4ZAH

Crystal structure of sugar aminotransferase WecE with External Aldimine VII from Escherichia coli K-12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structural Basis for the Stereochemical Control of Amine Installation in Nucleotide Sugar Aminotransferases.

Wang, F.Singh, S.Xu, W.Helmich, K.E.Miller, M.D.Cao, H.Bingman, C.A.Thorson, J.S.Phillips, G.N.

(2015) ACS Chem Biol 10: 2048-2056

  • DOI: 10.1021/acschembio.5b00244
  • Primary Citation of Related Structures:  
    4ZAH

  • PubMed Abstract: 
  • Sugar aminotransferases (SATs) are an important class of tailoring enzymes that catalyze the 5'-pyridoxal phosphate (PLP)-dependent stereo- and regiospecific installation of an amino group from an amino acid donor (typically L-Glu or L-Gln) to a corresponding ketosugar nucleotide acceptor ...

    Sugar aminotransferases (SATs) are an important class of tailoring enzymes that catalyze the 5'-pyridoxal phosphate (PLP)-dependent stereo- and regiospecific installation of an amino group from an amino acid donor (typically L-Glu or L-Gln) to a corresponding ketosugar nucleotide acceptor. Herein we report the strategic structural study of two homologous C4 SATs (Micromonospora echinospora CalS13 and Escherichia coli WecE) that utilize identical substrates but differ in their stereochemistry of aminotransfer. This study reveals for the first time a new mode of SAT sugar nucleotide binding and, in conjunction with previously reported SAT structural studies, provides the basis from which to propose a universal model for SAT stereo- and regiochemical control of amine installation. Specifically, the universal model put forth highlights catalytic divergence to derive solely from distinctions within nucleotide sugar orientation upon binding within a relatively fixed SAT active site where the available ligand bound structures of the three out of four representative C3 and C4 SAT examples provide a basis for the overall model. Importantly, this study presents a new predictive model to support SAT functional annotation, biochemical study and rational engineering.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
dTDP-4-amino-4,6-dideoxygalactose transaminase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
396Escherichia coli K-12Mutation(s): 0 
Gene Names: rffAwecEyifIb3791JW3765
EC: 2.6.1.59
UniProt
Find proteins for P27833 (Escherichia coli (strain K12))
Explore P27833 
Go to UniProtKB:  P27833
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27833
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T5K
Query on T5K

Download Ideal Coordinates CCD File 
I [auth A],
J [auth B],
K [auth C],
L [auth D],
M [auth E],
I [auth A],
J [auth B],
K [auth C],
L [auth D],
M [auth E],
N [auth F],
O [auth G],
P [auth H]
[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4S,5R,6R)-6-methyl-5-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3,4-bis(oxidanyl)oxan-2-yl] hydrogen phosphate
C24 H35 N4 O19 P3
LEIRFGMKEVPNBT-QBLVGKJYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 1
  • Diffraction Data DOI: 10.18430/m34zah Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.071α = 72.1
b = 103.935β = 73.55
c = 109.386γ = 74.08
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU01GM098248
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA84374

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references
  • Version 1.2: 2015-07-01
    Changes: Database references
  • Version 1.3: 2015-10-07
    Changes: Database references
  • Version 1.4: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.5: 2019-12-04
    Changes: Author supporting evidence