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PDBsum entry 1hpc
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Transit peptide
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PDB id
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1hpc
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Refined structures at 2 and 2.2 a resolution of two forms of the h-Protein, A lipoamide-Containing protein of the glycine decarboxylase complex.
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Authors
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S.Pares,
C.Cohen-Addad,
L.C.Sieker,
M.Neuburger,
R.Douce.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1995,
51,
1041-1051.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
86%.
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Abstract
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H-protein, a 14 kDa lipoic acid-containing protein is a component of the glycine
decarboxylase complex. This complex which consists of four protein components
(P-, H-, T- and L-protein) catalyzes the oxidative decarboxylation of glycine.
The mechanistic heart of the complex is provided by the lipoic acid attached to
a lysine residue of the H-protein. It undergoes a cycle of transformations, i.e.
reductive methylamination, methylamine transfer, and electron transfer. We
present details of the crystal structures of the H-protein, in its two forms,
H-Pro(Ox) with oxidized lipoamide and H-Pro(Met) with methylamine-loaded
lipoamide. X-ray diffraction data were collected from crystals of H-Pro(Ox) to 2
and H-Pro(Met) to 2.2 A resolution. The final R-factor value for the H-Pro(Ox)
is 18.5% for data with F > 2sigma. in the range of 8.0-2.0 A resolution. The
refinement confirmed our previous model, refined to 2.6 A, of a beta-fold
sandwich structure with two beta-sheets. The lipoamide arm attached to Lys63,
located in the loop of a hairpin conformation, is clearly visible at the surface
of the protein. The H-Pro(Met) has been crystallized in orthorhombic and
monoclinic forms and the structures were solved by molecular replacement,
starting from the H-Pro(Ox) model. The orthorhombic structure has been refined
with a final R-factor value of 18.5% for data with F > 2sigma in the range of
8.0-2.2 A resolution. The structure of the monoclinic form has been refined with
a final R-factor value of 17.5% for data with F > 2sigma in the range of
15.0-3.0 A. In these two structures which have similar packing, the protein
conformation is identical to the conformation found in the H-Pro(Ox). The main
change lies in the position of the lipoamide group which has moved significantly
when loaded with methylamine. In this case the methylamine-lipoamide group is
tucked into a cleft at the surface of the protein where it is stabilized by
hydrogen bonds and hydrophobic contacts. Thus, it is totally protected and not
free to move in aqueous solvent. In addition, the H-protein presents some
sequence and structural analogies with other lipoate- and biotin-containing
proteins and also with proteins of the phosphoenolpyruvate:sugar
phosphotransferase system.
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Figure 6.
Fig. 6. H-PrOMet orthorhombic crystl form. Plot of the average B-factor
values. Same represenaton as in Fig. 3.
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Figure 9.
Fig. 9. Stereo viw of the structure of the H-protein an location of the
lipoamide arm. (a H-Proox, (b) H-PrOMet.
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Figure 11.
Fig. 11. Connolly surface of the cavity containing the lipoamide group.
This cavity is essentially identical in H-PrOMet and H-Proox. The
figue was generated with the program MS (Connolly, 1983) and
TURBO-FRODO (Roussel & Cambiau, 1989).
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1995,
51,
1041-1051)
copyright 1995.
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Secondary reference #1
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Title
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The lipoamide arm in the glycine decarboxylase complex is not freely swinging.
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Authors
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C.Cohen-Addad,
S.Pares,
L.Sieker,
M.Neuburger,
R.Douce.
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Ref.
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Nat Struct Biol, 1995,
2,
63-68.
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PubMed id
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Secondary reference #2
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Title
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X-Ray structure determination at 2.6-A resolution of a lipoate-Containing protein: the h-Protein of the glycine decarboxylase complex from pea leaves.
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Authors
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S.Pares,
C.Cohen-Addad,
L.Sieker,
M.Neuburger,
R.Douce.
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Ref.
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Proc Natl Acad Sci U S A, 1994,
91,
4850-4853.
[DOI no: ]
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PubMed id
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Secondary reference #3
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Title
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Crystallographic data for h-Protein from the glycine decarboxylase complex.
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Authors
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L.Sieker,
C.Cohen-Addad,
M.Neuburger,
R.Douce.
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Ref.
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J Mol Biol, 1991,
220,
223-224.
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PubMed id
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Secondary reference #4
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Title
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Cdna cloning, Primary structure and gene expression for h-Protein, A component of the glycine-Cleavage system (glycine decarboxylase) of pea (pisum sativum) leaf mitochondria.
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Authors
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D.Macherel,
M.Lebrun,
J.Gagnon,
M.Neuburger,
R.Douce.
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Ref.
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Biochem J, 1990,
268,
783-789.
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PubMed id
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