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1YGY
Biol. Unit 1
Info
Asym.Unit (170 KB)
Biol.Unit 1 (323 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF D-3-PHOSPHOGLYCERATE DEHYDROGENASE FROM MYCOBACTERIUM TUBERCULOSIS
Authors
:
S. Dey, G. A. Grant, J. C. Sacchettini, Tb Structural Genomics Conso (Tbsgc)
Date
:
05 Jan 05 (Deposition) - 25 Jan 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Oxidoreductase, Phosphoglycerate Dehydrogenase, Serine Biosynthesis, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Dey, G. A. Grant, J. C. Sacchettini
Crystal Structure Of Mycobacterium Tuberculosis D-3-Phosphoglycerate Dehydrogenase: Extreme Asymmetry In A Tetramer Of Identical Subunits
J. Biol. Chem. V. 280 14892 2005
(for further references see the
PDB file header
)
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Hetero Components
(1, 6)
Info
All Hetero Components
1a: D(-)-TARTARIC ACID (TARa)
1b: D(-)-TARTARIC ACID (TARb)
1c: D(-)-TARTARIC ACID (TARc)
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Label:
No.
Name
Count
Type
Full Name
1
TAR
6
Ligand/Ion
D(-)-TARTARIC ACID
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:446 , HIS A:447 , LYS B:439 , ASP B:449 , LEU B:450 , ARG B:451 , ARG B:501
BINDING SITE FOR RESIDUE TAR A 600
2
AC2
SOFTWARE
LYS A:439 , ASP A:449 , LEU A:450 , ARG A:451 , ARG A:501 , ARG B:446 , HIS B:447 , SER B:488 , GLU B:489
BINDING SITE FOR RESIDUE TAR B 1600
3
AC3
SOFTWARE
GLU B:361 , VAL B:362 , GLU B:363 , LYS B:402
BINDING SITE FOR RESIDUE TAR B 2600
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(4, 32)
Info
All PROSITE Patterns/Profiles
1: D_2_HYDROXYACID_DH_1 (A:145-172,B:145-172)
2: D_2_HYDROXYACID_DH_2 (A:193-215,B:193-215)
3: D_2_HYDROXYACID_DH_3 (A:222-238,B:222-238)
4: ACT (A:456-528,B:456-528)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
D_2_HYDROXYACID_DH_1
PS00065
D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.
SERA_MYCTO
144-171
4
A:145-172
B:145-172
SERA_MYCTU
144-171
4
A:145-172
B:145-172
2
D_2_HYDROXYACID_DH_2
PS00670
D-isomer specific 2-hydroxyacid dehydrogenases signature 2.
SERA_MYCTO
192-214
4
A:193-215
B:193-215
SERA_MYCTU
192-214
4
A:193-215
B:193-215
3
D_2_HYDROXYACID_DH_3
PS00671
D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
SERA_MYCTO
221-237
4
A:222-238
B:222-238
SERA_MYCTU
221-237
4
A:222-238
B:222-238
4
ACT
PS51671
ACT domain profile.
SERA_MYCTO
455-527
4
A:456-528
B:456-528
SERA_MYCTU
455-527
4
A:456-528
B:456-528
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1ygya3 (A:452-529)
1b: SCOP_d1ygyb3 (B:452-529)
2a: SCOP_d1ygya4 (A:317-451)
2b: SCOP_d1ygyb4 (B:317-451)
3a: SCOP_d1ygya2 (A:3-98,A:283-316)
3b: SCOP_d1ygyb2 (B:3-98,B:283-316)
4a: SCOP_d1ygya1 (A:99-282)
4b: SCOP_d1ygyb1 (B:99-282)
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)
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)
(
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
ACT-like
(63)
Family
:
Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
(9)
Protein domain
:
Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
(9)
Mycobacterium tuberculosis [TaxId: 1773]
(2)
1a
d1ygya3
A:452-529
1b
d1ygyb3
B:452-529
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Serine metabolism enzymes domain
(5)
Family
:
SerA intervening domain-like
(2)
Protein domain
:
D-3-phosphoglycerate dehydrogenase SerA
(2)
Mycobacterium tuberculosis [TaxId: 1773]
(2)
2a
d1ygya4
A:317-451
2b
d1ygyb4
B:317-451
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Formate/glycerate dehydrogenase catalytic domain-like
(49)
Family
:
Formate/glycerate dehydrogenases, substrate-binding domain
(21)
Protein domain
:
Phosphoglycerate dehydrogenase
(9)
Mycobacterium tuberculosis [TaxId: 1773]
(2)
3a
d1ygya2
A:3-98,A:283-316
3b
d1ygyb2
B:3-98,B:283-316
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Formate/glycerate dehydrogenases, NAD-domain
(49)
Protein domain
:
Phosphoglycerate dehydrogenase
(9)
Mycobacterium tuberculosis [TaxId: 1773]
(2)
4a
d1ygya1
A:99-282
4b
d1ygyb1
B:99-282
[
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1ygyB03 (B:316-454)
1b: CATH_1ygyA03 (A:321-453)
2a: CATH_1ygyA02 (A:99-280)
2b: CATH_1ygyB02 (B:100-280)
2c: CATH_1ygyA01 (A:3-98,A:281-320)
2d: CATH_1ygyB01 (B:3-99,B:281-315)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
60s Ribosomal Protein L30; Chain: A;
(235)
Homologous Superfamily
:
D-3-phosphoglycerate dehydrogenase; domain 3
(5)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(1)
1a
1ygyB03
B:316-454
1b
1ygyA03
A:321-453
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(22)
2a
1ygyA02
A:99-280
2b
1ygyB02
B:100-280
2c
1ygyA01
A:3-98,A:281-320
2d
1ygyB01
B:3-99,B:281-315
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_ACT_1ygyB01 (B:455-519)
1b: PFAM_ACT_1ygyB02 (B:455-519)
2a: PFAM_2_Hacid_dh_1ygyB03 (B:7-314)
2b: PFAM_2_Hacid_dh_1ygyB04 (B:7-314)
3a: PFAM_2_Hacid_dh_C_1ygyB05 (B:108-282)
3b: PFAM_2_Hacid_dh_C_1ygyB06 (B:108-282)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ACT
(34)
Family
:
ACT
(19)
Mycobacterium tuberculosis
(1)
1a
ACT-1ygyB01
B:455-519
1b
ACT-1ygyB02
B:455-519
Clan
:
Form_Glyc_dh
(56)
Family
:
2-Hacid_dh
(21)
Mycobacterium tuberculosis
(1)
2a
2-Hacid_dh-1ygyB03
B:7-314
2b
2-Hacid_dh-1ygyB04
B:7-314
Clan
:
NADP_Rossmann
(1239)
Family
:
2-Hacid_dh_C
(23)
Mycobacterium tuberculosis
(1)
3a
2-Hacid_dh_C-1ygyB05
B:108-282
3b
2-Hacid_dh_C-1ygyB06
B:108-282
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