3ES8

Crystal structure of divergent enolase from Oceanobacillus Iheyensis complexed with Mg and L-malate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis .

Rakus, J.F.Kalyanaraman, C.Fedorov, A.A.Fedorov, E.V.Mills-Groninger, F.P.Toro, R.Bonanno, J.Bain, K.Sauder, J.M.Burley, S.K.Almo, S.C.Jacobson, M.P.Gerlt, J.A.

(2009) Biochemistry 48: 11546-11558

  • DOI: 10.1021/bi901731c
  • Primary Citation of Related Structures:  
    3HPF, 3FYY, 3ES7, 3ES8, 2OQY

  • PubMed Abstract: 
  • The structure of an uncharacterized member of the enolase superfamily from Oceanobacillus iheyensis (GI 23100298, IMG locus tag Ob2843, PDB entry 2OQY ) was determined by the New York SGX Research Center for Structural Genomics (NYSGXRC). The structure contained two Mg(2+) ions located 10 ...

    The structure of an uncharacterized member of the enolase superfamily from Oceanobacillus iheyensis (GI 23100298, IMG locus tag Ob2843, PDB entry 2OQY ) was determined by the New York SGX Research Center for Structural Genomics (NYSGXRC). The structure contained two Mg(2+) ions located 10.4 A from one another, with one located in the canonical position in the (beta/alpha)(7)beta-barrel domain (although the ligand at the end of the fifth beta-strand is His, unprecedented in structurally characterized members of the superfamily); the second is located in a novel site within the capping domain. In silico docking of a library of mono- and diacid sugars to the active site predicted a diacid sugar as a likely substrate. Activity screening of a physical library of acid sugars identified galactarate as the substrate (k(cat) = 6.8 s(-1), K(M) = 620 microM, k(cat)/K(M) = 1.1 x 10(4) M(-1) s(-1)), allowing functional assignment of Ob2843 as galactarate dehydratase (GalrD-II). The structure of a complex of the catalytically impaired Y90F mutant with Mg(2+) and galactarate allowed identification of a Tyr 164-Arg 162 dyad as the base that initiates the reaction by abstraction of the alpha-proton and Tyr 90 as the acid that facilitates departure of the beta-OH leaving group. The enzyme product is 2-keto-d-threo-4,5-dihydroxyadipate, the enantiomer of the product obtained in the GalrD reaction catalyzed by a previously characterized bifunctional l-talarate/galactarate dehydratase (TalrD/GalrD). On the basis of the different active site structures and different regiochemistries, we recognize that these functions represent an example of apparent, not actual, convergent evolution of function. The structure of GalrD-II and its active site architecture allow identification of the seventh functionally and structurally characterized subgroup in the enolase superfamily. This study provides an additional example in which an integrated sequence- and structure-based strategy employing computational approaches is a viable approach for directing functional assignment of unknown enzymes discovered in genome projects.


    Organizational Affiliation

    Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Muconate cycloisomeraseA, B, C, D, E, F, G, H391Oceanobacillus iheyensisMutation(s): 0 
Gene Names: OB2843
EC: 4.2.1.158
UniProt
Find proteins for Q8EMJ9 (Oceanobacillus iheyensis (strain DSM 14371 / CIP 107618 / JCM 11309 / KCTC 3954 / HTE831))
Explore Q8EMJ9 
Go to UniProtKB:  Q8EMJ9
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.584α = 109.31
b = 105.695β = 109.47
c = 105.718γ = 109.66
Software Package:
Software NamePurpose
ADSCdata collection
BALBESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2018-11-14
    Changes: Data collection, Structure summary
  • Version 1.4: 2021-02-10
    Changes: Database references, Derived calculations, Structure summary