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1G1L
Asym. Unit
Info
Asym.Unit (903 KB)
Biol.Unit 1 (452 KB)
Biol.Unit 2 (449 KB)
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(1)
Title
:
THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). TDP-GLUCOSE COMPLEX.
Authors
:
W. Blankenfeldt, M. Asuncion, J. S. Lam, J. H. Naimsmith
Date
:
12 Oct 00 (Deposition) - 27 Dec 00 (Release) - 23 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.77
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
:
L-Rhamnose, Nucleotidyltransferase, Pyrophosphorylase, Thymidylyltransferase, Allostery, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Blankenfeldt, M. Asuncion, J. S. Lam, J. H. Naismith
The Structural Basis Of The Catalytic Mechanism And Regulation Of Glucose-1-Phosphate Thymidylyltransferase (Rmla).
Embo J. V. 19 6652 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 41)
Info
All Hetero Components
1a: CITRIC ACID (CITa)
1b: CITRIC ACID (CITb)
2a: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUa)
2b: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUb)
2c: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUc)
2d: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUd)
2e: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUe)
2f: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUf)
2g: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUg)
2h: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUh)
2i: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUi)
2j: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUj)
2k: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUk)
2l: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUl)
2m: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUm)
2n: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUn)
2o: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUo)
2p: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUp)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
3t: SULFATE ION (SO4t)
3u: SULFATE ION (SO4u)
3v: SULFATE ION (SO4v)
3w: SULFATE ION (SO4w)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CIT
2
Ligand/Ion
CITRIC ACID
2
DAU
16
Ligand/Ion
2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
3
SO4
23
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(41, 41)
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)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:12 , GLY A:13 , THR A:14 , ARG A:15 , LYS A:25 , HOH A:4062
BINDING SITE FOR RESIDUE SO4 A 3700
02
AC2
SOFTWARE
SER B:12 , GLY B:13 , THR B:14 , ARG B:15 , LYS B:25 , HOH B:3986 , HOH B:4080 , HOH B:4153 , HOH B:4203 , HOH B:4205
BINDING SITE FOR RESIDUE SO4 B 3701
03
AC3
SOFTWARE
SER G:12 , GLY G:13 , THR G:14 , ARG G:15 , LYS G:25 , HOH G:3946 , HOH G:4117 , HOH G:4139 , HOH G:4157 , HOH G:4204
BINDING SITE FOR RESIDUE SO4 G 3702
04
AC4
SOFTWARE
SER H:12 , GLY H:13 , THR H:14 , ARG H:15
BINDING SITE FOR RESIDUE SO4 H 3703
05
AC5
SOFTWARE
ARG A:62 , HOH A:3985 , ARG B:62 , HOH C:4051
BINDING SITE FOR RESIDUE SO4 A 3802
06
AC6
SOFTWARE
ARG A:128 , GLU A:215 , HOH A:4030 , HOH A:4084 , ASP F:151 , GLN F:152 , HOH F:4059
BINDING SITE FOR RESIDUE SO4 A 3803
07
AC7
SOFTWARE
GLU B:160 , GLU B:161 , ARG B:194 , ARG B:204 , HOH B:3899 , HOH B:3925 , HOH B:4108
BINDING SITE FOR RESIDUE SO4 B 3804
08
AC8
SOFTWARE
HOH B:4118 , ARG C:62 , HOH C:3935 , HOH C:4021 , ARG D:62 , HOH D:3955
BINDING SITE FOR RESIDUE SO4 C 3805
09
AC9
SOFTWARE
GLN C:127 , ARG C:128 , GLN C:129 , THR C:130
BINDING SITE FOR RESIDUE SO4 C 3806
10
BC1
SOFTWARE
GLN D:127 , ARG D:128 , GLN D:129 , THR D:130
BINDING SITE FOR RESIDUE SO4 D 3807
11
BC2
SOFTWARE
ARG E:62 , HOH E:3885 , ARG F:62
BINDING SITE FOR RESIDUE SO4 E 3808
12
BC3
SOFTWARE
GLN E:127 , ARG E:128 , GLN E:129 , THR E:130 , HOH E:3980
BINDING SITE FOR RESIDUE SO4 E 3809
13
BC4
SOFTWARE
ARG B:128 , GLU B:215 , ASP E:151 , GLN E:152 , HOH E:3989 , HOH E:3990
BINDING SITE FOR RESIDUE SO4 E 3810
14
BC5
SOFTWARE
GLN F:129 , THR F:130
BINDING SITE FOR RESIDUE SO4 F 3811
15
BC6
SOFTWARE
ASP C:151 , GLN C:152 , HOH C:4014 , HOH C:4093 , ARG G:128 , GLU G:215 , HOH G:3951 , HOH G:4101
BINDING SITE FOR RESIDUE SO4 G 3812
16
BC7
SOFTWARE
GLU G:160 , GLU G:161 , ARG G:194 , ARG G:204 , HOH G:3880 , HOH G:3941 , HOH G:4134
BINDING SITE FOR RESIDUE SO4 G 3813
17
BC8
SOFTWARE
ARG G:62 , ARG H:62
BINDING SITE FOR RESIDUE SO4 H 3814
18
BC9
SOFTWARE
ASP D:151 , GLN D:152 , HOH D:3943 , HOH D:3949 , HOH D:4074 , ARG H:128 , GLU H:215 , HOH H:3892
BINDING SITE FOR RESIDUE SO4 H 3815
19
CC1
SOFTWARE
GLU H:160 , GLU H:161 , ARG H:204 , HOH H:3919 , HOH H:4149
BINDING SITE FOR RESIDUE SO4 H 3816
20
CC2
SOFTWARE
GLU A:160 , GLU A:161 , ARG A:194 , ARG A:204 , HOH A:3908 , HOH A:3914 , HOH A:3992 , HOH A:4201 , HOH B:4183
BINDING SITE FOR RESIDUE SO4 A 3817
21
CC3
SOFTWARE
HIS A:116 , DAU A:3501 , HOH A:3829 , HOH A:3921 , HOH A:3927 , HOH A:3997 , LEU C:121 , TYR C:221 , HOH C:3905
BINDING SITE FOR RESIDUE SO4 A 3818
22
CC4
SOFTWARE
LEU B:121 , TYR B:221 , HOH B:3816 , HIS D:116 , DAU D:3507 , HOH D:3892 , HOH D:3933
BINDING SITE FOR RESIDUE SO4 D 3819
23
CC5
SOFTWARE
HIS E:116 , DAU E:3509 , HOH E:3831 , HOH E:3894 , HOH E:4034 , LEU H:121 , TYR H:221 , HOH H:3871
BINDING SITE FOR RESIDUE SO4 E 3820
24
CC6
SOFTWARE
LEU A:8 , GLY A:10 , GLY A:11 , GLN A:26 , GLN A:82 , PRO A:85 , ASP A:86 , GLY A:87 , LEU A:88 , LEU A:108 , GLY A:109 , ASP A:110 , ASN A:111 , TYR A:145 , GLY A:146 , GLU A:161 , LYS A:162 , VAL A:172 , GLU A:196 , THR A:200 , HOH A:3819 , HOH A:3904 , HOH A:4168 , HOH A:4203 , HOH A:4224
BINDING SITE FOR RESIDUE DAU A 3500
25
CC7
SOFTWARE
LEU A:45 , TYR A:114 , GLY A:115 , HIS A:116 , ASP A:117 , PHE A:118 , HIS A:119 , GLU A:120 , VAL A:250 , ALA A:251 , GLU A:255 , ILE A:256 , ARG A:259 , TYR A:293 , SO4 A:3818 , HOH A:3839 , HOH A:3847 , HOH A:3850 , HOH A:3862 , HOH A:3900 , HOH A:3927 , HOH A:4023 , HOH A:4049 , HOH A:4184 , ILE C:216 , GLY C:218 , ARG C:219 , GLY C:220
BINDING SITE FOR RESIDUE DAU A 3501
26
CC8
SOFTWARE
LEU B:8 , GLY B:10 , GLY B:11 , ARG B:15 , GLN B:26 , GLN B:82 , PRO B:85 , ASP B:86 , GLY B:87 , LEU B:88 , LEU B:108 , GLY B:109 , ASP B:110 , ASN B:111 , TYR B:145 , GLY B:146 , GLU B:161 , LYS B:162 , VAL B:172 , THR B:200 , HOH B:3832 , HOH B:3856 , HOH B:3915 , HOH B:3969 , HOH B:4199 , HOH B:4200 , HOH B:4201
BINDING SITE FOR RESIDUE DAU B 3502
27
CC9
SOFTWARE
LEU B:45 , TYR B:114 , GLY B:115 , HIS B:116 , ASP B:117 , PHE B:118 , HIS B:119 , GLU B:120 , VAL B:250 , ALA B:251 , GLU B:255 , ILE B:256 , TYR B:293 , HOH B:3817 , HOH B:3826 , HOH B:3835 , HOH B:3863 , HOH B:3876 , HOH B:3887 , HOH B:3971 , HOH B:4112 , ILE D:216 , GLY D:218 , ARG D:219 , GLY D:220
BINDING SITE FOR RESIDUE DAU B 3503
28
DC1
SOFTWARE
LEU C:8 , GLY C:10 , GLY C:11 , LYS C:25 , GLN C:26 , GLN C:82 , PRO C:85 , ASP C:86 , GLY C:87 , LEU C:88 , LEU C:108 , GLY C:109 , ASP C:110 , ASN C:111 , TYR C:145 , GLY C:146 , GLU C:161 , LYS C:162 , VAL C:172 , THR C:200 , HOH C:3814 , HOH C:3852 , HOH C:3977 , HOH C:4121 , HOH C:4146 , HOH C:4147 , HOH C:4149 , HOH C:4154
BINDING SITE FOR RESIDUE DAU C 3504
29
DC2
SOFTWARE
ILE A:216 , GLY A:218 , ARG A:219 , GLY A:220 , LEU C:45 , TYR C:114 , GLY C:115 , HIS C:116 , ASP C:117 , PHE C:118 , HIS C:119 , GLU C:120 , VAL C:250 , ALA C:251 , GLU C:255 , ILE C:256 , ARG C:259 , TYR C:293 , HOH C:3810 , HOH C:3826 , HOH C:3832 , HOH C:3850 , HOH C:3880 , HOH C:3979
BINDING SITE FOR RESIDUE DAU C 3505
30
DC3
SOFTWARE
LEU D:8 , GLY D:10 , GLY D:11 , LYS D:25 , GLN D:26 , GLN D:82 , PRO D:85 , ASP D:86 , GLY D:87 , LEU D:88 , LEU D:108 , ASP D:110 , ASN D:111 , TYR D:145 , GLY D:146 , GLU D:161 , LYS D:162 , VAL D:172 , GLU D:196 , THR D:200 , HOH D:3820 , HOH D:3958 , HOH D:3988 , HOH D:4107 , HOH D:4108
BINDING SITE FOR RESIDUE DAU D 3506
31
DC4
SOFTWARE
ILE B:216 , GLY B:218 , ARG B:219 , GLY B:220 , LEU D:45 , TYR D:114 , GLY D:115 , HIS D:116 , ASP D:117 , PHE D:118 , HIS D:119 , GLU D:120 , VAL D:250 , ALA D:251 , GLU D:255 , ILE D:256 , ARG D:259 , TYR D:293 , SO4 D:3819 , HOH D:3827 , HOH D:3833 , HOH D:3840 , HOH D:3857 , HOH D:3886 , HOH D:3892 , HOH D:3940
BINDING SITE FOR RESIDUE DAU D 3507
32
DC5
SOFTWARE
LEU E:8 , GLY E:10 , GLY E:11 , LYS E:25 , GLN E:26 , GLN E:82 , PRO E:85 , ASP E:86 , GLY E:87 , LEU E:88 , LEU E:108 , ASP E:110 , ASN E:111 , TYR E:145 , GLY E:146 , GLU E:161 , LYS E:162 , VAL E:172 , GLU E:196 , THR E:200 , HOH E:3825 , HOH E:4126 , HOH E:4127 , HOH E:4128
BINDING SITE FOR RESIDUE DAU E 3508
33
DC6
SOFTWARE
LEU E:45 , TYR E:114 , GLY E:115 , HIS E:116 , ASP E:117 , PHE E:118 , HIS E:119 , GLU E:120 , VAL E:250 , ALA E:251 , GLU E:255 , ILE E:256 , TYR E:293 , SO4 E:3820 , HOH E:3827 , HOH E:3832 , HOH E:3833 , HOH E:3873 , HOH E:3894 , HOH E:3937 , ILE H:216 , GLY H:218 , ARG H:219 , GLY H:220
BINDING SITE FOR RESIDUE DAU E 3509
34
DC7
SOFTWARE
LEU F:8 , GLY F:10 , GLY F:11 , LYS F:25 , GLN F:26 , GLN F:82 , PRO F:85 , ASP F:86 , GLY F:87 , LEU F:88 , LEU F:108 , ASP F:110 , ASN F:111 , TYR F:145 , GLY F:146 , GLU F:161 , LYS F:162 , VAL F:172 , ARG F:194 , GLU F:196 , THR F:200 , TRP F:223 , HOH F:3828 , HOH F:3922 , HOH F:3990 , HOH F:4001 , HOH F:4118 , HOH F:4119
BINDING SITE FOR RESIDUE DAU F 3510
35
DC8
SOFTWARE
LEU F:45 , TYR F:114 , GLY F:115 , HIS F:116 , ASP F:117 , PHE F:118 , HIS F:119 , GLU F:120 , VAL F:250 , ALA F:251 , GLU F:255 , ILE F:256 , TYR F:293 , HOH F:3818 , HOH F:3826 , HOH F:3832 , HOH F:3876 , HOH F:3878 , HOH F:3926 , ILE G:216 , GLY G:218 , ARG G:219 , GLY G:220
BINDING SITE FOR RESIDUE DAU F 3511
36
DC9
SOFTWARE
LEU H:8 , GLY H:10 , GLY H:11 , GLN H:26 , GLN H:82 , PRO H:85 , ASP H:86 , GLY H:87 , LEU H:88 , LEU H:108 , ASP H:110 , ASN H:111 , TYR H:145 , GLY H:146 , GLU H:161 , LYS H:162 , VAL H:172 , THR H:200 , HOH H:3825 , HOH H:3884 , HOH H:4002 , HOH H:4068 , HOH H:4139 , HOH H:4193
BINDING SITE FOR RESIDUE DAU H 3512
37
EC1
SOFTWARE
ILE E:216 , GLY E:218 , ARG E:219 , GLY E:220 , LEU H:45 , TYR H:114 , GLY H:115 , HIS H:116 , ASP H:117 , PHE H:118 , HIS H:119 , GLU H:120 , VAL H:250 , ALA H:251 , GLU H:255 , ILE H:256 , ARG H:259 , TYR H:293 , HOH H:3832 , HOH H:3835 , HOH H:3851 , HOH H:3905 , HOH H:3908 , HOH H:3914 , HOH H:3949 , HOH H:3952 , HOH H:4076
BINDING SITE FOR RESIDUE DAU H 3513
38
EC2
SOFTWARE
LEU G:8 , GLY G:10 , GLY G:11 , GLN G:26 , GLN G:82 , PRO G:85 , ASP G:86 , GLY G:87 , LEU G:88 , LEU G:108 , GLY G:109 , ASP G:110 , ASN G:111 , TYR G:145 , GLY G:146 , GLU G:161 , LYS G:162 , VAL G:172 , THR G:200 , HOH G:3827 , HOH G:3895 , HOH G:3902 , HOH G:3965 , HOH G:3990 , HOH G:4052 , HOH G:4117 , HOH G:4126 , HOH G:4157
BINDING SITE FOR RESIDUE DAU G 3514
39
EC3
SOFTWARE
ILE F:216 , GLY F:218 , ARG F:219 , GLY F:220 , LEU G:45 , TYR G:114 , GLY G:115 , HIS G:116 , ASP G:117 , PHE G:118 , HIS G:119 , GLU G:120 , VAL G:250 , ALA G:251 , GLU G:255 , ILE G:256 , ARG G:259 , TYR G:293 , HOH G:3823 , HOH G:3829 , HOH G:3856 , HOH G:3879 , HOH G:3891 , HOH G:3907 , HOH G:3997 , HOH G:4142
BINDING SITE FOR RESIDUE DAU G 3515
40
EC4
SOFTWARE
TYR A:31 , LYS A:249 , GLY A:279 , HOH A:3955 , HOH A:4205 , HOH A:4206 , HOH A:4221 , ARG B:15 , HIS B:229
BINDING SITE FOR RESIDUE CIT A 3800
41
EC5
SOFTWARE
HIS A:229 , HOH A:3905 , HOH A:3912 , HOH A:4063 , HOH A:4214 , HOH A:4215 , HOH A:4216 , HOH A:4217 , TYR B:31 , ASP B:32 , LYS B:249 , GLY B:279
BINDING SITE FOR RESIDUE CIT A 3801
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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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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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1g1la_ (A:)
1b: SCOP_d1g1lc_ (C:)
1c: SCOP_d1g1ld_ (D:)
1d: SCOP_d1g1le_ (E:)
1e: SCOP_d1g1lf_ (F:)
1f: SCOP_d1g1lg_ (G:)
1g: SCOP_d1g1lh_ (H:)
1h: SCOP_d1g1lb_ (B:)
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Folds
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Superfamilies
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)
(
)
Families
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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
:
glucose-1-phosphate thymidylyltransferase
(43)
Protein domain
:
RmlA (RfbA)
(27)
Pseudomonas aeruginosa [TaxId: 287]
(9)
1a
d1g1la_
A:
1b
d1g1lc_
C:
1c
d1g1ld_
D:
1d
d1g1le_
E:
1e
d1g1lf_
F:
1f
d1g1lg_
G:
1g
d1g1lh_
H:
1h
d1g1lb_
B:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1g1lA00 (A:2-293)
1b: CATH_1g1lD00 (D:2-293)
1c: CATH_1g1lE00 (E:2-293)
1d: CATH_1g1lG00 (G:2-293)
1e: CATH_1g1lH00 (H:2-293)
1f: CATH_1g1lB00 (B:1-293)
1g: CATH_1g1lF00 (F:1-293)
1h: CATH_1g1lC00 (C:2-293)
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Architectures
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Topologies
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Homologous Superfamilies
(
)
(
)
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)
Pseudomonas aeruginosa. Organism_taxid: 287.
(7)
1a
1g1lA00
A:2-293
1b
1g1lD00
D:2-293
1c
1g1lE00
E:2-293
1d
1g1lG00
G:2-293
1e
1g1lH00
H:2-293
1f
1g1lB00
B:1-293
1g
1g1lF00
F:1-293
1h
1g1lC00
C:2-293
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Asymmetric Unit 1
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