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Biol. Unit 2
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Asym.Unit (385 KB)
Biol.Unit 1 (193 KB)
Biol.Unit 2 (192 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PYRUVATE DECARBOXYLASE VARIANT D28A IN COMPLEX WITH ITS SUBSTRATE
Authors
:
S. Kutter, M. Weik, M. S. Weiss, S. Konig
Date
:
16 Dec 07 (Deposition) - 27 Jan 09 (Release) - 05 May 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.71
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
(2, 6)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: PYRUVIC ACID (PYRa)
2b: PYRUVIC ACID (PYRb)
2c: PYRUVIC ACID (PYRc)
2d: PYRUVIC ACID (PYRd)
2e: PYRUVIC ACID (PYRe)
2f: PYRUVIC ACID (PYRf)
2g: PYRUVIC ACID (PYRg)
2h: PYRUVIC ACID (PYRh)
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
PYR
4
Ligand/Ion
PYRUVIC ACID
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
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 , GLU C:477 , MG C:601 , PYR C:602 , HOH C:2287 , HOH C:2407 , HOH C:2408 , 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:2407
BINDING SITE FOR RESIDUE MG C 601
3
BC2
SOFTWARE
GLU C:477 , TPP C:600 , GLY D:27 , ALA D:28 , HIS D:114 , HIS D:115
BINDING SITE FOR RESIDUE PYR 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 , HOH C:2218
BINDING SITE FOR RESIDUE PYR C 603
5
BC4
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 , GLU D:477 , MG D:601 , PYR D:602 , HOH D:2335 , HOH D:2336 , HOH D:2337
BINDING SITE FOR RESIDUE TPP D 600
6
BC5
SOFTWARE
ASP D:444 , ASN D:471 , GLY D:473 , TPP D:600 , HOH D:2336
BINDING SITE FOR RESIDUE MG D 601
7
BC6
SOFTWARE
GLY C:27 , ALA C:28 , HIS C:114 , HIS C:115 , GLU D:477 , TPP D:600
BINDING SITE FOR RESIDUE PYR D 602
8
BC7
SOFTWARE
HIS D:92 , CYS D:221 , GLY D:286 , ALA D:287 , HIS D:310 , SER D:311
BINDING SITE FOR RESIDUE PYR D 603
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: TPP_ENZYMES (C:427-446,D:427-446)
;
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
2
-
-
C:427-446
D:427-446
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d2vk1a2 (A:182-360)
1b: SCOP_d2vk1c2 (C:182-360)
1c: SCOP_d2vk1d2 (D:182-360)
1d: SCOP_d2vk1b2 (B:182-360)
2a: SCOP_d2vk1a1 (A:2-181)
2b: SCOP_d2vk1a3 (A:361-563)
2c: SCOP_d2vk1b1 (B:2-181)
2d: SCOP_d2vk1b3 (B:361-563)
2e: SCOP_d2vk1c1 (C:2-181)
2f: SCOP_d2vk1c3 (C:361-563)
2g: SCOP_d2vk1d1 (D:2-181)
2h: SCOP_d2vk1d3 (D:361-563)
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)
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)
(
)
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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
d2vk1a2
A:182-360
1b
d2vk1c2
C:182-360
1c
d2vk1d2
D:182-360
1d
d2vk1b2
B: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
d2vk1a1
A:2-181
2b
d2vk1a3
A:361-563
2c
d2vk1b1
B:2-181
2d
d2vk1b3
B:361-563
2e
d2vk1c1
C:2-181
2f
d2vk1c3
C:361-563
2g
d2vk1d1
D:2-181
2h
d2vk1d3
D:361-563
[
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2vk1A03 (A:353-554)
1b: CATH_2vk1B03 (B:353-554)
1c: CATH_2vk1C03 (C:353-554)
1d: CATH_2vk1D03 (D:353-554)
1e: CATH_2vk1A01 (A:2-188)
1f: CATH_2vk1B01 (B:2-188)
1g: CATH_2vk1C01 (C:2-188)
1h: CATH_2vk1D01 (D:2-188)
2a: CATH_2vk1A02 (A:189-352)
2b: CATH_2vk1B02 (B:189-352)
2c: CATH_2vk1C02 (C:189-352)
2d: CATH_2vk1D02 (D:189-352)
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Topologies
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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)
Yeast (Saccharomyces cerevisiae)
(1)
1a
2vk1A03
A:353-554
1b
2vk1B03
B:353-554
1c
2vk1C03
C:353-554
1d
2vk1D03
D:353-554
1e
2vk1A01
A:2-188
1f
2vk1B01
B:2-188
1g
2vk1C01
C:2-188
1h
2vk1D01
D:2-188
Homologous Superfamily
:
TPP-binding domain
(120)
Yeast (Saccharomyces cerevisiae)
(1)
2a
2vk1A02
A:189-352
2b
2vk1B02
B:189-352
2c
2vk1C02
C:189-352
2d
2vk1D02
D:189-352
[
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Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_2vk1D01 (D:201-339)
1b: PFAM_TPP_enzyme_M_2vk1D02 (D:201-339)
1c: PFAM_TPP_enzyme_M_2vk1D03 (D:201-339)
1d: PFAM_TPP_enzyme_M_2vk1D04 (D:201-339)
2a: PFAM_TPP_enzyme_C_2vk1D05 (D:387-526)
2b: PFAM_TPP_enzyme_C_2vk1D06 (D:387-526)
2c: PFAM_TPP_enzyme_C_2vk1D07 (D:387-526)
2d: PFAM_TPP_enzyme_C_2vk1D08 (D:387-526)
3a: PFAM_TPP_enzyme_N_2vk1D09 (D:4-180)
3b: PFAM_TPP_enzyme_N_2vk1D10 (D:4-180)
3c: PFAM_TPP_enzyme_N_2vk1D11 (D:4-180)
3d: PFAM_TPP_enzyme_N_2vk1D12 (D:4-180)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD_DHS
(82)
Family
:
TPP_enzyme_M
(50)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(12)
1a
TPP_enzyme_M-2vk1D01
D:201-339
1b
TPP_enzyme_M-2vk1D02
D:201-339
1c
TPP_enzyme_M-2vk1D03
D:201-339
1d
TPP_enzyme_M-2vk1D04
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-2vk1D05
D:387-526
2b
TPP_enzyme_C-2vk1D06
D:387-526
2c
TPP_enzyme_C-2vk1D07
D:387-526
2d
TPP_enzyme_C-2vk1D08
D:387-526
Family
:
TPP_enzyme_N
(54)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(12)
3a
TPP_enzyme_N-2vk1D09
D:4-180
3b
TPP_enzyme_N-2vk1D10
D:4-180
3c
TPP_enzyme_N-2vk1D11
D:4-180
3d
TPP_enzyme_N-2vk1D12
D:4-180
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Asymmetric Unit 1
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