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2W93
Biol. Unit 2
Info
Asym.Unit (379 KB)
Biol.Unit 1 (190 KB)
Biol.Unit 2 (189 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PYRUVATE DECARBOXYLASE VARIANT E477Q IN COMPLEX WITH THE SURROGATE PYRUVAMIDE
Authors
:
S. Kutter, M. S. Weiss, S. Konig
Date
:
21 Jan 09 (Deposition) - 03 Feb 09 (Release) - 30 Jul 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Substrate Activation, Substrate Regulation, Lyase, Nucleus, Cytoplasm, Magnesium, Acetylation, Phosphoprotein, Allosteric Enzyme, Thiamine Pyrophosphate, Phenylalanine Catabolism, Tryptophan Catabolism, Pyruvate Decarboxylase, Branched-Chain Amino Acid Catabolism, Metal-Binding, Thiohemiketal, Decarboxylase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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Reference
:
S. Konig, M. Spinka, S. Kutter
Allosteric Activation Of Pyruvate Decarboxylases. A Never-Ending Story.
J. Mol. Catal. , B Enzym. V. 61 100 2014
[
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: (1S,2S)-1-AMINO-1,2-DIHYDROXYPROPA... (PY0a)
2b: (1S,2S)-1-AMINO-1,2-DIHYDROXYPROPA... (PY0b)
2c: (1S,2S)-1-AMINO-1,2-DIHYDROXYPROPA... (PY0c)
2d: (1S,2S)-1-AMINO-1,2-DIHYDROXYPROPA... (PY0d)
2e: (1S,2S)-1-AMINO-1,2-DIHYDROXYPROPA... (PY0e)
2f: (1S,2S)-1-AMINO-1,2-DIHYDROXYPROPA... (PY0f)
2g: (1S,2S)-1-AMINO-1,2-DIHYDROXYPROPA... (PY0g)
2h: (1S,2S)-1-AMINO-1,2-DIHYDROXYPROPA... (PY0h)
3a: THIAMINE DIPHOSPHATE (TPPa)
3b: THIAMINE DIPHOSPHATE (TPPb)
3c: THIAMINE DIPHOSPHATE (TPPc)
3d: THIAMINE DIPHOSPHATE (TPPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
PY0
4
Ligand/Ion
(1S,2S)-1-AMINO-1,2-DIHYDROXYPROPAN-1-OLATE
3
TPP
2
Ligand/Ion
THIAMINE DIPHOSPHATE
[
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Sites
(8, 8)
Info
All Sites
1: AC9 (SOFTWARE)
2: BC1 (SOFTWARE)
3: BC2 (SOFTWARE)
4: BC3 (SOFTWARE)
5: BC4 (SOFTWARE)
6: BC5 (SOFTWARE)
7: BC6 (SOFTWARE)
8: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC9
SOFTWARE
THR C:390 , GLY C:413 , SER C:414 , ILE C:415 , GLY C:443 , ASP C:444 , GLY C:445 , SER C:446 , ASN C:471 , GLY C:473 , TYR C:474 , THR C:475 , ILE C:476 , GLN C:477 , MG C:601 , PY0 C:602 , HOH C:2249 , HOH C:2352 , HOH C:2353 , PRO D:26 , GLY D:27 , GLU D:51 , VAL D:76 , HIS D:115
BINDING SITE FOR RESIDUE TPP C 600
2
BC1
SOFTWARE
ASP C:444 , ASN C:471 , GLY C:473 , TPP C:600 , HOH C:2353
BINDING SITE FOR RESIDUE MG C 601
3
BC2
SOFTWARE
THR C:388 , GLN C:477 , TPP C:600 , GLY D:27 , ASP D:28 , HIS D:114 , HIS D:115
BINDING SITE FOR RESIDUE PY0 C 602
4
BC3
SOFTWARE
HIS C:92 , CYS C:221 , HIS C:225 , GLY C:286 , ALA C:287 , HIS C:310 , SER C:311
BINDING SITE FOR RESIDUE PY0 C 603
5
BC4
SOFTWARE
PRO C:26 , GLY C:27 , GLU C:51 , VAL C:76 , HIS C:115 , THR D:390 , GLY D:413 , SER D:414 , ILE D:415 , GLY D:443 , ASP D:444 , GLY D:445 , SER D:446 , ASN D:471 , GLY D:473 , TYR D:474 , THR D:475 , ILE D:476 , GLN D:477 , MG D:601 , PY0 D:602 , HOH D:2295 , HOH D:2296 , HOH D:2297
BINDING SITE FOR RESIDUE TPP D 600
6
BC5
SOFTWARE
ASP D:444 , ASN D:471 , GLY D:473 , TPP D:600 , HOH D:2296
BINDING SITE FOR RESIDUE MG D 601
7
BC6
SOFTWARE
GLY C:27 , ASP C:28 , HIS C:115 , HOH C:2069 , THR D:388 , GLN D:477 , ILE D:480 , TPP D:600
BINDING SITE FOR RESIDUE PY0 D 602
8
BC7
SOFTWARE
HIS D:92 , CYS D:221 , HIS D:225 , GLY D:286 , ALA D:287 , HIS D:310 , SER D:311 , HOH D:2298
BINDING SITE FOR RESIDUE PY0 D 603
[
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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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: TPP_ENZYMES (C:427-446,D:427-446)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TPP_ENZYMES
PS00187
Thiamine pyrophosphate enzymes signature.
PDC1_YEAST
427-446
2
-
-
C:427-446
D:427-446
[
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Exons
(0, 0)
Info
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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
(2, 12)
Info
All SCOP Domains
1a: SCOP_d2w93a2 (A:182-360)
1b: SCOP_d2w93b2 (B:182-360)
1c: SCOP_d2w93c2 (C:182-360)
1d: SCOP_d2w93d2 (D:182-360)
2a: SCOP_d2w93a1 (A:2-181)
2b: SCOP_d2w93b1 (B:2-181)
2c: SCOP_d2w93b3 (B:361-563)
2d: SCOP_d2w93c1 (C:2-181)
2e: SCOP_d2w93c3 (C:361-558)
2f: SCOP_d2w93d1 (D:2-181)
2g: SCOP_d2w93d3 (D:361-563)
2h: SCOP_d2w93a3 (A:361-559)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
DHS-like NAD/FAD-binding domain
(176)
Superfamily
:
DHS-like NAD/FAD-binding domain
(176)
Family
:
automated matches
(36)
Protein domain
:
automated matches
(36)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(3)
1a
d2w93a2
A:182-360
1b
d2w93b2
B:182-360
1c
d2w93c2
C:182-360
1d
d2w93d2
D:182-360
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
automated matches
(65)
Protein domain
:
automated matches
(65)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(3)
2a
d2w93a1
A:2-181
2b
d2w93b1
B:2-181
2c
d2w93b3
B:361-563
2d
d2w93c1
C:2-181
2e
d2w93c3
C:361-558
2f
d2w93d1
D:2-181
2g
d2w93d3
D:361-563
2h
d2w93a3
A:361-559
[
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2w93A03 (A:353-554)
1b: CATH_2w93B03 (B:353-554)
1c: CATH_2w93C03 (C:353-554)
1d: CATH_2w93D03 (D:353-554)
1e: CATH_2w93A01 (A:2-188)
1f: CATH_2w93B01 (B:2-188)
1g: CATH_2w93C01 (C:2-188)
1h: CATH_2w93D01 (D:2-188)
2a: CATH_2w93B02 (B:189-352)
2b: CATH_2w93C02 (C:189-352)
2c: CATH_2w93D02 (D:189-352)
2d: CATH_2w93A02 (A:189-352)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Baker's yeast (Saccharomyces cerevisiae)
(17)
1a
2w93A03
A:353-554
1b
2w93B03
B:353-554
1c
2w93C03
C:353-554
1d
2w93D03
D:353-554
1e
2w93A01
A:2-188
1f
2w93B01
B:2-188
1g
2w93C01
C:2-188
1h
2w93D01
D:2-188
Homologous Superfamily
:
TPP-binding domain
(120)
Baker's yeast (Saccharomyces cerevisiae)
(20)
2a
2w93B02
B:189-352
2b
2w93C02
C:189-352
2c
2w93D02
D:189-352
2d
2w93A02
A:189-352
[
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Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_2w93D01 (D:201-339)
1b: PFAM_TPP_enzyme_M_2w93D02 (D:201-339)
1c: PFAM_TPP_enzyme_M_2w93D03 (D:201-339)
1d: PFAM_TPP_enzyme_M_2w93D04 (D:201-339)
2a: PFAM_TPP_enzyme_C_2w93D05 (D:387-526)
2b: PFAM_TPP_enzyme_C_2w93D06 (D:387-526)
2c: PFAM_TPP_enzyme_C_2w93D07 (D:387-526)
2d: PFAM_TPP_enzyme_C_2w93D08 (D:387-526)
3a: PFAM_TPP_enzyme_N_2w93D09 (D:4-180)
3b: PFAM_TPP_enzyme_N_2w93D10 (D:4-180)
3c: PFAM_TPP_enzyme_N_2w93D11 (D:4-180)
3d: PFAM_TPP_enzyme_N_2w93D12 (D:4-180)
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Clans
(
)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD_DHS
(82)
Family
:
TPP_enzyme_M
(50)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(12)
1a
TPP_enzyme_M-2w93D01
D:201-339
1b
TPP_enzyme_M-2w93D02
D:201-339
1c
TPP_enzyme_M-2w93D03
D:201-339
1d
TPP_enzyme_M-2w93D04
D:201-339
Clan
:
THDP-binding
(106)
Family
:
TPP_enzyme_C
(54)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(12)
2a
TPP_enzyme_C-2w93D05
D:387-526
2b
TPP_enzyme_C-2w93D06
D:387-526
2c
TPP_enzyme_C-2w93D07
D:387-526
2d
TPP_enzyme_C-2w93D08
D:387-526
Family
:
TPP_enzyme_N
(54)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(12)
3a
TPP_enzyme_N-2w93D09
D:4-180
3b
TPP_enzyme_N-2w93D10
D:4-180
3c
TPP_enzyme_N-2w93D11
D:4-180
3d
TPP_enzyme_N-2w93D12
D:4-180
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Asymmetric Unit 1
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