2PAN

Crystal structure of E. coli glyoxylate carboligase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

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This is version 2.0 of the entry. See complete history. 


Literature

Glyoxylate carboligase lacks the canonical active site glutamate of thiamine-dependent enzymes.

Kaplun, A., Binshtein, E., Vyazmensky, M., Steinmetz, A., Barak, Z., Chipman, D.M., Tittmann, K., Shaanan, B.

(2008) Nat Chem Biol 4: 113-118

  • DOI: 10.1038/nchembio.62
  • Primary Citation of Related Structures:  
    2PAN

  • PubMed Abstract: 

    • Thiamine diphosphate (ThDP), a derivative of vitamin B1, is an enzymatic cofactor whose special chemical properties allow it to play critical mechanistic roles in a number of essential metabolic enzymes. It has been assumed that all ThDP-dependent enzymes exploit a polar interaction between a strictly conserved glutamate and the N1' of the ThDP moiety ...

    Thiamine diphosphate (ThDP), a derivative of vitamin B1, is an enzymatic cofactor whose special chemical properties allow it to play critical mechanistic roles in a number of essential metabolic enzymes. It has been assumed that all ThDP-dependent enzymes exploit a polar interaction between a strictly conserved glutamate and the N1' of the ThDP moiety. The crystal structure of glyoxylate carboligase challenges this paradigm by revealing that valine replaces the conserved glutamate. Through kinetic, spectroscopic and site-directed mutagenesis studies, we show that although this extreme change lowers the rate of the initial step of the enzymatic reaction, it ensures efficient progress through subsequent steps. Glyoxylate carboligase thus provides a unique illustration of the fine tuning between catalytic stages imposed during evolution on enzymes catalyzing multistep processes.

    Organizational Affiliation: 

    Department of Life Sciences, Ben-Gurion University of the Negev, 1 Ben-Gurion Avenue, Beer-Sheva 84105, Israel.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glyoxylate carboligase
A, B, C, D, E, F
A, B, C, D, E, F
616Escherichia coliMutation(s): 0 
Gene Names: gcl
EC: 4.1.1.47
UniProt
Find proteins for P0AEP7 (Escherichia coli (strain K12))
Explore P0AEP7 
Go to UniProtKB:  P0AEP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEP7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
BA [auth E],
GA [auth F],
I [auth A],
O [auth B],
S [auth C],
BA [auth E],
GA [auth F],
I [auth A],
O [auth B],
S [auth C],
W [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
TPP
Query on TPP
Download Ideal Coordinates CCD File 
CA [auth E],
HA [auth F],
J [auth A],
P [auth B],
T [auth C],
CA [auth E],
HA [auth F],
J [auth A],
P [auth B],
T [auth C],
X [auth D]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O		 Ligand Interaction
1PE
Query on 1PE
Download Ideal Coordinates CCD File 
L [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N		 Ligand Interaction
DTT
Query on DTT
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DA [auth E],
IA [auth F],
K [auth A],
Q [auth B],
U [auth C],
DA [auth E],
IA [auth F],
K [auth A],
Q [auth B],
U [auth C],
Y [auth D]
2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N		 Ligand Interaction
MG
Query on MG
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AA [auth E],
EA [auth F],
FA [auth F],
G [auth A],
H [auth A],
AA [auth E],
EA [auth F],
FA [auth F],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
R [auth C],
V [auth D],
Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.18α = 90
b = 188.18β = 90
c = 249.4γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2021-08-04
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary