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3G1H
Asym. Unit
Info
Asym.Unit (449 KB)
Biol.Unit 1 (76 KB)
Biol.Unit 2 (75 KB)
Biol.Unit 3 (74 KB)
Biol.Unit 4 (73 KB)
Biol.Unit 5 (74 KB)
Biol.Unit 6 (73 KB)
Biol.Unit 7 (75 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH 5,6-DIHYDROURIDINE 5'-MONOPHOSPHATE
Authors
:
A. A. Fedorov, E. V. Fedorov, K. K. Chan, J. A. Gerlt, S. C. Almo
Date
:
29 Jan 09 (Deposition) - 23 Jun 09 (Release) - 23 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: I,J (1x)
Biol. Unit 6: K,L (1x)
Biol. Unit 7: M (2x)
Keywords
:
Orotidine 5'-Monophosphate Decarboxylase, H2-Ump, Crystal Structure, Decarboxylase, Pyrimidine Biosynthesis, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. K. Chan, B. M. Wood, A. A. Fedorov, E. V. Fedorov, H. J. Imker, T. L. Amyes, J. P. Richard, S. C. Almo, J. A. Gerlt
Mechanism Of The Orotidine 5'-Monophosphate Decarboxylase-Catalyzed Reaction: Evidence For Substrate Destabilization.
Biochemistry V. 48 5518 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 13)
Info
All Hetero Components
1a: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ua)
1b: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ub)
1c: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Uc)
1d: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ud)
1e: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ue)
1f: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Uf)
1g: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ug)
1h: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Uh)
1i: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ui)
1j: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Uj)
1k: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Uk)
1l: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Ul)
1m: 5,6-DIHYDROURIDINE-5'-MONOPHOSPHAT... (H2Um)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
H2U
13
Mod. Residue
5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:20 , LYS A:42 , ASP A:70 , LYS A:72 , MET A:126 , SER A:127 , PRO A:180 , GLN A:185 , GLY A:202 , ARG A:203 , HOH A:236 , HOH A:251 , HOH A:255 , ASP B:75 , ILE B:76 , THR B:79
BINDING SITE FOR RESIDUE H2U A 229
02
AC2
SOFTWARE
ASP A:75 , ILE A:76 , THR A:79 , ASP B:20 , LYS B:42 , ASP B:70 , LYS B:72 , MET B:126 , SER B:127 , PRO B:180 , GLN B:185 , GLY B:202 , ARG B:203 , HOH B:237 , HOH B:278 , HOH B:316
BINDING SITE FOR RESIDUE H2U B 229
03
AC3
SOFTWARE
ASP C:20 , LYS C:42 , ASP C:70 , LYS C:72 , MET C:126 , SER C:127 , PRO C:180 , GLN C:185 , VAL C:201 , GLY C:202 , ARG C:203 , HOH C:235 , HOH C:242 , ASP D:75 , ILE D:76 , THR D:79
BINDING SITE FOR RESIDUE H2U C 229
04
AC4
SOFTWARE
ASP C:75 , ILE C:76 , THR C:79 , ASP D:20 , LYS D:42 , ASP D:70 , LYS D:72 , MET D:126 , SER D:127 , PRO D:180 , GLN D:185 , GLY D:202 , ARG D:203 , HOH D:239 , HOH D:269
BINDING SITE FOR RESIDUE H2U D 229
05
AC5
SOFTWARE
ASP E:20 , LYS E:42 , ASP E:70 , LYS E:72 , MET E:126 , SER E:127 , PRO E:180 , GLN E:185 , GLY E:202 , ARG E:203 , ASP F:75 , ILE F:76 , THR F:79
BINDING SITE FOR RESIDUE H2U E 229
06
AC6
SOFTWARE
ASP E:75 , ILE E:76 , THR E:79 , ASP F:20 , LYS F:42 , ASP F:70 , LYS F:72 , MET F:126 , SER F:127 , PRO F:180 , GLN F:185 , VAL F:201 , GLY F:202 , ARG F:203
BINDING SITE FOR RESIDUE H2U F 229
07
AC7
SOFTWARE
ASP G:20 , LYS G:42 , ASP G:70 , LYS G:72 , MET G:126 , SER G:127 , PRO G:180 , ALA G:184 , GLN G:185 , GLY G:202 , ARG G:203 , ASP H:75 , ILE H:76 , THR H:79
BINDING SITE FOR RESIDUE H2U G 229
08
AC8
SOFTWARE
ASP G:75 , ILE G:76 , THR G:79 , ASP H:20 , LYS H:42 , ASP H:70 , LYS H:72 , MET H:126 , SER H:127 , PRO H:180 , GLN H:185 , VAL H:201 , GLY H:202 , ARG H:203
BINDING SITE FOR RESIDUE H2U H 229
09
AC9
SOFTWARE
ASP I:20 , LYS I:42 , ASP I:70 , LYS I:72 , MET I:126 , SER I:127 , VAL I:182 , ALA I:184 , GLN I:185 , GLY I:202 , ARG I:203 , TYR I:206 , ASP J:75 , THR J:79
BINDING SITE FOR RESIDUE H2U I 229
10
BC1
SOFTWARE
ASP I:75 , ILE I:76 , THR I:79 , ASP J:20 , LYS J:42 , ASP J:70 , LYS J:72 , MET J:126 , SER J:127 , PRO J:180 , GLN J:185 , GLY J:202 , ARG J:203 , HOH J:242 , HOH J:250
BINDING SITE FOR RESIDUE H2U J 229
11
BC2
SOFTWARE
ASP K:20 , LYS K:42 , ASP K:70 , LYS K:72 , MET K:126 , SER K:127 , PRO K:180 , VAL K:182 , ALA K:184 , GLN K:185 , GLY K:202 , ARG K:203 , ASP L:75 , THR L:79
BINDING SITE FOR RESIDUE H2U K 229
12
BC3
SOFTWARE
ASP K:75 , ILE K:76 , THR K:79 , ASP L:20 , LYS L:42 , ASP L:70 , LYS L:72 , MET L:126 , SER L:127 , PRO L:180 , GLN L:185 , VAL L:201 , GLY L:202 , ARG L:203
BINDING SITE FOR RESIDUE H2U L 229
13
BC4
SOFTWARE
ASP M:20 , LYS M:42 , ASP M:70 , LYS M:72 , ASP M:75 , THR M:79 , MET M:126 , SER M:127 , PRO M:180 , GLN M:185 , VAL M:201 , GLY M:202 , ARG M:203 , HOH M:244 , HOH M:255
BINDING SITE FOR RESIDUE H2U M 229
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 13)
Info
All PROSITE Patterns/Profiles
1: OMPDECASE (A:67-80,B:67-80,C:67-80,D:67-80,E:...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
OMPDECASE
PS00156
Orotidine 5'-phosphate decarboxylase active site.
PYRF_METTH
67-80
13
A:67-80
B:67-80
C:67-80
D:67-80
E:67-80
F:67-80
G:67-80
H:67-80
I:67-80
J:67-80
K:67-80
L:67-80
M:67-80
[
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Exons
(0, 0)
Info
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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, 13)
Info
All SCOP Domains
1a: SCOP_d3g1ha_ (A:)
1b: SCOP_d3g1hb_ (B:)
1c: SCOP_d3g1hc_ (C:)
1d: SCOP_d3g1hd_ (D:)
1e: SCOP_d3g1he_ (E:)
1f: SCOP_d3g1hf_ (F:)
1g: SCOP_d3g1hg_ (G:)
1h: SCOP_d3g1hh_ (H:)
1i: SCOP_d3g1hi_ (I:)
1j: SCOP_d3g1hj_ (J:)
1k: SCOP_d3g1hk_ (K:)
1l: SCOP_d3g1hl_ (L:)
1m: SCOP_d3g1hm_ (M:)
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)
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(
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Ribulose-phoshate binding barrel
(356)
Family
:
Decarboxylase
(172)
Protein domain
:
automated matches
(117)
Methanothermobacter thermautotrophicus [TaxId: 187420]
(66)
1a
d3g1ha_
A:
1b
d3g1hb_
B:
1c
d3g1hc_
C:
1d
d3g1hd_
D:
1e
d3g1he_
E:
1f
d3g1hf_
F:
1g
d3g1hg_
G:
1h
d3g1hh_
H:
1i
d3g1hi_
I:
1j
d3g1hj_
J:
1k
d3g1hk_
K:
1l
d3g1hl_
L:
1m
d3g1hm_
M:
[
close SCOP info
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CATH Domains
(1, 13)
Info
all CATH domains
1a: CATH_3g1hA00 (A:5-225)
1b: CATH_3g1hC00 (C:8-225)
1c: CATH_3g1hJ00 (J:8-225)
1d: CATH_3g1hE00 (E:9-225)
1e: CATH_3g1hF00 (F:9-225)
1f: CATH_3g1hG00 (G:9-225)
1g: CATH_3g1hM00 (M:9-225)
1h: CATH_3g1hB00 (B:10-225)
1i: CATH_3g1hH00 (H:10-225)
1j: CATH_3g1hK00 (K:10-225)
1k: CATH_3g1hL00 (L:10-225)
1l: CATH_3g1hD00 (D:11-225)
1m: CATH_3g1hI00 (I:14-225)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Delta h (Methanothermobacter thermautotrophicus str)
(13)
1a
3g1hA00
A:5-225
1b
3g1hC00
C:8-225
1c
3g1hJ00
J:8-225
1d
3g1hE00
E:9-225
1e
3g1hF00
F:9-225
1f
3g1hG00
G:9-225
1g
3g1hM00
M:9-225
1h
3g1hB00
B:10-225
1i
3g1hH00
H:10-225
1j
3g1hK00
K:10-225
1k
3g1hL00
L:10-225
1l
3g1hD00
D:11-225
1m
3g1hI00
I:14-225
[
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Pfam Domains
(0, 0)
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Asym.Unit (449 KB)
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