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1LY8
Asym. Unit
Info
Asym.Unit (126 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (62 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF A MUTANT ENZYME OF COPRINUS CINEREUS PEROXIDASE PROVIDES AN UNDERSTANDING OF ITS INCREASED THERMOSTABILITY AND INSIGHT INTO MODELLING OF PROTEIN STRUCTURES
Authors
:
K. Houborg, P. Harris, J. -C. N. Poulsen, A. Svendsen, P. Schneider, S. L
Date
:
07 Jun 02 (Deposition) - 14 Jun 02 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Peroxidase, Mutant, Thermostability, Coprinus Cinereus, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Houborg, P. Harris, J. C. Poulsen, P. Schneider, A. Svendsen, S. Larsen
The Structure Of A Mutant Enzyme Of Coprinus Cinereus Peroxidase Provides An Understanding Of Its Increased Thermostability.
Acta Crystallogr. , Sect. D V. 59 997 2003
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Hetero Components
(6, 24)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
4a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
4b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
CA
4
Ligand/Ion
CALCIUM ION
3
GOL
12
Ligand/Ion
GLYCEROL
4
HEM
2
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
5
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(24, 24)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:81 , GLY A:110 , PHE A:113 , SER A:141 , ASN A:142 , SER A:143 , HOH A:9073 , HOH A:9223 , HOH A:9224 , HOH A:9331 , HOH A:9332
BINDING SITE FOR RESIDUE NAG A 500
02
AC2
SOFTWARE
THR A:313 , THR A:331 , SER A:333 , GLY A:334
BINDING SITE FOR RESIDUE BMA A 600
03
AC3
SOFTWARE
GLY A:238 , SER A:338 , LEU A:339 , ALA A:340 , HOH A:9024 , HOH A:9061 , HOH A:9133 , HOH A:9219 , HOH A:9242 , HOH A:9305
BINDING SITE FOR RESIDUE MAN A 700
04
AC4
SOFTWARE
ALA B:81 , ILE B:107 , GLY B:110 , PHE B:113 , ASN B:142 , HOH B:9062 , HOH B:9118 , HOH B:9221
BINDING SITE FOR RESIDUE NAG B 500
05
AC5
SOFTWARE
THR B:313 , THR B:331
BINDING SITE FOR RESIDUE BMA B 600
06
AC6
SOFTWARE
GLY B:238 , SER B:338 , LEU B:339 , GOL B:803 , HOH B:9042 , HOH B:9074
BINDING SITE FOR RESIDUE MAN B 700
07
AC7
SOFTWARE
ASP A:56 , GLY A:74 , ASP A:76 , SER A:78 , HOH A:9029 , HOH A:9218
BINDING SITE FOR RESIDUE CA A 9001
08
AC8
SOFTWARE
ASP B:56 , GLY B:74 , ASP B:76 , SER B:78 , HOH B:9017 , HOH B:9196
BINDING SITE FOR RESIDUE CA B 9002
09
AC9
SOFTWARE
SER B:184 , ASP B:201 , THR B:203 , VAL B:206 , ASP B:208
BINDING SITE FOR RESIDUE CA B 9003
10
BC1
SOFTWARE
SER A:184 , ASP A:201 , THR A:203 , VAL A:206 , ASP A:208
BINDING SITE FOR RESIDUE CA A 9004
11
BC2
SOFTWARE
ARG A:47 , LYS A:48 , LEU A:50 , PHE A:54 , GLY A:154 , PRO A:155 , PHE A:166 , LEU A:180 , ALA A:182 , HIS A:183 , LEU A:185 , ALA A:186 , SER A:187 , GLN A:188 , GLU A:189 , GLY A:190 , LEU A:191 , SER A:244 , MET A:276 , HOH A:9005 , HOH A:9006 , HOH A:9071 , HOH A:9115
BINDING SITE FOR RESIDUE HEM A 344
12
BC3
SOFTWARE
ARG B:47 , LEU B:50 , PHE B:54 , PRO B:153 , GLY B:154 , PRO B:155 , PHE B:166 , LEU B:179 , LEU B:180 , ALA B:182 , HIS B:183 , ALA B:186 , SER B:187 , GLN B:188 , GLU B:189 , GLY B:190 , LEU B:191 , SER B:244 , MET B:276 , HOH B:9004 , HOH B:9005 , HOH B:9049 , HOH B:9131
BINDING SITE FOR RESIDUE HEM B 344
13
BC4
SOFTWARE
GLN B:38 , THR B:158 , THR B:160 , HOH B:9226 , HOH B:9265 , HOH B:9287
BINDING SITE FOR RESIDUE GOL B 800
14
BC5
SOFTWARE
HIS A:82 , ASN A:84 , ILE A:85 , HOH A:9088
BINDING SITE FOR RESIDUE GOL A 801
15
BC6
SOFTWARE
HIS B:82 , ASN B:84 , ILE B:85 , HOH B:9304
BINDING SITE FOR RESIDUE GOL B 802
16
BC7
SOFTWARE
ALA B:66 , SER B:338 , MAN B:700 , HOH B:9264
BINDING SITE FOR RESIDUE GOL B 803
17
BC8
SOFTWARE
ASP B:97 , SER B:252 , ARG B:253 , HOH B:9086 , HOH B:9137 , HOH B:9151 , HOH B:9269
BINDING SITE FOR RESIDUE GOL B 804
18
BC9
SOFTWARE
HOH A:9206 , CYS B:42 , ASN B:127 , GLN B:205 , HOH B:9041 , HOH B:9175 , HOH B:9258
BINDING SITE FOR RESIDUE GOL B 805
19
CC1
SOFTWARE
PHE A:36 , ASP A:97 , SER A:252 , ARG A:253 , HOH A:9020 , HOH A:9114 , HOH A:9165 , HOH A:9329
BINDING SITE FOR RESIDUE GOL A 806
20
CC2
SOFTWARE
SER A:264 , HOH A:9093 , SER B:260 , SER B:264 , VAL B:267 , ARG B:271
BINDING SITE FOR RESIDUE GOL B 807
21
CC3
SOFTWARE
SER B:263 , SER B:264 , ASN B:265 , GLU B:266 , PRO B:306 , HOH B:9307
BINDING SITE FOR RESIDUE GOL B 808
22
CC4
SOFTWARE
PRO B:90 , ALA B:91 , PRO B:155 , PHE B:229 , HOH B:9131
BINDING SITE FOR RESIDUE GOL B 809
23
CC5
SOFTWARE
SER A:150 , ILE A:152 , ARG A:165 , HOH A:9233 , HOH A:9304 , HOH A:9316
BINDING SITE FOR RESIDUE GOL A 810
24
CC6
SOFTWARE
PHE A:60 , ALA A:169 , GLY A:170 , LYS A:278 , LEU A:282 , HOH A:9045 , HOH A:9200
BINDING SITE FOR RESIDUE GOL A 811
[
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]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_PER_COPCI_001 (I79V, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_PER_COPCI_001
*
I
99
V
PER_COPCI
---
---
A/B
I
79
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_2 (A:46-57,B:46-57)
2: PEROXIDASE_4 (A:50-296,B:50-296)
3: PEROXIDASE_1 (A:175-185,B:175-185)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEROXIDASE_2
PS00436
Peroxidases active site signature.
PER_COPCI
66-77
2
A:46-57
B:46-57
2
PEROXIDASE_4
PS50873
Plant heme peroxidase family profile.
PER_COPCI
69-316
2
A:50-296
B:50-296
3
PEROXIDASE_1
PS00435
Peroxidases proximal heme-ligand signature.
PER_COPCI
195-205
2
A:175-185
B:175-185
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
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_d1ly8a_ (A:)
1b: SCOP_d1ly8b_ (B:)
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Classes
(
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(
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Folds
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(
)
Superfamilies
(
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Heme-dependent peroxidases
(402)
Superfamily
:
Heme-dependent peroxidases
(402)
Family
:
CCP-like
(292)
Protein domain
:
Fungal peroxidase (ligninase)
(28)
Inky cap (Coprinus cinereus) [TaxId: 5346]
(5)
1a
d1ly8a_
A:
1b
d1ly8b_
B:
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1ly8A01 (A:19-152,A:276-303)
1b: CATH_1ly8B01 (B:19-152,B:276-303)
2a: CATH_1ly8A02 (A:153-275,A:304-343)
2b: CATH_1ly8B02 (B:153-275,B:304-343)
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(
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(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Peroxidase; domain 1
(244)
Homologous Superfamily
:
[code=1.10.520.10, no name defined]
(241)
Coprinopsis cinerea. Organism_taxid: 5346.
(4)
1a
1ly8A01
A:19-152,A:276-303
1b
1ly8B01
B:19-152,B:276-303
Topology
:
Peroxidase; domain 2
(241)
Homologous Superfamily
:
Peroxidase, domain 2
(241)
Coprinopsis cinerea. Organism_taxid: 5346.
(4)
2a
1ly8A02
A:153-275,A:304-343
2b
1ly8B02
B:153-275,B:304-343
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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