3A8K

Crystal Structure of ETD97N-EHred complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of aminomethyltransferase in complex with dihydrolipoyl-H-protein of the glycine cleavage system: implications for recognition of lipoyl protein substrate, disease-related mutations, and reaction mechanism

Okamura-Ikeda, K., Hosaka, H., Maita, N., Fujiwara, K., Yoshizawa, A.C., Nakagawa, A., Taniguchi, H.

(2010) J Biol Chem 285: 18684-18692

  • DOI: 10.1074/jbc.M110.110718
  • Primary Citation of Related Structures:  
    3A8I, 3A8J, 3A8K, 3AB9

  • PubMed Abstract: 

    • Aminomethyltransferase, a component of the glycine cleavage system termed T-protein, reversibly catalyzes the degradation of the aminomethyl moiety of glycine attached to the lipoate cofactor of H-protein, resulting in the production of ammonia, 5,10 ...

    Aminomethyltransferase, a component of the glycine cleavage system termed T-protein, reversibly catalyzes the degradation of the aminomethyl moiety of glycine attached to the lipoate cofactor of H-protein, resulting in the production of ammonia, 5,10-methylenetetrahydrofolate, and dihydrolipoate-bearing H-protein in the presence of tetrahydrofolate. Several mutations in the human T-protein gene are known to cause nonketotic hyperglycinemia. Here, we report the crystal structure of Escherichia coli T-protein in complex with dihydrolipoate-bearing H-protein and 5-methyltetrahydrofolate, a complex mimicking the ternary complex in the reverse reaction. The structure of the complex shows a highly interacting intermolecular interface limited to a small area and the protein-bound dihydrolipoyllysine arm inserted into the active site cavity of the T-protein. Invariant Arg(292) of the T-protein is essential for complex assembly. The structure also provides novel insights in understanding the disease-causing mutations, in addition to the disease-related impairment in the cofactor-enzyme interactions reported previously. Furthermore, structural and mutational analyses suggest that the reversible transfer of the methylene group between the lipoate and tetrahydrofolate should proceed through the electron relay-assisted iminium intermediate formation.

    Organizational Affiliation: 

    Institute for Enzyme Research, the University of Tokushima, Tokushima 770-8503, Japan. ikeda@ier.tokushima-u.ac.jp



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AminomethyltransferaseA, B, C, D364Escherichia coli K-12Mutation(s): 1 
Gene Names: gcvT, b2905, JW2873
EC: 2.1.2.10
Find proteins for P27248 (Escherichia coli (strain K12))
Explore P27248 
Go to UniProtKB:  P27248
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glycine cleavage system H proteinE, F129Escherichia coli K-12Mutation(s): 0 
Gene Names: gcvH, b2904, JW2872
Find proteins for P0A6T9 (Escherichia coli (strain K12))
Explore P0A6T9 
Go to UniProtKB:  P0A6T9
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LA2
Query on LA2		E,FL-PEPTIDE LINKINGC14 H28 N2 O3 S2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.122α = 91.56
b = 88.412β = 102.42
c = 97.863γ = 89.59
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-08-21
    Changes: Database references