6TH8 | pdb_00006th8

Reconstructing the Origins of the HemD-like fold

PDB DOI: https://doi.org/10.2210/pdb6TH8/pdb
BMRB: 34452

Classification: FLAVOPROTEIN
Organism(s): Thermus thermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-11-19 Released: 2019-11-27
Deposition Author(s): Coles, M., Toledo-Patino, S., Chaubey, M., Hocker, B.
Funding Organization(s): European Research Council

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 50
Conformers Submitted: 21
Selection Criteria: structures with the least restraint violations

wwPDB Validation 3D Report Full Report

Validation slider image for 6TH8

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

Literature

Reconstructing the Remote Origins of a Fold Singleton from a Flavodoxin-Like Ancestor.

Toledo-Patino, S., Chaubey, M., Coles, M., Hocker, B.

(2019) Biochemistry 58: 4790-4793

PubMed: 31724394 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.biochem.9b00900
Primary Citation Related Structures:
6TH8

PubMed Abstract:
Evolutionary processes that led to the emergence of structured protein domains left footprints in the sequences of modern proteins. We searched for such hints employing state-of-the-art sequence analysis and found evidence that the HemD-like fold emerged from the flavodoxin-like fold through segment swap and gene duplication. To verify this hypothesis, we reverted these evolutionary steps experimentally, constructing a HemD-half that resulted in a protein with the canonical flavodoxin-like architecture. These results of fold reconstruction from the sequence of a different fold strongly support our hypothesis of common ancestry. It further illustrates the plasticity of modern proteins to form new folded proteins.

Organizational Affiliation

Department of Biochemistry , University of Bayreuth , 95447 Bayreuth , Germany.

Macromolecule Content

Total Structure Weight: 13.65 kDa
Atom Count: 960
Modeled Residue Count: 125
Deposited Residue Count: 125
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cU3Sd	A	125	Thermus thermophilus	Mutation(s): 0 EC: 4.2.1.75
UniProt
Find proteins for P48246 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P48246 Go to UniProtKB: P48246
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48246
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 50
Conformers Submitted: 21
Selection Criteria: structures with the least restraint violations

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-11-27

Deposition Author(s):

Toledo-Patino, S.

Funding Organization	Location	Grant Number
European Research Council	Germany	647548

Revision History (Full details and data files)

Version 1.0: 2019-11-27
Type: Initial release
Version 1.1: 2019-12-11
Changes: Database references
Version 1.2: 2023-06-14
Changes: Database references, Other
Version 1.3: 2024-06-19
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.