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2R8O
Asym. Unit
Info
Asym.Unit (235 KB)
Biol.Unit 1 (229 KB)
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(1)
Title
:
TRANSKETOLASE FROM E. COLI IN COMPLEX WITH SUBSTRATE D-XYLULOSE-5-PHOSPHATE
Authors
:
G. Wille, P. Asztalos, M. S. Weiss, K. Tittmann
Date
:
11 Sep 07 (Deposition) - 11 Dec 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.47
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Reaction Intermediate, Calcium, Metal-Binding, Thiamine Pyrophosphate, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Asztalos, C. Parthier, R. Golbik, M. Kleinschmidt, G. Hubner, M. S. Weiss, R. Friedemann, G. Wille, K. Tittmann
Strain And Near Attack Conformers In Enzymic Thiamin Catalysis: X-Ray Crystallographic Snapshots Of Bacterial Transketolase In Covalent Complex With Donor Ketoses Xylulose 5-Phosphate And Fructose 6-Phosphate, And In Noncovalent Complex With Acceptor Aldose Ribose 5-Phosphate.
Biochemistry V. 46 12037 2007
(for further references see the
PDB file header
)
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Hetero Components
(3, 15)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
3a: 2-C-{3-[(4-AMINO-2-METHYLPYRIMIDIN... (T5Xa)
3b: 2-C-{3-[(4-AMINO-2-METHYLPYRIMIDIN... (T5Xb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
EDO
11
Ligand/Ion
1,2-ETHANEDIOL
3
T5X
2
Ligand/Ion
2-C-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-2-YL}-5-O-PHOSPHONO-D-XYLITOL
[
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Sites
(15, 15)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:155 , ASN A:185 , ILE A:187 , T5X A:671 , HOH A:680
BINDING SITE FOR RESIDUE CA A 670
02
AC2
SOFTWARE
ASP B:155 , ASN B:185 , ILE B:187 , T5X B:671 , HOH B:730
BINDING SITE FOR RESIDUE CA B 670
03
AC3
SOFTWARE
HIS A:26 , ALA A:29 , HIS A:66 , HIS A:100 , GLY A:114 , LEU A:116 , ASP A:155 , GLY A:156 , GLU A:160 , ASN A:185 , ILE A:187 , ILE A:189 , ILE A:247 , HIS A:261 , CA A:670 , HOH A:677 , HOH A:680 , HOH A:681 , HOH A:682 , HOH A:687 , HOH A:691 , HOH A:697 , HOH A:703 , HOH A:747 , HOH A:793 , ASP B:381 , SER B:385 , GLU B:411 , PHE B:434 , PHE B:437 , TYR B:440 , HIS B:461 , ASP B:469 , HIS B:473 , ARG B:520 , HOH B:1232
BINDING SITE FOR RESIDUE T5X A 671
04
AC4
SOFTWARE
ASP A:381 , SER A:385 , GLU A:411 , PHE A:434 , PHE A:437 , TYR A:440 , HIS A:461 , ASP A:469 , HIS A:473 , ARG A:520 , HOH A:700 , HOH A:943 , HIS B:26 , ALA B:29 , HIS B:66 , HIS B:100 , GLY B:114 , LEU B:116 , ASP B:155 , GLY B:156 , GLU B:160 , ASN B:185 , ILE B:187 , ILE B:189 , ILE B:247 , HIS B:261 , CA B:670 , HOH B:682 , HOH B:690 , HOH B:693 , HOH B:695 , HOH B:699 , HOH B:736 , HOH B:763 , HOH B:1252
BINDING SITE FOR RESIDUE T5X B 671
05
AC5
SOFTWARE
GLU B:6 , GLY B:278 , TRP B:279 , LYS B:280 , TYR B:281 , HOH B:913 , HOH B:1215
BINDING SITE FOR RESIDUE EDO B 672
06
AC6
SOFTWARE
ALA B:271 , TYR B:505 , GLU B:508 , ARG B:509 , HOH B:783 , HOH B:816
BINDING SITE FOR RESIDUE EDO B 673
07
AC7
SOFTWARE
ARG B:274 , GLU B:275 , TRP B:279 , GLN B:592 , HOH B:822 , HOH B:1124 , HOH B:1224
BINDING SITE FOR RESIDUE EDO B 674
08
AC8
SOFTWARE
LEU B:272 , GLU B:275 , ARG B:509 , ASP B:511 , HOH B:1103
BINDING SITE FOR RESIDUE EDO B 675
09
AC9
SOFTWARE
PHE B:375 , TRP B:390 , SER B:393 , ASN B:403 , TYR B:404 , TYR B:430
BINDING SITE FOR RESIDUE EDO B 676
10
BC1
SOFTWARE
PRO B:52 , GLY B:108 , VAL B:109
BINDING SITE FOR RESIDUE EDO B 677
11
BC2
SOFTWARE
ILE A:615 , ASP A:617 , THR A:633 , HOH A:898 , ARG B:483 , HOH B:906
BINDING SITE FOR RESIDUE EDO A 672
12
BC3
SOFTWARE
SER B:559 , GLU B:560 , PHE B:645 , PHE B:650 , HOH B:917 , HOH B:1088
BINDING SITE FOR RESIDUE EDO B 678
13
BC4
SOFTWARE
LYS B:131 , THR B:172 , LYS B:174 , ASN B:397 , HOH B:842 , HOH B:1094
BINDING SITE FOR RESIDUE EDO B 679
14
BC5
SOFTWARE
LEU B:435 , ASP B:462 , PRO B:475 , VAL B:479 , ARG B:492 , ALA B:613 , GLY B:614 , HOH B:752
BINDING SITE FOR RESIDUE EDO B 680
15
BC6
SOFTWARE
PHE B:325 , THR B:326 , HOH B:881
BINDING SITE FOR RESIDUE EDO B 681
[
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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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: TRANSKETOLASE_1 (A:12-32,B:12-32)
2: TRANSKETOLASE_2 (A:467-483,B:467-483)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRANSKETOLASE_1
PS00801
Transketolase signature 1.
TKT1_ECOLI
12-32
2
A:12-32
B:12-32
2
TRANSKETOLASE_2
PS00802
Transketolase signature 2.
TKT1_ECOLI
467-483
2
A:467-483
B:467-483
[
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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.
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2r8oa1 (A:333-527)
1b: SCOP_d2r8ob1 (B:333-527)
2a: SCOP_d2r8oa2 (A:2-332)
2b: SCOP_d2r8ob2 (B:2-332)
3a: SCOP_d2r8oa3 (A:528-663)
3b: SCOP_d2r8ob3 (B:528-668)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
automated matches
(65)
Protein domain
:
automated matches
(65)
Escherichia coli K-12 [TaxId: 83333]
(2)
1a
d2r8oa1
A:333-527
1b
d2r8ob1
B:333-527
Family
:
TK-like PP module
(24)
Protein domain
:
Transketolase (TK), PP module
(13)
Escherichia coli [TaxId: 562]
(4)
2a
d2r8oa2
A:2-332
2b
d2r8ob2
B:2-332
Fold
:
TK C-terminal domain-like
(79)
Superfamily
:
TK C-terminal domain-like
(79)
Family
:
Transketolase C-terminal domain-like
(21)
Protein domain
:
Transketolase (TK), C-domain
(13)
Escherichia coli [TaxId: 562]
(4)
3a
d2r8oa3
A:528-663
3b
d2r8ob3
B:528-668
[
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]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2r8oB03 (B:538-668)
1b: CATH_2r8oA03 (A:538-663)
2a: CATH_2r8oA02 (A:327-537)
2b: CATH_2r8oB02 (B:327-537)
2c: CATH_2r8oA01 (A:2-326)
2d: CATH_2r8oB01 (B:2-326)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.920, no name defined]
(73)
Escherichia coli k12. Organism_taxid: 83333. Strain: k-12.
(2)
1a
2r8oB03
B:538-668
1b
2r8oA03
A:538-663
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Escherichia coli k12. Organism_taxid: 83333. Strain: k-12.
(2)
2a
2r8oA02
A:327-537
2b
2r8oB02
B:327-537
2c
2r8oA01
A:2-326
2d
2r8oB01
B:2-326
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Transket_pyr_2r8oB01 (B:353-526)
1b: PFAM_Transket_pyr_2r8oB02 (B:353-526)
2a: PFAM_Transketolase_N_2r8oB03 (B:3-334)
2b: PFAM_Transketolase_N_2r8oB04 (B:3-334)
3a: PFAM_Transketolase_C_2r8oB05 (B:540-655)
3b: PFAM_Transketolase_C_2r8oB06 (B:540-655)
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Clans
(
)
(
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(
)
(
)
Organisms
(
)
(
)
Clan
:
THDP-binding
(106)
Family
:
Transket_pyr
(45)
Escherichia coli (strain K12)
(5)
1a
Transket_pyr-2r8oB01
B:353-526
1b
Transket_pyr-2r8oB02
B:353-526
Family
:
Transketolase_N
(22)
Escherichia coli (strain K12)
(6)
2a
Transketolase_N-2r8oB03
B:3-334
2b
Transketolase_N-2r8oB04
B:3-334
Clan
:
no clan defined [family: Transketolase_C]
(40)
Family
:
Transketolase_C
(40)
Escherichia coli (strain K12)
(4)
3a
Transketolase_C-2r8oB05
B:540-655
3b
Transketolase_C-2r8oB06
B:540-655
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Asym.Unit (235 KB)
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