6BLM

Crystal Structure of Native Fused 4-OT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.488 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1074/jbc.M117.815340
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The tautomerase superfamily (TSF) consists of more than 11,000 non-redundant 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 ...

    The tautomerase superfamily (TSF) consists of more than 11,000 non-redundant 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 indicated 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, while the macrophagemigration 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 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 discovery of sequence/structure/function transitions in other enzyme superfamilies.


    Organizational Affiliation

    University of California, San Francisco, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-oxalocrotonate tautomerase
A, B, C
127Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383)Mutation(s): 0 
Find proteins for Q392K7 (Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383))
Go to UniProtKB:  Q392K7
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.488 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.814α = 90.00
b = 67.229β = 90.00
c = 94.840γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM-65324
Robert A. Welch FoundationUnited StatesF-1334

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Author supporting evidence
  • Version 1.3: 2018-02-28
    Type: Database references