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8PRK
Asym. Unit
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Asym.Unit (102 KB)
Biol.Unit 1 (97 KB)
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(1)
Title
:
THE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISIAE SOLUBLE INORGANIC PYROPHOSPHATASE: STRUCTURAL STUDIES AND MECHANISTIC IMPLICATIONS
Authors
:
V. Tuominen, P. Heikinheimo, T. Kajander, T. Torkkel, T. Hyytia, J. Kapyla, R. Lahti, B. S. Cooperman, A. Goldman
Date
:
16 Sep 98 (Deposition) - 23 Dec 98 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Enzyme Mechanism, Iorganic Pyrophosphatase, Mutant Structures, 2-Metal Ion Mechanism, Hydrolase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Tuominen, P. Heikinheimo, T. Kajander, T. Torkkel, T. Hyytia, J. Kapyla, R. Lahti, B. S. Cooperman, A. Goldman
The R78K And D117E Active-Site Variants Of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies And Mechanistic Implications.
J. Mol. Biol. V. 284 1565 1998
(for further references see the
PDB file header
)
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
1e: MANGANESE (II) ION (MNe)
1f: MANGANESE (II) ION (MNf)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
View:
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No.
Name
Count
Type
Full Name
1
MN
6
Ligand/Ion
MANGANESE (II) ION
2
PO4
2
Ligand/Ion
PHOSPHATE ION
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Sites
(11, 11)
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: MN1 (AUTHOR)
10: MN2 (AUTHOR)
11: MN4 (AUTHOR)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP B:1115 , ASP B:1120 , ASP B:1152 , MN B:2008 , PO4 B:3004 , HOH B:4008
BINDING SITE FOR RESIDUE MN B 2005
02
AC2
SOFTWARE
ASP A:147 , ASP A:152 , PO4 A:3002
BINDING SITE FOR RESIDUE MN A 2004
03
AC3
SOFTWARE
ASP B:1147 , ASP B:1152 , MN B:2005 , PO4 B:3004 , HOH B:4012
BINDING SITE FOR RESIDUE MN B 2008
04
AC4
SOFTWARE
ASP B:1120 , PO4 B:3004 , HOH B:4009 , HOH B:4010 , HOH B:4011
BINDING SITE FOR RESIDUE MN B 2006
05
AC5
SOFTWARE
ASP A:120 , PO4 A:3002 , HOH A:4002 , HOH A:4003 , HOH A:4004
BINDING SITE FOR RESIDUE MN A 2002
06
AC6
SOFTWARE
ASP A:115 , ASP A:120 , ASP A:152 , PO4 A:3002 , HOH A:4001
BINDING SITE FOR RESIDUE MN A 2001
07
AC7
SOFTWARE
LYS A:56 , TYR A:93 , ASP A:115 , ASP A:117 , ASP A:120 , ASP A:152 , LYS A:154 , MN A:2001 , MN A:2002 , MN A:2004 , HOH A:4021 , HOH A:4262
BINDING SITE FOR RESIDUE PO4 A 3002
08
AC8
SOFTWARE
LYS B:1056 , TYR B:1093 , ASP B:1115 , ASP B:1117 , ASP B:1120 , ASP B:1152 , LYS B:1154 , MN B:2005 , MN B:2006 , MN B:2008 , HOH B:4012 , HOH B:4202
BINDING SITE FOR RESIDUE PO4 B 3004
09
MN1
AUTHOR
ASP A:117 , ASP A:152 , ASP A:115 , ASP A:120
METAL 1 BINDING SITE
10
MN2
AUTHOR
ASP A:117 , TYR A:93 , ASP A:120
METAL 2 BINDING SITE
11
MN4
AUTHOR
ASP A:152 , ASP A:147
METAL 4 BINDING SITE
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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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.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d8prka_ (A:)
1b: SCOP_d8prkb_ (B:)
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Protein Domains
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Organisms
(
)
(
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Class
:
All beta proteins
(24004)
Fold
:
OB-fold
(1179)
Superfamily
:
Inorganic pyrophosphatase
(69)
Family
:
Inorganic pyrophosphatase
(56)
Protein domain
:
Inorganic pyrophosphatase
(41)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(19)
1a
d8prka_
A:
1b
d8prkb_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_8prkA00 (A:1-282)
1b: CATH_8prkB00 (B:1001-1282)
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Organisms
(
)
(
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Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Inorganic Pyrophosphatase
(59)
Homologous Superfamily
:
Inorganic Pyrophosphatase
(59)
Baker's yeast (Saccharomyces cerevisiae)
(17)
1a
8prkA00
A:1-282
1b
8prkB00
B:1001-1282
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Asym.Unit (102 KB)
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