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1WYU
Asym. Unit
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Asym.Unit (609 KB)
Biol.Unit 1 (305 KB)
Biol.Unit 2 (307 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GLYCINE DECARBOXYLASE (P-PROTEIN) OF THE GLYCINE CLEAVAGE SYSTEM, IN HOLO FORM
Authors
:
T. Nakai, N. Nakagawa, N. Maoka, R. Masui, S. Kuramitsu, N. Kamiya, Rike Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
17 Feb 05 (Deposition) - 05 Apr 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Alpha(2)Beta(2) Tetramer, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxidoreductase
(Keyword Search:
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Reference
:
T. Nakai, N. Nakagawa, N. Maoka, R. Masui, S. Kuramitsu, N. Kamiya
Structure Of P-Protein Of The Glycine Cleavage System: Implications For Nonketotic Hyperglycinemia
Embo J. V. 24 1523 2005
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
1b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
1c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
1d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
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No.
Name
Count
Type
Full Name
1
PLP
4
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:320 , THR A:321 , HOH A:459 , SER B:73 , ALA B:131 , GLY B:132 , ALA B:133 , GLU B:136 , HIS B:166 , SER B:168 , ASP B:239 , ALA B:241 , ASN B:263 , HIS B:265 , LYS B:266 , HOH B:631
BINDING SITE FOR RESIDUE PLP B 475
2
AC2
SOFTWARE
THR C:320 , THR C:321 , HOH C:454 , SER D:73 , ALA D:131 , GLY D:132 , ALA D:133 , GLU D:136 , HIS D:166 , SER D:168 , ASP D:239 , ALA D:241 , ASN D:263 , HIS D:265 , LYS D:266
BINDING SITE FOR RESIDUE PLP D 475
3
AC3
SOFTWARE
THR E:320 , THR E:321 , HOH E:440 , SER F:73 , ALA F:131 , GLY F:132 , ALA F:133 , GLU F:136 , HIS F:166 , SER F:168 , ASP F:239 , ALA F:241 , ASN F:263 , HIS F:265 , LYS F:266 , HOH F:746
BINDING SITE FOR RESIDUE PLP F 475
4
AC4
SOFTWARE
THR G:320 , THR G:321 , SER H:73 , ALA H:131 , GLY H:132 , ALA H:133 , GLU H:136 , HIS H:166 , SER H:168 , ASP H:239 , ALA H:241 , ASN H:263 , HIS H:265 , LYS H:266 , HOH H:482 , HOH H:632
BINDING SITE FOR RESIDUE PLP H 475
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SAPs(SNPs)/Variants
(0, 0)
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PROSITE Patterns/Profiles
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1wyua_ (A:)
1b: SCOP_d1wyuc_ (C:)
1c: SCOP_d1wyue_ (E:)
1d: SCOP_d1wyug_ (G:)
2a: SCOP_d1wyub_ (B:)
2b: SCOP_d1wyud_ (D:)
2c: SCOP_d1wyuf_ (F:)
2d: SCOP_d1wyuh_ (H:)
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Protein Domains
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Organisms
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(
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
Glycine dehydrogenase subunits (GDC-P)
(6)
Protein domain
:
Glycine dehydrogenase (decarboxylating) subunit 1
(3)
Thermus thermophilus [TaxId: 274]
(3)
1a
d1wyua_
A:
1b
d1wyuc_
C:
1c
d1wyue_
E:
1d
d1wyug_
G:
Protein domain
:
Glycine dehydrogenase subunit 2 (P-protein)
(3)
Thermus thermophilus [TaxId: 274]
(3)
2a
d1wyub_
B:
2b
d1wyud_
D:
2c
d1wyuf_
F:
2d
d1wyuh_
H:
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CATH Domains
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_GDC_P_1wyuH01 (H:18-433)
1b: PFAM_GDC_P_1wyuH02 (H:18-433)
1c: PFAM_GDC_P_1wyuH03 (H:18-433)
1d: PFAM_GDC_P_1wyuH04 (H:18-433)
1e: PFAM_GDC_P_1wyuG01 (G:1-433)
1f: PFAM_GDC_P_1wyuG02 (G:1-433)
1g: PFAM_GDC_P_1wyuG03 (G:1-433)
1h: PFAM_GDC_P_1wyuG04 (G:1-433)
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Clan
:
PLP_aminotran
(240)
Family
:
GDC-P
(3)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(3)
1a
GDC-P-1wyuH01
H:18-433
1b
GDC-P-1wyuH02
H:18-433
1c
GDC-P-1wyuH03
H:18-433
1d
GDC-P-1wyuH04
H:18-433
1e
GDC-P-1wyuG01
G:1-433
1f
GDC-P-1wyuG02
G:1-433
1g
GDC-P-1wyuG03
G:1-433
1h
GDC-P-1wyuG04
G:1-433
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