3AB9 | pdb_00003ab9

Crystal Structure of lipoylated E. coli H-protein (reduced form)

• PDB DOI: https://doi.org/10.2210/pdb3AB9/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-12-04 Released: 2010-04-07 
• Deposition Author(s): Okamura-Ikeda, K., Maita, N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.216 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

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 Biological Chem 285: 18684-18692

• PubMed: 20375021 
• DOI: https://doi.org/10.1074/jbc.M110.110718
• Primary Citation 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-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. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.08 kDa 
• Atom Count: 1,016 
• Modeled Residue Count: 127 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine cleavage system H protein	A	129	Escherichia coli K-12	Mutation(s): 0  Gene Names: gcvH
UniProt
Find proteins for P0A6T9 (Escherichia coli (strain K12)) Explore P0A6T9  Go to UniProtKB:  P0A6T9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LA2	A	L-PEPTIDE LINKING	C14 H28 N2 O3 S2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.216 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.255	α = 90
b = 60.255	β = 90
c = 68.586	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-07 
Deposition Author(s): Okamura-Ikeda, K., Maita, N.

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
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description