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PDBsum entry 1wyu

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1wyu
Jmol
Contents
Protein chains
437 a.a. *
473 a.a. *
Ligands
PLP ×4
Waters ×2145
* Residue conservation analysis
PDB id:
1wyu
Name: Oxidoreductase
Title: Crystal structure of glycine decarboxylase (p-protein) of th cleavage system, in holo form
Structure: Glycine dehydrogenase (decarboxylating) subunit 1 chain: a, c, e, g. Synonym: p-protein of the glycine cleavage system subunit 1 engineered: yes. Glycine dehydrogenase subunit 2 (p-protein). Chain: b, d, f, h. Synonym: p-protein of the glycine cleavage system subunit 2 engineered: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: gcsa. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: gcsb.
Biol. unit: Tetramer (from PQS)
Resolution:
2.10Å     R-factor:   0.189     R-free:   0.229
Authors: T.Nakai,N.Nakagawa,N.Maoka,R.Masui,S.Kuramitsu,N.Kamiya,Rike Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
T.Nakai et al. (2005). Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia. EMBO J, 24, 1523-1536. PubMed id: 15791207 DOI: 10.1038/sj.emboj.7600632
Date:
17-Feb-05     Release date:   05-Apr-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5SKW8  (Q5SKW8_THET8) -  Probable glycine dehydrogenase [decarboxylating] subunit 1
Seq:
Struc:
438 a.a.
437 a.a.
Protein chains
Pfam   ArchSchema ?
Q5SKW7  (GCSPB_THET8) -  Probable glycine dehydrogenase (decarboxylating) subunit 2
Seq:
Struc:
474 a.a.
473 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H: E.C.1.4.4.2  - Glycine dehydrogenase (aminomethyl-transferring).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Glycine Cleavage System
      Reaction: Glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine = [glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L- lysine + CO2
Glycine
+ [glycine-cleavage complex H protein]-N(6)-lipoyl-L-lysine
= [glycine-cleavage complex H protein]-S-aminomethyl-N(6)-dihydrolipoyl-L- lysine
+ CO(2)
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1038/sj.emboj.7600632 EMBO J 24:1523-1536 (2005)
PubMed id: 15791207  
 
 
Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia.
T.Nakai, N.Nakagawa, N.Maoka, R.Masui, S.Kuramitsu, N.Kamiya.
 
  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. 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.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Overall structures of P-protein and GluDC, the closest homolog with a known structure. Front view (A), top view (B) and side view (C) of ( N C)[2]-tetrameric P-protein, and side view of I[6] hexameric GluDC (D). PLP molecules are represented by yellow spheres.
Figure 3.
Figure 3 Dimer and subunit structures of P-protein and GluDC. Stereoview of the N C dimer of the P-protein (A) and view of I[2] dimer of GluDC (B). Stereoviews of N (C) and C (D) of the P-protein. Superposition of N (green) and C (orange) of the P-protein, and I of GluDC (purple) (E). PLP molecules and their bound lysine residues are shown as ball-and-stick models. In panels C and D, topology diagrams are included, in which -helices and -strands are represented by circles and triangles, respectively. The diagrams were generated by Tops (Westhead et al, 1999) with manual modifications.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2005, 24, 1523-1536) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17981801 D.A.Scott, S.M.Hickerson, T.J.Vickers, and S.M.Beverley (2008).
The role of the mitochondrial glycine cleavage complex in the metabolism and virulence of the protozoan parasite Leishmania major.
  J Biol Chem, 283, 155-165.  
18941301 G.Kikuchi, Y.Motokawa, T.Yoshida, and K.Hiraga (2008).
Glycine cleavage system: reaction mechanism, physiological significance, and hyperglycinemia.
  Proc Jpn Acad Ser B Phys Biol Sci, 84, 246-263.  
18316329 T.Nakai, S.Kuramitsu, and N.Kamiya (2008).
Structural bases for the specific interactions between the E2 and E3 components of the Thermus thermophilus 2-oxo acid dehydrogenase complexes.
  J Biochem, 143, 747-758.  
16450403 S.Kure, K.Kato, A.Dinopoulos, C.Gail, T.J.DeGrauw, J.Christodoulou, V.Bzduch, R.Kalmanchey, G.Fekete, A.Trojovsky, B.Plecko, G.Breningstall, J.Tohyama, Y.Aoki, and Y.Matsubara (2006).
Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia.
  Hum Mutat, 27, 343-352.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.