino, S., Goetz, S.K., Farias-Rico, J.A., Hocker, B.
• This entry supersedes: 4QWV

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	HO 4022/1-2
European Research Council (ERC)	European Union	647548 'Protein Lego'
Volkswagen Foundation	Germany	94747
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)	Mexico	IA204622
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	319320

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Structure summary