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3CU0
Asym. Unit
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Asym.Unit (93 KB)
Biol.Unit 1 (86 KB)
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Title
:
HUMAN BETA 1,3-GLUCURONYLTRANSFERASE I (GLCAT-I) IN COMPLEX WITH UDP AND GAL-GAL(6-SO4)-XYL(2-PO4)-O-SER
Authors
:
Y. Tone, L. C. Pedersen, T. Yamamoto, H. Kitagawa, J. Nishihara- Shimizu, J. Tamura, M. Negishi, K. Sugahara
Date
:
15 Apr 08 (Deposition) - 06 May 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Glcat-I, Glycosyltransferase, Heparan Sulfate Biosynthesis, Glycoprotein, Golgi Apparatus, Manganese, Membrane, Metal- Binding, Signal-Anchor, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Tone, L. C. Pedersen, T. Yamamoto, T. Izumikawa, H. Kitagawa, J. Nishihara, J. Tamura, M. Negishi, K. Sugahara
2-O-Phosphorylation Of Xylose And 6-O-Sulfation Of Galactose In The Protein Linkage Region Of Glycosaminoglycans Influence The Glucuronyltransferase-I Activity Involved In The Linkage Region Synthesis.
J. Biol. Chem. V. 283 16801 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 10)
Info
All Hetero Components
1a: BETA-D-GALACTOSE (GALa)
1b: BETA-D-GALACTOSE (GALb)
1c: BETA-D-GALACTOSE (GALc)
1d: BETA-D-GALACTOSE (GALd)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
4a: URIDINE-5'-DIPHOSPHATE (UDPa)
4b: URIDINE-5'-DIPHOSPHATE (UDPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GAL
4
Ligand/Ion
BETA-D-GALACTOSE
2
MN
2
Ligand/Ion
MANGANESE (II) ION
3
SO4
2
Ligand/Ion
SULFATE ION
4
UDP
2
Ligand/Ion
URIDINE-5'-DIPHOSPHATE
[
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Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY B:222 , GLU B:227 , TRP B:243 , ARG B:247 , ASP B:252 , GLU B:281 , HOH B:552 , HOH B:586
BINDING SITE FOR RESIDUE GAL B 1
02
AC2
SOFTWARE
TRP B:243 , ARG B:277 , HOH B:507 , HOH B:586
BINDING SITE FOR RESIDUE GAL B 2
03
AC3
SOFTWARE
GLU A:227 , ARG A:247 , ASP A:252 , GLU A:281 , HOH A:508 , HOH A:532 , HOH A:558 , HOH A:569 , HOH A:581
BINDING SITE FOR RESIDUE GAL A 1
04
AC4
SOFTWARE
GLY A:222 , TRP A:243 , ARG A:277 , HOH A:532 , HOH A:569
BINDING SITE FOR RESIDUE GAL A 2
05
AC5
SOFTWARE
LYS A:317 , GLN A:318 , GLY B:223 , TRP B:243
BINDING SITE FOR RESIDUE SO4 B 3
06
AC6
SOFTWARE
GLY A:223 , TRP A:243 , LYS B:317 , GLN B:318
BINDING SITE FOR RESIDUE SO4 A 3
07
AC7
SOFTWARE
ASP A:196 , HOH A:504 , HOH A:505
BINDING SITE FOR RESIDUE MN A 502
08
AC8
SOFTWARE
ASP B:196 , HOH B:505 , HOH B:506
BINDING SITE FOR RESIDUE MN B 504
09
AC9
SOFTWARE
PRO A:82 , THR A:83 , TYR A:84 , ARG A:86 , ASP A:113 , ARG A:156 , GLY A:157 , ASP A:194 , ASP A:195 , ASP A:196 , HIS A:308 , ARG A:310 , HOH A:505 , HOH A:508 , HOH A:540 , HOH A:547 , HOH A:588 , HOH A:600 , HOH A:615 , HOH A:631
BINDING SITE FOR RESIDUE UDP A 501
10
BC1
SOFTWARE
HOH A:514 , HOH A:571 , HOH A:597 , HOH A:623 , PRO B:82 , THR B:83 , TYR B:84 , ASP B:113 , PRO B:155 , ARG B:156 , GLY B:157 , ASP B:194 , ASP B:195 , ASP B:196 , HIS B:308 , ARG B:310 , HOH B:529
BINDING SITE FOR RESIDUE UDP A 503
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_066624 (R277Q, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_066624
R
277
Q
B3GA3_HUMAN
Disease (JDSSDHD)
---
A/B
R
277
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(4, 8)
Info
All Exons
Exon 1.3 (A:75-86 | B:75-86)
Exon 1.4c (A:86-206 (gaps) | B:86-206 (gaps))
Exon 1.5b (A:207-303 | B:207-303)
Exon 1.6d (A:304-335 | B:304-335)
View:
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All Exon Boundaries
1: Boundary 1.1a/1.3
2: Boundary 1.3/1.4c
3: Boundary 1.4c/1.5b
4: Boundary 1.5b/1.6d
5: Boundary 1.6d/-
View:
Label:
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
1.1a
ENST00000265471
1a
ENSE00002142592
chr11:
62389647-62389338
310
B3GA3_HUMAN
1-28
28
0
-
-
1.3
ENST00000265471
3
ENSE00001118980
chr11:
62388143-62387969
175
B3GA3_HUMAN
28-86
59
2
A:75-86
B:75-86
12
12
1.4c
ENST00000265471
4c
ENSE00000991160
chr11:
62384819-62384459
361
B3GA3_HUMAN
86-206
121
2
A:86-206 (gaps)
B:86-206 (gaps)
121
121
1.5b
ENST00000265471
5b
ENSE00000991161
chr11:
62384268-62383978
291
B3GA3_HUMAN
207-303
97
2
A:207-303
B:207-303
97
97
1.6d
ENST00000265471
6d
ENSE00001293049
chr11:
62383271-62382768
504
B3GA3_HUMAN
304-335
32
2
A:304-335
B:304-335
32
32
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3cu0a_ (A:)
1b: SCOP_d3cu0b_ (B:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleotide-diphospho-sugar transferases
(408)
Superfamily
:
Nucleotide-diphospho-sugar transferases
(408)
Family
:
1,3-glucuronyltransferase
(7)
Protein domain
:
1,3-Glucuronyltransferase I (glcAT-I)
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d3cu0a_
A:
1b
d3cu0b_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3cu0A00 (A:75-335)
1b: CATH_3cu0B00 (B:75-335)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Homologous Superfamily
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Human (Homo sapiens)
(73)
1a
3cu0A00
A:75-335
1b
3cu0B00
B:75-335
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Pfam Domains
(0, 0)
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all PFAM domains
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Asymmetric Unit 1
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Asym.Unit (93 KB)
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