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1UP6
Biol. Unit 1
Info
Asym.Unit (548 KB)
Biol.Unit 1 (281 KB)
Biol.Unit 2 (264 KB)
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(1)
Title
:
STRUCTURE OF THE 6-PHOSPHO-BETA GLUCOSIDASE FROM THERMOTOGA MARITIMA AT 2.55 ANGSTROM RESOLUTION IN THE TETRAGONAL FORM WITH MANGANESE, NAD+ AND GLUCOSE-6-PHOSPHATE
Authors
:
A. Varrot, V. L. Yip, S. G. Withers, G. J. Davies
Date
:
29 Sep 03 (Deposition) - 02 Aug 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.55
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Hydrolase, 6-Phospho-Beta-Glucosidase, Family4 Hydrolase, Nad Dependent
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. L. Yip, A. Varrot, G. J. Davies, S. S. Rajan, X. Yang, J. Thompson, W. F. Anderson, S. G. Withers
An Unusual Mechanism Of Glycoside Hydrolysis Involving Redox And Elimination Steps By A Family 4 Beta-Glycosidase From Thermotoga Maritima.
J. Am. Chem. Soc. V. 126 8354 2004
[
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Hetero Components
(4, 34)
Info
All Hetero Components
1a: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Pa)
1b: ALPHA-D-GLUCOSE-6-PHOSPHATE (G6Pb)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3ag: SELENOMETHIONINE (MSEag)
3ah: SELENOMETHIONINE (MSEah)
3ai: SELENOMETHIONINE (MSEai)
3aj: SELENOMETHIONINE (MSEaj)
3ak: SELENOMETHIONINE (MSEak)
3al: SELENOMETHIONINE (MSEal)
3am: SELENOMETHIONINE (MSEam)
3an: SELENOMETHIONINE (MSEan)
3ao: SELENOMETHIONINE (MSEao)
3ap: SELENOMETHIONINE (MSEap)
3aq: SELENOMETHIONINE (MSEaq)
3ar: SELENOMETHIONINE (MSEar)
3as: SELENOMETHIONINE (MSEas)
3at: SELENOMETHIONINE (MSEat)
3au: SELENOMETHIONINE (MSEau)
3av: SELENOMETHIONINE (MSEav)
3aw: SELENOMETHIONINE (MSEaw)
3ax: SELENOMETHIONINE (MSEax)
3ay: SELENOMETHIONINE (MSEay)
3az: SELENOMETHIONINE (MSEaz)
3b: SELENOMETHIONINE (MSEb)
3ba: SELENOMETHIONINE (MSEba)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
4a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
4b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
4c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
G6P
2
Ligand/Ion
ALPHA-D-GLUCOSE-6-PHOSPHATE
2
MN
-1
Ligand/Ion
MANGANESE (II) ION
3
MSE
28
Mod. Amino Acid
SELENOMETHIONINE
4
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
5
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
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: BC3 (SOFTWARE)
10: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:87 , GLU A:103 , ASN A:140 , ASN A:163 , HIS A:192 , TYR A:241 , ARG A:261 , GLY A:290 , NAD A:1416 , MN A:1417 , HOH A:2134
BINDING SITE FOR RESIDUE G6P A1418
02
AC2
SOFTWARE
ARG C:87 , GLU C:103 , ASN C:140 , CYS C:162 , ASN C:163 , HIS C:192 , TYR C:241 , ARG C:261 , NAD C:1416 , MN C:1417
BINDING SITE FOR RESIDUE G6P C1418
03
AC3
SOFTWARE
CYS A:162 , ASN A:163 , HIS A:192 , NAD A:1416 , G6P A:1418
BINDING SITE FOR RESIDUE MN A1417
04
AC4
SOFTWARE
ILE A:37 , GLU A:39 , MN A:1420 , HOH A:2135 , ILE C:37
BINDING SITE FOR RESIDUE MN A1419
05
AC5
SOFTWARE
ILE A:37 , MN A:1419 , ILE C:37 , HOH C:2004
BINDING SITE FOR RESIDUE MN A1420
06
AC6
SOFTWARE
GLU A:248 , HOH A:2067 , PRO B:389 , GLY B:391 , ASP B:393 , HOH B:2082 , HOH B:2083
BINDING SITE FOR RESIDUE SO4 B1416
07
AC7
SOFTWARE
CYS C:162 , ASN C:163 , HIS C:192 , NAD C:1416 , G6P C:1418
BINDING SITE FOR RESIDUE MN C1417
08
AC8
SOFTWARE
GLU C:248 , GLU D:248 , PRO D:389 , GLY D:391 , HOH D:2093 , HOH D:2095
BINDING SITE FOR RESIDUE SO4 D1416
09
BC3
SOFTWARE
GLY A:9 , SER A:10 , TYR A:12 , TYR A:35 , ASP A:36 , ILE A:37 , ASP A:38 , LYS A:41 , GLN A:78 , PHE A:79 , ARG A:80 , GLU A:103 , ILE A:119 , TYR A:123 , PHE A:138 , THR A:139 , ASN A:140 , LEU A:161 , CYS A:162 , ASN A:163 , GLU A:269 , MN A:1417 , G6P A:1418
BINDING SITE FOR RESIDUE NAD A1416
10
BC4
SOFTWARE
GLY C:9 , SER C:10 , TYR C:12 , ASP C:36 , ILE C:37 , ASP C:38 , LYS C:41 , GLN C:78 , PHE C:79 , ARG C:80 , GLU C:103 , ILE C:119 , TYR C:123 , PHE C:138 , ASN C:140 , LEU C:161 , CYS C:162 , ASN C:163 , GLU C:269 , MN C:1417 , G6P C:1418 , HOH C:2106
BINDING SITE FOR RESIDUE NAD C1416
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GLYCOSYL_HYDROL_F4 (A:131-162,B:131-162,C:131-162,D:13...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLYCOSYL_HYDROL_F4
PS01324
Glycosyl hydrolases family 4 signature.
BGLT_THEMA
131-162
4
A:131-162
B:131-162
C:131-162
D:131-162
-
-
-
-
[
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1up6a2 (A:163-415)
1b: SCOP_d1up6c2 (C:163-415)
1c: SCOP_d1up6d2 (D:163-415)
1d: SCOP_d1up6e2 (E:163-415)
1e: SCOP_d1up6f2 (F:163-415)
1f: SCOP_d1up6g2 (G:163-415)
1g: SCOP_d1up6h2 (H:163-415)
1h: SCOP_d1up6b2 (B:163-415)
2a: SCOP_d1up6a1 (A:2-162)
2b: SCOP_d1up6c1 (C:2-162)
2c: SCOP_d1up6d1 (D:2-162)
2d: SCOP_d1up6e1 (E:2-162)
2e: SCOP_d1up6f1 (F:2-162)
2f: SCOP_d1up6g1 (G:2-162)
2g: SCOP_d1up6h1 (H:2-162)
2h: SCOP_d1up6b1 (B:2-162)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LDH C-terminal domain-like
(172)
Superfamily
:
LDH C-terminal domain-like
(172)
Family
:
AglA-like glucosidase
(9)
Protein domain
:
6-phospho-beta-glucosidase
(4)
Thermotoga maritima [TaxId: 2336]
(3)
1a
d1up6a2
A:163-415
1b
d1up6c2
C:163-415
1c
d1up6d2
D:163-415
1d
d1up6e2
E:163-415
1e
d1up6f2
F:163-415
1f
d1up6g2
G:163-415
1g
d1up6h2
H:163-415
1h
d1up6b2
B:163-415
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
LDH N-terminal domain-like
(117)
Protein domain
:
6-phospho-beta-glucosidase
(4)
Thermotoga maritima [TaxId: 2336]
(3)
2a
d1up6a1
A:2-162
2b
d1up6c1
C:2-162
2c
d1up6d1
D:2-162
2d
d1up6e1
E:2-162
2e
d1up6f1
F:2-162
2f
d1up6g1
G:2-162
2g
d1up6h1
H:2-162
2h
d1up6b1
B:2-162
[
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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, 16)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_4C_1up6H01 (H:181-391)
1b: PFAM_Glyco_hydro_4C_1up6H02 (H:181-391)
1c: PFAM_Glyco_hydro_4C_1up6H03 (H:181-391)
1d: PFAM_Glyco_hydro_4C_1up6H04 (H:181-391)
1e: PFAM_Glyco_hydro_4C_1up6H05 (H:181-391)
1f: PFAM_Glyco_hydro_4C_1up6H06 (H:181-391)
1g: PFAM_Glyco_hydro_4C_1up6H07 (H:181-391)
1h: PFAM_Glyco_hydro_4C_1up6H08 (H:181-391)
2a: PFAM_Glyco_hydro_4_1up6H09 (H:2-178)
2b: PFAM_Glyco_hydro_4_1up6H10 (H:2-178)
2c: PFAM_Glyco_hydro_4_1up6H11 (H:2-178)
2d: PFAM_Glyco_hydro_4_1up6H12 (H:2-178)
2e: PFAM_Glyco_hydro_4_1up6H13 (H:2-178)
2f: PFAM_Glyco_hydro_4_1up6H14 (H:2-178)
2g: PFAM_Glyco_hydro_4_1up6H15 (H:2-178)
2h: PFAM_Glyco_hydro_4_1up6H16 (H:2-178)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
LDH_C
(56)
Family
:
Glyco_hydro_4C
(5)
Thermotoga maritima
(4)
1a
Glyco_hydro_4C-1up6H01
H:181-391
1b
Glyco_hydro_4C-1up6H02
H:181-391
1c
Glyco_hydro_4C-1up6H03
H:181-391
1d
Glyco_hydro_4C-1up6H04
H:181-391
1e
Glyco_hydro_4C-1up6H05
H:181-391
1f
Glyco_hydro_4C-1up6H06
H:181-391
1g
Glyco_hydro_4C-1up6H07
H:181-391
1h
Glyco_hydro_4C-1up6H08
H:181-391
Clan
:
NADP_Rossmann
(1239)
Family
:
Glyco_hydro_4
(5)
Thermotoga maritima
(4)
2a
Glyco_hydro_4-1up6H09
H:2-178
2b
Glyco_hydro_4-1up6H10
H:2-178
2c
Glyco_hydro_4-1up6H11
H:2-178
2d
Glyco_hydro_4-1up6H12
H:2-178
2e
Glyco_hydro_4-1up6H13
H:2-178
2f
Glyco_hydro_4-1up6H14
H:2-178
2g
Glyco_hydro_4-1up6H15
H:2-178
2h
Glyco_hydro_4-1up6H16
H:2-178
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Asym.Unit (548 KB)
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