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Asym. Unit
Info
Asym.Unit (388 KB)
Biol.Unit 1 (194 KB)
Biol.Unit 2 (194 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PYRUVATE DECARBOXYLASE VARIANT E477Q IN COMPLEX WITH ITS SUBSTRATE
Authors
:
S. Kutter, M. Weik, M. S. Weiss, S. Konig
Date
:
17 Dec 07 (Deposition) - 27 Jan 09 (Release) - 11 Sep 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.42
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Asymmetric Active Sites, Phenylalanine Catabolism, Tryptophan Catabolism, Thiamine Pyrophosphate, Dimer Of Dimers, Phosphorylation, Allosteric Enzyme, Tdp, Tpp, Lyase, Nucleus, Pyruvate, Cytoplasm, Branched-Chain Amino Acid Catabolism, Substrate Activation, Thiamine Diphosphate, Magnesium, Acetylation, Metal-Binding, Decarboxylase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Kutter, M. S. Weiss, G. Wille, R. Golbik, M. Spinka, S. Konig
Covalently Bound Substrate At The Regulatory Site Of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation.
J. Biol. Chem. V. 284 12136 2009
[
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: (2S)-2-HYDROXYPROPANOIC ACID (2OPa)
1b: (2S)-2-HYDROXYPROPANOIC ACID (2OPb)
1c: (2S)-2-HYDROXYPROPANOIC ACID (2OPc)
1d: (2S)-2-HYDROXYPROPANOIC ACID (2OPd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
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
2OP
4
Ligand/Ion
(2S)-2-HYDROXYPROPANOIC ACID
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
TPP
4
Ligand/Ion
THIAMINE DIPHOSPHATE
[
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]
Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:389 , THR A:390 , GLY A:413 , SER A:414 , ILE A:415 , GLY A:443 , ASP A:444 , GLY A:445 , SER A:446 , ASN A:471 , GLY A:473 , TYR A:474 , THR A:475 , ILE A:476 , GLN A:477 , MG A:1565 , HOH A:2295 , HOH A:2421 , HOH A:2422 , HOH A:2423 , PRO B:26 , GLY B:27 , GLU B:51 , VAL B:76 , HIS B:115
BINDING SITE FOR RESIDUE TPP A1564
02
AC2
SOFTWARE
ASP A:444 , ASN A:471 , GLY A:473 , TPP A:1564 , HOH A:2421
BINDING SITE FOR RESIDUE MG A1565
03
AC3
SOFTWARE
HIS A:92 , CYS A:221 , GLY A:286 , ALA A:287 , HIS A:310 , SER A:311
BINDING SITE FOR RESIDUE 2OP A1566
04
AC4
SOFTWARE
PRO A:26 , GLY A:27 , GLU A:51 , VAL A:76 , HIS A:115 , GLY B:389 , THR B:390 , GLY B:413 , SER B:414 , ILE B:415 , GLY B:443 , ASP B:444 , GLY B:445 , SER B:446 , ASN B:471 , GLY B:473 , TYR B:474 , THR B:475 , ILE B:476 , GLN B:477 , MG B:1565 , HOH B:2375 , HOH B:2376 , HOH B:2421 , HOH B:2533
BINDING SITE FOR RESIDUE TPP B1564
05
AC5
SOFTWARE
ASP B:444 , ASN B:471 , GLY B:473 , TPP B:1564 , HOH B:2421
BINDING SITE FOR RESIDUE MG B1565
06
AC6
SOFTWARE
HIS B:92 , CYS B:221 , HIS B:225 , GLY B:286 , ALA B:287 , HIS B:310 , SER B:311 , HOH B:2288
BINDING SITE FOR RESIDUE 2OP B1566
07
AC7
SOFTWARE
GLY C:389 , 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:1565 , HOH C:2289 , HOH C:2325 , HOH C:2432 , HOH C:2433 , PRO D:26 , GLY D:27 , GLU D:51 , VAL D:76 , HIS D:115
BINDING SITE FOR RESIDUE TPP C1564
08
AC8
SOFTWARE
ASP C:444 , ASN C:471 , GLY C:473 , TPP C:1564 , HOH C:2325
BINDING SITE FOR RESIDUE MG C1565
09
AC9
SOFTWARE
CYS C:221 , GLY C:286 , ALA C:287 , HIS C:310 , SER C:311
BINDING SITE FOR RESIDUE 2OP C1566
10
BC1
SOFTWARE
PRO C:26 , GLY C:27 , GLU C:51 , VAL C:76 , HIS C:115 , GLY D:389 , 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:1565 , HOH D:2296 , HOH D:2427 , HOH D:2428 , HOH D:2429
BINDING SITE FOR RESIDUE TPP D1564
11
BC2
SOFTWARE
ASP D:444 , ASN D:471 , GLY D:473 , TPP D:1564 , HOH D:2428
BINDING SITE FOR RESIDUE MG D1565
12
BC3
SOFTWARE
HIS D:92 , CYS D:221 , HIS D:225 , GLY D:286 , ALA D:287 , HIS D:310 , SER D:311 , HOH D:2225
BINDING SITE FOR RESIDUE 2OP D1566
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: TPP_ENZYMES (A:427-446,B:427-446,C:427-446,D:42...)
;
View:
Select:
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
4
A:427-446
B:427-446
C:427-446
D:427-446
[
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Exons
(1, 4)
Info
All Exons
Exon 1.1 (A:2-563 | B:2-563 | C:2-563 | D:2-...)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
YLR044C
1
YLR044C.1
XII:234082-232391
1692
PDC1_YEAST
1-563
563
4
A:2-563
B:2-563
C:2-563
D:2-563
562
562
562
562
[
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SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d2vk8a2 (A:182-360)
1b: SCOP_d2vk8b2 (B:182-360)
1c: SCOP_d2vk8c2 (C:182-360)
1d: SCOP_d2vk8d2 (D:182-360)
2a: SCOP_d2vk8a1 (A:2-181)
2b: SCOP_d2vk8a3 (A:361-563)
2c: SCOP_d2vk8b1 (B:2-181)
2d: SCOP_d2vk8b3 (B:361-563)
2e: SCOP_d2vk8c1 (C:2-181)
2f: SCOP_d2vk8c3 (C:361-563)
2g: SCOP_d2vk8d1 (D:2-181)
2h: SCOP_d2vk8d3 (D:361-563)
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)
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)
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)
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)
(
)
Families
(
)
(
)
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
d2vk8a2
A:182-360
1b
d2vk8b2
B:182-360
1c
d2vk8c2
C:182-360
1d
d2vk8d2
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
d2vk8a1
A:2-181
2b
d2vk8a3
A:361-563
2c
d2vk8b1
B:2-181
2d
d2vk8b3
B:361-563
2e
d2vk8c1
C:2-181
2f
d2vk8c3
C:361-563
2g
d2vk8d1
D:2-181
2h
d2vk8d3
D:361-563
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2vk8A03 (A:353-554)
1b: CATH_2vk8B03 (B:353-554)
1c: CATH_2vk8C03 (C:353-554)
1d: CATH_2vk8D03 (D:353-554)
1e: CATH_2vk8A01 (A:2-188)
1f: CATH_2vk8B01 (B:2-188)
1g: CATH_2vk8C01 (C:2-188)
1h: CATH_2vk8D01 (D:2-188)
2a: CATH_2vk8A02 (A:189-352)
2b: CATH_2vk8B02 (B:189-352)
2c: CATH_2vk8C02 (C:189-352)
2d: CATH_2vk8D02 (D:189-352)
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)
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)
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)
Topologies
(
)
(
)
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
2vk8A03
A:353-554
1b
2vk8B03
B:353-554
1c
2vk8C03
C:353-554
1d
2vk8D03
D:353-554
1e
2vk8A01
A:2-188
1f
2vk8B01
B:2-188
1g
2vk8C01
C:2-188
1h
2vk8D01
D:2-188
Homologous Superfamily
:
TPP-binding domain
(120)
Baker's yeast (Saccharomyces cerevisiae)
(20)
2a
2vk8A02
A:189-352
2b
2vk8B02
B:189-352
2c
2vk8C02
C:189-352
2d
2vk8D02
D:189-352
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_2vk8D01 (D:201-339)
1b: PFAM_TPP_enzyme_M_2vk8D02 (D:201-339)
1c: PFAM_TPP_enzyme_M_2vk8D03 (D:201-339)
1d: PFAM_TPP_enzyme_M_2vk8D04 (D:201-339)
2a: PFAM_TPP_enzyme_C_2vk8D05 (D:387-526)
2b: PFAM_TPP_enzyme_C_2vk8D06 (D:387-526)
2c: PFAM_TPP_enzyme_C_2vk8D07 (D:387-526)
2d: PFAM_TPP_enzyme_C_2vk8D08 (D:387-526)
3a: PFAM_TPP_enzyme_N_2vk8D09 (D:4-180)
3b: PFAM_TPP_enzyme_N_2vk8D10 (D:4-180)
3c: PFAM_TPP_enzyme_N_2vk8D11 (D:4-180)
3d: PFAM_TPP_enzyme_N_2vk8D12 (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-2vk8D01
D:201-339
1b
TPP_enzyme_M-2vk8D02
D:201-339
1c
TPP_enzyme_M-2vk8D03
D:201-339
1d
TPP_enzyme_M-2vk8D04
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-2vk8D05
D:387-526
2b
TPP_enzyme_C-2vk8D06
D:387-526
2c
TPP_enzyme_C-2vk8D07
D:387-526
2d
TPP_enzyme_C-2vk8D08
D:387-526
Family
:
TPP_enzyme_N
(54)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(12)
3a
TPP_enzyme_N-2vk8D09
D:4-180
3b
TPP_enzyme_N-2vk8D10
D:4-180
3c
TPP_enzyme_N-2vk8D11
D:4-180
3d
TPP_enzyme_N-2vk8D12
D:4-180
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Asym.Unit (388 KB)
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