1WYU

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Literature

Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia

Nakai, T., Nakagawa, N., Maoka, N., Masui, R., Kuramitsu, S., Kamiya, N.

(2005) EMBO J 24: 1523-1536

  • DOI: 10.1038/sj.emboj.7600632
  • Primary Citation of Related Structures:  
    1WYT, 1WYU, 1WYV

  • PubMed Abstract: 

    • The crystal structure of the P-protein of the glycine cleavage system from Thermus thermophilus HB8 has been determined. This is the first reported crystal structure of a P-protein, and it reveals that P-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (PLP)-dependent enzymes ...

    The crystal structure of the P-protein of the glycine cleavage system from Thermus thermophilus HB8 has been determined. This is the first reported crystal structure of a P-protein, and it reveals that P-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (PLP)-dependent enzymes. Instead, novel alphabeta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally similar and appear to have arisen by gene duplication and subsequent divergence with a loss of one active site. The binding of PLP to the apoenzyme induces large open-closed conformational changes, with residues moving up to 13.5 A. The structure of the complex formed by the holoenzyme bound to an inhibitor, (aminooxy)acetate, suggests residues that may be responsible for substrate recognition. The molecular surface around the lipoamide-binding channel shows conservation of positively charged residues, which are possibly involved in complex formation with the H-protein. These results provide insights into the molecular basis of nonketotic hyperglycinemia.

    Organizational Affiliation: 

    RIKEN Harima Institute at SPring-8, Mikazuki, Sayo, Hyogo, Japan. nakaix@spring8.or.jp



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
glycine dehydrogenase (decarboxylating) subunit 1A, C, E, G438Thermus thermophilus HB8Mutation(s): 0 
Gene Names: GCSA, gcvPA, TTHA0525
EC: 1.4.4.2
UniProt
Find proteins for Q5SKW8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKW8 
Go to UniProtKB:  Q5SKW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SKW8
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
glycine dehydrogenase subunit 2 (P-protein)B, D, F, H474Thermus thermophilus HB8Mutation(s): 0 
Gene Names: GCSB, gcvPB, TTHA0526
EC: 1.4.4.2
UniProt
Find proteins for Q5SKW7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKW7 
Go to UniProtKB:  Q5SKW7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SKW7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP
Download Ideal Coordinates CCD File 
I [auth B],
J [auth D],
K [auth F],
L [auth H]		PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.874α = 90
b = 166.673β = 90
c = 189.007γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance