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3M5Q
Asym. Unit
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Asym.Unit (137 KB)
Biol.Unit 1 (132 KB)
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(1)
Title
:
0.93 A STRUCTURE OF MANGANESE-BOUND MANGANESE PEROXIDASE
Authors
:
M. Sundaramoorthy, M. H. Gold, T. L. Poulos
Date
:
12 Mar 10 (Deposition) - 14 Apr 10 (Release) - 26 May 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
0.93
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Peroxidase, Heme, Mn(Ii)-Binding Site, Ca(Ii)-Binding Site, Glycosylation, Ultrahigh Resolution, Calcium, Disulfide Bond, Glycoprotein, Hydrogen Peroxide, Iron, Lignin Degradation, Manganese, Metal-Binding, Oxidoreductase, Secreted
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
M. Sundaramoorthy, M. H. Gold, T. L. Poulos
Ultrahigh (0. 93A) Resolution Structure Of Manganese Peroxidase From Phanerochaete Chrysosporium: Implications For The Catalytic Mechanism.
J. Inorg. Biochem. V. 104 683 2010
(for further references see the
PDB file header
)
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Hetero Components
(6, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: GLYCEROL (GOLa)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
4a: ALPHA-D-MANNOSE (MANa)
5a: MANGANESE (II) ION (MNa)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
GOL
1
Ligand/Ion
GLYCEROL
3
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
5
MN
1
Ligand/Ion
MANGANESE (II) ION
6
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:98 , THR A:99 , ASN A:131 , NAG A:362 , HOH A:1090 , HOH A:1117 , HOH A:1240 , HOH A:1297
BINDING SITE FOR RESIDUE NAG A 361
2
AC2
SOFTWARE
MET A:94 , GLN A:95 , ASN A:98 , NAG A:361 , HOH A:1226 , HOH A:1409 , HOH A:1557 , HOH A:1558 , HOH A:1566
BINDING SITE FOR RESIDUE NAG A 362
3
AC3
SOFTWARE
HIS A:11 , PRO A:331 , GLY A:332 , SER A:334 , GLN A:335 , SER A:336 , HOH A:1238
BINDING SITE FOR RESIDUE MAN A 364
4
AC4
SOFTWARE
SER A:174 , ASP A:191 , THR A:193 , THR A:196 , ASP A:198
BINDING SITE FOR RESIDUE CA A 371
5
AC5
SOFTWARE
ASP A:47 , GLY A:62 , ASP A:64 , SER A:66 , HOH A:1085 , HOH A:1127
BINDING SITE FOR RESIDUE CA A 372
6
AC6
SOFTWARE
GLU A:35 , GLU A:39 , ASP A:179 , HEM A:396 , HOH A:1040 , HOH A:1108
BINDING SITE FOR RESIDUE MN A 381
7
AC7
SOFTWARE
ASP A:23 , THR A:27 , PRO A:92 , LYS A:96 , GLU A:156 , HOH A:1092
BINDING SITE FOR RESIDUE GOL A 391
8
AC8
SOFTWARE
GLU A:35 , HIS A:38 , GLU A:39 , ARG A:42 , PHE A:45 , GLU A:143 , PRO A:144 , PHE A:155 , LEU A:169 , LEU A:170 , SER A:172 , HIS A:173 , ALA A:176 , ARG A:177 , ALA A:178 , ASP A:179 , LYS A:180 , VAL A:181 , SER A:241 , MN A:381 , HOH A:1074 , HOH A:1108 , HOH A:1137 , HOH A:1190 , HOH A:1223
BINDING SITE FOR RESIDUE HEM A 396
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_2 (A:37-48)
2: PEROXIDASE_4 (A:37-293)
3: PEROXIDASE_1 (A:165-175)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEROXIDASE_2
PS00436
Peroxidases active site signature.
PEM1_PHACH
58-69
1
A:37-48
2
PEROXIDASE_4
PS50873
Plant heme peroxidase family profile.
PEM1_PHACH
58-314
1
A:37-293
3
PEROXIDASE_1
PS00435
Peroxidases proximal heme-ligand signature.
PEM1_PHACH
186-196
1
A:165-175
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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.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3m5qa_ (A:)
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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
:
automated matches
(48)
Basidomycetes fungus (Phanerochaete chrysosporium) [TaxId: 5306]
(6)
1a
d3m5qa_
A:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_DUF3415_3m5qA01 (A:263-343)
2a: PFAM_peroxidase_3m5qA02 (A:20-261)
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Clan
:
no clan defined [family: DUF3415]
(12)
Family
:
DUF3415
(12)
Phanerochaete chrysosporium (White-rot fungus) (Sporotrichum pruinosum)
(7)
1a
DUF3415-3m5qA01
A:263-343
Clan
:
no clan defined [family: peroxidase]
(92)
Family
:
peroxidase
(92)
Phanerochaete chrysosporium (White-rot fungus) (Sporotrichum pruinosum)
(7)
2a
peroxidase-3m5qA02
A:20-261
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Chain A
Asymmetric Unit 1
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