8T8K

Structure of Domain of Unknown Function 507 (DUF507) in Space Group C222(1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold.

McKay, C.E.Cheng, J.Tanner, J.J.

(2023) Sci Rep 13: 13496-13496

  • DOI: https://doi.org/10.1038/s41598-023-40558-y
  • Primary Citation of Related Structures:  
    8T8K, 8T8L

  • PubMed Abstract: 

    The crystal structure of the domain of unknown function family 507 protein from Aquifex aeolicus is reported (AaDUF507, UniProt O67633, 183 residues). The structure was determined in two space groups (C222 1 and P3 2 21) at 1.9 Å resolution. The phase problem was solved by molecular replacement using an AlphaFold model as the search model. AaDUF507 is a Y-shaped α-helical protein consisting of an anti-parallel 4-helix bundle base and two helical arms that extend 30-Å from the base. The two crystal structures differ by a 25° rigid body rotation of the C-terminal arm. The tertiary structure exhibits pseudo-twofold symmetry. The structural symmetry mirrors internal sequence similarity: residues 11-57 and 102-148 are 30% identical and 53% similar with an E-value of 0.002. In one of the structures, electron density for an unknown ligand, consistent with nicotinamide or similar molecule, may indicate a functional site. Docking calculations suggest potential ligand binding hot spots in the region between the helical arms. Structure-based query of the Protein Data Bank revealed no other protein with a similar tertiary structure, leading us to propose that AaDUF507 represents a new protein fold.


  • Organizational Affiliation

    Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUF507 family protein184Aquifex aeolicusMutation(s): 0 
Gene Names: aq_1752
UniProt
Find proteins for O67633 (Aquifex aeolicus (strain VF5))
Explore O67633 
Go to UniProtKB:  O67633
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67633
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
B [auth A]HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.714α = 90
b = 86.534β = 90
c = 79.139γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM093123

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release