5UNQ

Crystal Structure of Pt0534 Inactivated by 2-Oxo-3-pentynoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A global view of structure-function relationships in the tautomerase superfamily.

Davidson, R.Baas, B.J.Akiva, E.Holliday, G.L.Polacco, B.J.LeVieux, J.A.Pullara, C.R.Zhang, Y.J.Whitman, C.P.Babbitt, P.C.

(2018) J Biol Chem 293: 2342-2357

  • DOI: https://doi.org/10.1074/jbc.M117.815340
  • Primary Citation of Related Structures:  
    5UNQ, 6BLM

  • PubMed Abstract: 

    The tautomerase superfamily (TSF) consists of more than 11,000 nonredundant sequences present throughout the biosphere. Characterized members have attracted much attention because of the unusual and key catalytic role of an N-terminal proline. These few characterized members catalyze a diverse range of chemical reactions, but the full scale of their chemical capabilities and biological functions remains unknown. To gain new insight into TSF structure-function relationships, we performed a global analysis of similarities across the entire superfamily and computed a sequence similarity network to guide classification into distinct subgroups. Our results indicate that TSF members are found in all domains of life, with most being present in bacteria. The eukaryotic members of the cis -3-chloroacrylic acid dehalogenase subgroup are limited to fungal species, whereas the macrophage migration inhibitory factor subgroup has wide eukaryotic representation (including mammals). Unexpectedly, we found that 346 TSF sequences lack Pro-1, of which 85% are present in the malonate semialdehyde decarboxylase subgroup. The computed network also enabled the identification of similarity paths, namely sequences that link functionally diverse subgroups and exhibit transitional structural features that may help explain reaction divergence. A structure-guided comparison of these linker proteins identified conserved transitions between them, and kinetic analysis paralleled these observations. Phylogenetic reconstruction of the linker set was consistent with these findings. Our results also suggest that contemporary TSF members may have evolved from a short 4-oxalocrotonate tautomerase-like ancestor followed by gene duplication and fusion. Our new linker-guided strategy can be used to enrich the discovery of sequence/structure/function transitions in other enzyme superfamilies.


  • Organizational Affiliation

    From the Department of Bioengineering and Therapeutic Sciences.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative tautomeraseA,
C [auth D],
D [auth E],
E [auth F],
F [auth C]
123Pusillimonas sp. T7-7Mutation(s): 0 
Gene Names: PT7_0534
UniProt
Find proteins for F4GMX9 (Pusillimonas sp. (strain T7-7))
Explore F4GMX9 
Go to UniProtKB:  F4GMX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4GMX9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative tautomerase123Pusillimonas sp. T7-7Mutation(s): 0 
Gene Names: PT7_0534
UniProt
Find proteins for F4GMX9 (Pusillimonas sp. (strain T7-7))
Explore F4GMX9 
Go to UniProtKB:  F4GMX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4GMX9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
DYJ
Query on DYJ
B
L-PEPTIDE LINKINGC10 H13 N O5PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.214α = 106.69
b = 57.586β = 104.54
c = 63.528γ = 94.03
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-65324
Robert A. Welch FoundationUnited StatesF-1334

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Author supporting evidence, Source and taxonomy
  • Version 1.2: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description