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1UHV
Asym. Unit
Info
Asym.Unit (365 KB)
Biol.Unit 1 (359 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BETA-D-XYLOSIDASE FROM THERMOANAEROBACTERIUM SACCHAROLYTICUM, A FAMILY 39 GLYCOSIDE HYDROLASE
Authors
:
J. K. Yang, H. J. Yoon, H. J. Ahn, B. Il Lee, J. D. Pedelacq, E. C. Liong, J. Berendzen, M. Laivenieks, C. Vieille, G. J. Zeikus, D. J. Vocadlo, S. G. Withers, S. W. Suh
Date
:
11 Jul 03 (Deposition) - 23 Dec 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Family 39 Glycoside Hydrolase, Xylosidase, Xylan, Xylose, Covalent Glycosyl-Enzyme Intermediate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. K. Yang, H. J. Yoon, H. J. Ahn, B. I. Lee, J. D. Pedelacq, E. C. Liong, J. Berendzen, M. Laivenieks, C. Vieille, G. J. Zeikus, D. J. Vocadlo, S. G. Withers, S. W. Suh
Crystal Structure Of Beta-D-Xylosidase From Thermoanaerobacterium Saccharolyticum, A Family 39 Glycoside Hydrolase.
J. Mol. Biol. V. 335 155 2004
(for further references see the
PDB file header
)
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: 1,2-DEOXY-2-FLUORO-XYLOPYRANOSE (DFXa)
1b: 1,2-DEOXY-2-FLUORO-XYLOPYRANOSE (DFXb)
1c: 1,2-DEOXY-2-FLUORO-XYLOPYRANOSE (DFXc)
1d: 1,2-DEOXY-2-FLUORO-XYLOPYRANOSE (DFXd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
DFX
4
Ligand/Ion
1,2-DEOXY-2-FLUORO-XYLOPYRANOSE
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:54 , PHE A:115 , ASN A:159 , GLU A:160 , PHE A:166 , TYR A:230 , GLU A:277 , TYR A:282 , TRP A:315 , GLU A:323 , PHE A:335
BINDING SITE FOR RESIDUE DFX A 3277
2
AC2
SOFTWARE
HIS B:54 , PHE B:115 , ASN B:159 , GLU B:160 , TYR B:230 , GLU B:277 , TYR B:282 , TRP B:315 , GLU B:323 , PHE B:335 , HOH B:2218
BINDING SITE FOR RESIDUE DFX B 3277
3
AC3
SOFTWARE
HIS C:54 , PHE C:115 , ASN C:159 , GLU C:160 , TYR C:230 , GLU C:277 , TYR C:282 , TRP C:315 , GLU C:323 , PHE C:335 , HOH C:2219
BINDING SITE FOR RESIDUE DFX C 3277
4
AC4
SOFTWARE
HIS D:54 , PHE D:115 , ASN D:159 , GLU D:160 , TYR D:230 , GLU D:277 , TYR D:282 , TRP D:315 , GLU D:323 , PHE D:335 , HOH D:2220
BINDING SITE FOR RESIDUE DFX D 3277
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GLYCOSYL_HYDROL_F39 (A:153-162,B:153-162,C:153-162,D:15...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLYCOSYL_HYDROL_F39
PS01027
Glycosyl hydrolases family 39 active site.
XYNB_THESA
153-162
4
A:153-162
B:153-162
C:153-162
D:153-162
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1uhva1 (A:1-13,A:360-500)
1b: SCOP_d1uhvb1 (B:1-13,B:360-500)
1c: SCOP_d1uhvc1 (C:1-13,C:360-500)
1d: SCOP_d1uhvd1 (D:1-13,D:360-500)
2a: SCOP_d1uhva2 (A:14-359)
2b: SCOP_d1uhvb2 (B:14-359)
2c: SCOP_d1uhvc2 (C:14-359)
2d: SCOP_d1uhvd2 (D:14-359)
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Classes
(
)
(
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)
(
)
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Glycosyl hydrolase domain
(397)
Superfamily
:
Glycosyl hydrolase domain
(397)
Family
:
Composite domain of glycosyl hydrolase families 5, 30, 39 and 51
(30)
Protein domain
:
Beta-D-xylosidase
(5)
Thermoanaerobacterium saccharolyticum [TaxId: 28896]
(2)
1a
d1uhva1
A:1-13,A:360-500
1b
d1uhvb1
B:1-13,B:360-500
1c
d1uhvc1
C:1-13,C:360-500
1d
d1uhvd1
D:1-13,D:360-500
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
beta-glycanases
(284)
Protein domain
:
Beta-D-xylosidase, catalytic domain
(5)
Thermoanaerobacterium saccharolyticum [TaxId: 28896]
(2)
2a
d1uhva2
A:14-359
2b
d1uhvb2
B:14-359
2c
d1uhvc2
C:14-359
2d
d1uhvd2
D:14-359
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1uhvA02 (A:15-358)
1b: CATH_1uhvB02 (B:15-358)
1c: CATH_1uhvC02 (C:15-358)
1d: CATH_1uhvD02 (D:15-358)
2a: CATH_1uhvA01 (A:1-14,A:359-500)
2b: CATH_1uhvB01 (B:1-14,B:359-500)
2c: CATH_1uhvC01 (C:1-14,C:359-500)
2d: CATH_1uhvD01 (D:1-14,D:359-500)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Thermoanaerobacterium saccharolyticum. Organism_taxid: 28896.
(2)
1a
1uhvA02
A:15-358
1b
1uhvB02
B:15-358
1c
1uhvC02
C:15-358
1d
1uhvD02
D:15-358
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Glycosyl hydrolase domain; family 39
(5)
Thermoanaerobacterium saccharolyticum. Organism_taxid: 28896.
(2)
2a
1uhvA01
A:1-14,A:359-500
2b
1uhvB01
B:1-14,B:359-500
2c
1uhvC01
C:1-14,C:359-500
2d
1uhvD01
D:1-14,D:359-500
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Asym.Unit (365 KB)
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