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2VQU
Biol. Unit 2
Info
Asym.Unit (317 KB)
Biol.Unit 1 (159 KB)
Biol.Unit 2 (157 KB)
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(1)
Title
:
STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA-MANNOSIDASES
Authors
:
L. E. Tailford, W. A. Offen, N. L. Smith, C. Dumon, C. Moreland, J. Gratien, M. P. Heck, R. V. Stick, Y. Bleriot, A. Vasella, H. J. Gilbert, G. J. Davies
Date
:
18 Mar 08 (Deposition) - 01 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Linear Free Energy Relationship, Transition State Mimic, Mannosidase, Glycoside Hydrolase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. E. Tailford, W. A. Offen, N. L. Smith, C. Dumon, C. Morland, J. Gratien, M. P. Heck, R. V. Stick, Y. Bleriot, A. Vasella, H. J. Gilbert, G. J. Davies
Structural And Biochemical Evidence For A Boat-Like Transition State In Beta-Mannosidases.
Nat. Chem. Biol. V. 4 306 2008
[
close entry info
]
Hetero Components
(2, 29)
Info
All Hetero Components
1a: BROMIDE ION (BRa)
1b: BROMIDE ION (BRb)
1c: BROMIDE ION (BRc)
1d: BROMIDE ION (BRd)
1e: BROMIDE ION (BRe)
1f: BROMIDE ION (BRf)
1g: BROMIDE ION (BRg)
1h: BROMIDE ION (BRh)
1i: BROMIDE ION (BRi)
1j: BROMIDE ION (BRj)
1k: BROMIDE ION (BRk)
1l: BROMIDE ION (BRl)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
2h: CHLORIDE ION (CLh)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3ab: 1,2-ETHANEDIOL (EDOab)
3ac: 1,2-ETHANEDIOL (EDOac)
3ad: 1,2-ETHANEDIOL (EDOad)
3ae: 1,2-ETHANEDIOL (EDOae)
3af: 1,2-ETHANEDIOL (EDOaf)
3ag: 1,2-ETHANEDIOL (EDOag)
3ah: 1,2-ETHANEDIOL (EDOah)
3ai: 1,2-ETHANEDIOL (EDOai)
3aj: 1,2-ETHANEDIOL (EDOaj)
3ak: 1,2-ETHANEDIOL (EDOak)
3al: 1,2-ETHANEDIOL (EDOal)
3am: 1,2-ETHANEDIOL (EDOam)
3an: 1,2-ETHANEDIOL (EDOan)
3ao: 1,2-ETHANEDIOL (EDOao)
3ap: 1,2-ETHANEDIOL (EDOap)
3aq: 1,2-ETHANEDIOL (EDOaq)
3ar: 1,2-ETHANEDIOL (EDOar)
3as: 1,2-ETHANEDIOL (EDOas)
3at: 1,2-ETHANEDIOL (EDOat)
3au: 1,2-ETHANEDIOL (EDOau)
3av: 1,2-ETHANEDIOL (EDOav)
3aw: 1,2-ETHANEDIOL (EDOaw)
3ax: 1,2-ETHANEDIOL (EDOax)
3ay: 1,2-ETHANEDIOL (EDOay)
3az: 1,2-ETHANEDIOL (EDOaz)
3b: 1,2-ETHANEDIOL (EDOb)
3ba: 1,2-ETHANEDIOL (EDOba)
3bb: 1,2-ETHANEDIOL (EDObb)
3bc: 1,2-ETHANEDIOL (EDObc)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
4a: (2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIP... (NOYa)
4b: (2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIP... (NOYb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BR
-1
Ligand/Ion
BROMIDE ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
EDO
28
Ligand/Ion
1,2-ETHANEDIOL
4
NOY
1
Ligand/Ion
(2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-2,3,4-TRIOL
[
close Hetero Component info
]
Sites
(44, 44)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC8 (SOFTWARE)
06: BC6 (SOFTWARE)
07: BC7 (SOFTWARE)
08: BC9 (SOFTWARE)
09: CC2 (SOFTWARE)
10: CC3 (SOFTWARE)
11: CC5 (SOFTWARE)
12: CC7 (SOFTWARE)
13: CC8 (SOFTWARE)
14: CC9 (SOFTWARE)
15: DC1 (SOFTWARE)
16: DC4 (SOFTWARE)
17: DC6 (SOFTWARE)
18: DC7 (SOFTWARE)
19: DC8 (SOFTWARE)
20: DC9 (SOFTWARE)
21: EC1 (SOFTWARE)
22: EC4 (SOFTWARE)
23: EC6 (SOFTWARE)
24: EC7 (SOFTWARE)
25: EC8 (SOFTWARE)
26: FC6 (SOFTWARE)
27: FC7 (SOFTWARE)
28: FC8 (SOFTWARE)
29: FC9 (SOFTWARE)
30: GC1 (SOFTWARE)
31: GC2 (SOFTWARE)
32: GC3 (SOFTWARE)
33: GC5 (SOFTWARE)
34: GC6 (SOFTWARE)
35: GC9 (SOFTWARE)
36: HC1 (SOFTWARE)
37: HC2 (SOFTWARE)
38: HC4 (SOFTWARE)
39: HC5 (SOFTWARE)
40: HC7 (SOFTWARE)
41: HC8 (SOFTWARE)
42: IC1 (SOFTWARE)
43: IC2 (SOFTWARE)
44: IC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
HIS B:326 , ARG B:327 , ASN B:450 , HIS B:451 , HOH B:2257 , HOH B:2323 , HOH B:2349
BINDING SITE FOR RESIDUE EDO B1868
02
AC4
SOFTWARE
ASN A:293 , PRO A:294 , GLY B:266 , THR B:267
BINDING SITE FOR RESIDUE EDO A1867
03
AC5
SOFTWARE
TRP B:198 , ASP B:199 , TRP B:200 , TRP B:395 , ASN B:461 , GLU B:462 , TRP B:533 , TYR B:537 , GLU B:555 , TRP B:656 , CL B:1892 , HOH B:2485
BINDING SITE FOR RESIDUE NOY B1869
04
AC6
SOFTWARE
ASN B:261 , SER B:311 , HOH B:2601
BINDING SITE FOR RESIDUE EDO B1870
05
AC8
SOFTWARE
TRP B:525 , SER B:530 , ASN B:532 , ASP B:548 , PRO B:550 , MET B:553 , HOH B:2604
BINDING SITE FOR RESIDUE EDO B1872
06
BC6
SOFTWARE
ASN B:337 , HIS B:511 , TYR B:515 , HOH B:2605 , HOH B:2606
BINDING SITE FOR RESIDUE EDO B1873
07
BC7
SOFTWARE
HIS A:157 , EDO A:1887 , ASP B:88 , HIS B:157 , ARG B:161 , GLN B:162 , EDO B:1887
BINDING SITE FOR RESIDUE EDO B1874
08
BC9
SOFTWARE
THR A:432 , ARG A:436 , EDO A:1894 , LEU B:126
BINDING SITE FOR RESIDUE EDO B1875
09
CC2
SOFTWARE
SER B:43 , GLN B:44 , SER B:45 , GLY B:46 , THR B:47 , GLU B:48 , GLU B:90
BINDING SITE FOR RESIDUE EDO B1876
10
CC3
SOFTWARE
TYR A:117 , ALA A:118 , ASP A:119 , LYS A:129 , ALA A:130 , HIS A:157 , EDO A:1894 , EDO A:1901 , HOH A:2590 , LYS B:129
BINDING SITE FOR RESIDUE EDO A1877
11
CC5
SOFTWARE
ARG B:331 , ASP B:506 , ARG B:507 , HOH B:2390 , HOH B:2607 , HOH B:2608
BINDING SITE FOR RESIDUE EDO B1877
12
CC7
SOFTWARE
GLN B:365 , ASN B:648 , ASP B:649 , ILE B:659 , ASP B:660
BINDING SITE FOR RESIDUE EDO B1878
13
CC8
SOFTWARE
GLU B:465 , LYS B:468 , TYR B:469 , PRO B:514 , LEU B:516 , ALA B:517
BINDING SITE FOR RESIDUE EDO B1879
14
CC9
SOFTWARE
ARG B:626 , HIS B:774 , PHE B:775 , HOH B:2609 , HOH B:2610 , HOH B:2611
BINDING SITE FOR RESIDUE EDO B1880
15
DC1
SOFTWARE
PHE B:356 , ARG B:633 , ARG B:636 , ILE B:695 , SER B:696 , ASP B:697 , ASN B:733 , THR B:734
BINDING SITE FOR RESIDUE EDO B1881
16
DC4
SOFTWARE
ILE B:328 , GLY B:329 , ARG B:449 , ASN B:450 , HIS B:451 , ALA B:452 , ARG B:507 , HOH B:2186
BINDING SITE FOR RESIDUE EDO B1882
17
DC6
SOFTWARE
HIS B:774 , PHE B:775 , PHE B:776 , ARG B:777 , LYS B:778 , CL B:1890 , HOH B:2612
BINDING SITE FOR RESIDUE EDO B1883
18
DC7
SOFTWARE
PHE B:42 , SER B:43 , GLN B:44 , LYS B:49 , HOH B:2016 , HOH B:2613
BINDING SITE FOR RESIDUE EDO B1884
19
DC8
SOFTWARE
PRO B:212 , HOH B:2070 , HOH B:2167 , HOH B:2319 , HOH B:2620
BINDING SITE FOR RESIDUE EDO B1885
20
DC9
SOFTWARE
ARG B:823 , SER B:825 , ILE B:840 , THR B:842 , HOH B:2306
BINDING SITE FOR RESIDUE EDO B1886
21
EC1
SOFTWARE
ASP A:119 , TYR A:121 , TYR A:155 , ARG B:161 , GLN B:162 , PRO B:165 , EDO B:1874
BINDING SITE FOR RESIDUE EDO B1887
22
EC4
SOFTWARE
ILE B:107 , LYS B:142
BINDING SITE FOR RESIDUE BR B1888
23
EC6
SOFTWARE
GLN B:685 , ASP B:688
BINDING SITE FOR RESIDUE BR B1889
24
EC7
SOFTWARE
ASP A:88 , HIS A:157 , ARG A:161 , HOH A:2596 , EDO B:1874
BINDING SITE FOR RESIDUE EDO A1887
25
EC8
SOFTWARE
ILE B:684 , GLN B:685 , HIS B:774 , EDO B:1883 , HOH B:2503
BINDING SITE FOR RESIDUE CL B1890
26
FC6
SOFTWARE
HOH B:2561 , HOH B:2562
BINDING SITE FOR RESIDUE CL B1891
27
FC7
SOFTWARE
TRP B:200 , ILE B:363 , TRP B:395 , NOY B:1869 , HOH B:2425
BINDING SITE FOR RESIDUE CL B1892
28
FC8
SOFTWARE
PHE B:476 , THR B:477 , VAL B:480
BINDING SITE FOR RESIDUE BR B1893
29
FC9
SOFTWARE
GLN B:274 , ILE B:285 , THR B:286
BINDING SITE FOR RESIDUE EDO B1894
30
GC1
SOFTWARE
MET B:298 , TRP B:302 , ASN B:351
BINDING SITE FOR RESIDUE CL A1893
31
GC2
SOFTWARE
TYR A:117 , ASP A:131 , GLN A:162 , ARG A:436 , EDO A:1877 , HOH A:2598 , LEU B:126 , LYS B:129 , EDO B:1875
BINDING SITE FOR RESIDUE EDO A1894
32
GC3
SOFTWARE
GLN B:108
BINDING SITE FOR RESIDUE BR B1896
33
GC5
SOFTWARE
ARG B:698
BINDING SITE FOR RESIDUE CL B1897
34
GC6
SOFTWARE
VAL B:372 , THR B:374 , TYR B:377 , ASN B:402 , LEU B:404 , HOH B:2618 , HOH B:2619 , HOH B:2620
BINDING SITE FOR RESIDUE EDO B1898
35
GC9
SOFTWARE
ASN B:300 , TRP B:302 , PHE B:356 , ASN B:390 , ASP B:697 , HOH B:2281 , HOH B:2621
BINDING SITE FOR RESIDUE EDO B1901
36
HC1
SOFTWARE
ASN B:337 , GLU B:338 , GLU B:344 , HOH B:2606
BINDING SITE FOR RESIDUE EDO B1902
37
HC2
SOFTWARE
PHE B:542 , GLU B:543 , ASP B:603 , GLY B:624 , HOH B:2461
BINDING SITE FOR RESIDUE EDO B1903
38
HC4
SOFTWARE
LYS A:540 , ASP A:548 , HOH A:2599 , HOH A:2600 , ASP B:340 , LYS B:341 , HOH B:2268
BINDING SITE FOR RESIDUE EDO A1899
39
HC5
SOFTWARE
VAL B:442 , TYR B:443 , ARG B:446 , HOH B:2622 , HOH B:2623 , HOH B:2624
BINDING SITE FOR RESIDUE EDO B1904
40
HC7
SOFTWARE
LYS A:129 , HIS A:157 , GLN A:162 , EDO A:1877 , HOH A:2602 , ASP B:119 , LYS B:129 , HIS B:157 , GLN B:162
BINDING SITE FOR RESIDUE EDO A1901
41
HC8
SOFTWARE
ARG B:597 , PRO B:607 , GLU B:608 , PHE B:610 , PHE B:613 , HOH B:2625
BINDING SITE FOR RESIDUE EDO B1905
42
IC1
SOFTWARE
HOH B:2267 , HOH B:2626 , HOH B:2628
BINDING SITE FOR RESIDUE EDO B1906
43
IC2
SOFTWARE
TYR B:661 , TYR B:662 , HOH B:2617
BINDING SITE FOR RESIDUE EDO B1907
44
IC3
SOFTWARE
HOH A:2579 , TRP B:519 , TRP B:533 , HOH B:2603
BINDING SITE FOR RESIDUE EDO A1903
[
close Site info
]
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
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
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
(3, 10)
Info
All SCOP Domains
1a: SCOP_d2vqua4 (A:28-219)
1b: SCOP_d2vqub4 (B:28-219)
2a: SCOP_d2vqua1 (A:679-783)
2b: SCOP_d2vqub2 (B:220-330)
2c: SCOP_d2vqub3 (B:784-867)
2d: SCOP_d2vqua2 (A:220-330)
2e: SCOP_d2vqua3 (A:784-864)
2f: SCOP_d2vqub1 (B:679-783)
3a: SCOP_d2vqua5 (A:331-678)
3b: SCOP_d2vqub5 (B:331-678)
View:
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Classes
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)
(
)
Folds
(
)
(
)
Superfamilies
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Galactose-binding domain-like
(314)
Superfamily
:
Galactose-binding domain-like
(314)
Family
:
beta-Galactosidase/glucuronidase, N-terminal domain
(49)
Protein domain
:
Beta-mannosidase
(2)
Bacteroides thetaiotaomicron [TaxId: 818]
(2)
1a
d2vqua4
A:28-219
1b
d2vqub4
B:28-219
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
beta-Galactosidase/glucuronidase domain
(79)
Family
:
beta-Galactosidase/glucuronidase domain
(49)
Protein domain
:
Beta-mannosidase, domains 2, 4 and 5
(2)
Bacteroides thetaiotaomicron [TaxId: 818]
(2)
2a
d2vqua1
A:679-783
2b
d2vqub2
B:220-330
2c
d2vqub3
B:784-867
2d
d2vqua2
A:220-330
2e
d2vqua3
A:784-864
2f
d2vqub1
B:679-783
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
beta-glycanases
(284)
Protein domain
:
Five-domain beta-mannosidase, domain 3
(2)
Bacteroides thetaiotaomicron [TaxId: 818]
(2)
3a
d2vqua5
A:331-678
3b
d2vqub5
B:331-678
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_2_N_2vquB01 (B:28-219)
1b: PFAM_Glyco_hydro_2_N_2vquB02 (B:28-219)
2a: PFAM_Glyco_hydro_2_C_2vquB03 (B:345-478)
2b: PFAM_Glyco_hydro_2_C_2vquB04 (B:345-478)
3a: PFAM_Glyco_hydro_2_2vquB05 (B:221-331)
3b: PFAM_Glyco_hydro_2_2vquB06 (B:221-331)
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Clans
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(
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Organisms
(
)
(
)
Clan
:
GBD
(153)
Family
:
Glyco_hydro_2_N
(32)
Bacteroides thetaiotaomicron
(9)
1a
Glyco_hydro_2_N-2vquB01
B:28-219
1b
Glyco_hydro_2_N-2vquB02
B:28-219
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_2_C
(27)
Bacteroides thetaiotaomicron
(9)
2a
Glyco_hydro_2_C-2vquB03
B:345-478
2b
Glyco_hydro_2_C-2vquB04
B:345-478
Clan
:
no clan defined [family: Glyco_hydro_2]
(31)
Family
:
Glyco_hydro_2
(31)
Bacteroides thetaiotaomicron
(9)
3a
Glyco_hydro_2-2vquB05
B:221-331
3b
Glyco_hydro_2-2vquB06
B:221-331
[
close Pfam info
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Asymmetric Unit 1
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