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117E
Asym. Unit
Info
Asym.Unit (104 KB)
Biol.Unit 1 (99 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
:
15 Sep 98 (Deposition) - 23 Dec 98 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Enzyme Mechanism, Iorganic Pyrophosphatase, Mutan Structures, 2-Metal Ion Mechanism, Hydrolase
(Keyword Search:
[
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, 11)
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)
1g: MANGANESE (II) ION (MNg)
1h: MANGANESE (II) ION (MNh)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
8
Ligand/Ion
MANGANESE (II) ION
2
PO4
3
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(17, 17)
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: MN1 (AUTHOR)
13: MN2 (AUTHOR)
14: MN4 (AUTHOR)
15: MN5 (AUTHOR)
16: MN6 (AUTHOR)
17: MN8 (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:115 , GLU A:117 , ASP A:120 , ASP A:152 , MN A:2002 , PO4 A:3002 , HOH A:4002
BINDING SITE FOR RESIDUE MN A 2001
02
AC2
SOFTWARE
GLU A:117 , ASP A:120 , MN A:2001 , PO4 A:3002 , HOH A:4003 , HOH A:4004 , HOH A:4005
BINDING SITE FOR RESIDUE MN A 2002
03
AC3
SOFTWARE
PO4 A:3001 , HOH A:4006 , HOH A:4008 , HOH A:4405 , HOH A:4414
BINDING SITE FOR RESIDUE MN A 2003
04
AC4
SOFTWARE
ASP A:147 , ASP A:152 , PO4 A:3001 , PO4 A:3002 , HOH A:4009 , HOH A:4010
BINDING SITE FOR RESIDUE MN A 2004
05
AC5
SOFTWARE
ASP B:1115 , GLU B:1117 , ASP B:1120 , ASP B:1152 , MN B:2006 , MN B:2008 , PO4 B:3004 , HOH B:4012
BINDING SITE FOR RESIDUE MN B 2005
06
AC6
SOFTWARE
GLU B:1117 , ASP B:1120 , MN B:2005 , PO4 B:3004 , HOH B:4013 , HOH B:4014 , HOH B:4015
BINDING SITE FOR RESIDUE MN B 2006
07
AC7
SOFTWARE
GLU B:1058 , GLU B:1117 , PO4 B:3004 , HOH B:4016 , HOH B:4017 , HOH B:4417
BINDING SITE FOR RESIDUE MN B 2007
08
AC8
SOFTWARE
ASP B:1147 , ASP B:1152 , MN B:2005 , PO4 B:3004 , HOH B:4019 , HOH B:4020 , HOH B:4416
BINDING SITE FOR RESIDUE MN B 2008
09
AC9
SOFTWARE
LYS A:56 , ARG A:78 , ASP A:147 , TYR A:192 , LYS A:193 , MN A:2003 , MN A:2004 , PO4 A:3002 , HOH A:4006 , HOH A:4182 , HOH A:4414
BINDING SITE FOR RESIDUE PO4 A 3001
10
BC1
SOFTWARE
LYS A:56 , TYR A:93 , ASP A:115 , GLU A:117 , ASP A:120 , ASP A:152 , MN A:2001 , MN A:2002 , MN A:2004 , PO4 A:3001 , HOH A:4006 , HOH A:4010 , HOH A:4401 , HOH A:4405
BINDING SITE FOR RESIDUE PO4 A 3002
11
BC2
SOFTWARE
LYS B:1056 , TYR B:1093 , ASP B:1115 , GLU B:1117 , ASP B:1120 , ASP B:1152 , LYS B:1154 , MN B:2005 , MN B:2006 , MN B:2007 , MN B:2008 , HOH B:4017 , HOH B:4020 , HOH B:4056 , HOH B:4409 , HOH B:4416
BINDING SITE FOR RESIDUE PO4 B 3004
12
MN1
AUTHOR
GLU A:117 , ASP A:152 , ASP A:115 , ASP A:120
NULL
13
MN2
AUTHOR
GLU A:117 , TYR A:93 , ASP A:120
NULL
14
MN4
AUTHOR
ASP A:152 , ASP A:147
NULL
15
MN5
AUTHOR
GLU B:1117 , ASP B:1152 , ASP B:1115 , ASP B:1120
NULL
16
MN6
AUTHOR
GLU B:1117 , TYR B:1093 , ASP B:1120
NULL
17
MN8
AUTHOR
ASP B:1152 , ASP B:1147
NULL
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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: PPASE (A:115-121,B:1115-1121)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PPASE
PS00387
Inorganic pyrophosphatase signature.
IPYR_YEAST
116-122
2
A:115-121
B:1115-1121
[
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]
Exons
(1, 2)
Info
All Exons
Exon 1.1 (A:1-282 | B:1001-1282)
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
View:
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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
YBR011C
1
YBR011C.1
II:257973-257110
864
IPYR_YEAST
1-287
287
2
A:1-282
B:1001-1282
282
282
[
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]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d117ea_ (A:)
1b: SCOP_d117eb_ (B:)
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)
(
)
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
d117ea_
A:
1b
d117eb_
B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_117eA00 (A:1-282)
1b: CATH_117eB00 (B:1001-1282)
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Topologies
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)
(
)
Organisms
(
)
(
)
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
117eA00
A:1-282
1b
117eB00
B:1001-1282
[
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]
Pfam Domains
(0, 0)
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all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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Example Commands
Example Command
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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