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3G1F
Biol. Unit 4
Info
Asym.Unit (447 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (74 KB)
Biol.Unit 3 (73 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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Title
:
CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM COMPLEXED WITH 5,6-DIHYDROOROTIDINE 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
:
2.50
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-Omp, 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, 2)
Info
All Hetero Components
1a: 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPH... (2OMa)
1b: 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPH... (2OMb)
1c: 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPH... (2OMc)
1d: 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPH... (2OMd)
1e: 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPH... (2OMe)
1f: 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPH... (2OMf)
1g: 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPH... (2OMg)
1h: 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPH... (2OMh)
1i: 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPH... (2OMi)
1j: 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPH... (2OMj)
1k: 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPH... (2OMk)
1l: 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPH... (2OMl)
1m: 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPH... (2OMm)
View:
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Label:
No.
Name
Count
Type
Full Name
1
2OM
2
Ligand/Ion
5,6-DIHYDROOROTIDINE 5'-MONOPHOSPHATE
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Sites
(2, 2)
Info
All Sites
1: AC7 (SOFTWARE)
2: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC7
SOFTWARE
ASP G:20 , LYS G:42 , ASP G:70 , LYS G:72 , ILE G:96 , MET G:126 , SER G:127 , PRO G:180 , VAL G:182 , GLN G:185 , GLY G:202 , ARG G:203 , ASP H:75 , ILE H:76 , THR H:79
BINDING SITE FOR RESIDUE 2OM G 229
2
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 , VAL H:182 , GLN H:185 , GLY H:202 , ARG H:203
BINDING SITE FOR RESIDUE 2OM H 229
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: OMPDECASE (G:67-80,H:67-80)
;
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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
2
-
-
-
-
-
-
G:67-80
H:67-80
-
-
-
-
-
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 13)
Info
All SCOP Domains
1a: SCOP_d3g1fa_ (A:)
1b: SCOP_d3g1fb_ (B:)
1c: SCOP_d3g1fc_ (C:)
1d: SCOP_d3g1fd_ (D:)
1e: SCOP_d3g1fe_ (E:)
1f: SCOP_d3g1ff_ (F:)
1g: SCOP_d3g1fg_ (G:)
1h: SCOP_d3g1fh_ (H:)
1i: SCOP_d3g1fi_ (I:)
1j: SCOP_d3g1fj_ (J:)
1k: SCOP_d3g1fk_ (K:)
1l: SCOP_d3g1fl_ (L:)
1m: SCOP_d3g1fm_ (M:)
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Protein Domains
(
)
(
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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
d3g1fa_
A:
1b
d3g1fb_
B:
1c
d3g1fc_
C:
1d
d3g1fd_
D:
1e
d3g1fe_
E:
1f
d3g1ff_
F:
1g
d3g1fg_
G:
1h
d3g1fh_
H:
1i
d3g1fi_
I:
1j
d3g1fj_
J:
1k
d3g1fk_
K:
1l
d3g1fl_
L:
1m
d3g1fm_
M:
[
close SCOP info
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CATH Domains
(1, 13)
Info
all CATH domains
1a: CATH_3g1fA00 (A:6-225)
1b: CATH_3g1fC00 (C:8-225)
1c: CATH_3g1fJ00 (J:8-225)
1d: CATH_3g1fE00 (E:9-225)
1e: CATH_3g1fF00 (F:9-225)
1f: CATH_3g1fG00 (G:9-225)
1g: CATH_3g1fM00 (M:9-225)
1h: CATH_3g1fB00 (B:10-225)
1i: CATH_3g1fH00 (H:10-225)
1j: CATH_3g1fK00 (K:10-225)
1k: CATH_3g1fL00 (L:10-225)
1l: CATH_3g1fD00 (D:11-225)
1m: CATH_3g1fI00 (I:14-225)
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Organisms
(
)
(
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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
3g1fA00
A:6-225
1b
3g1fC00
C:8-225
1c
3g1fJ00
J:8-225
1d
3g1fE00
E:9-225
1e
3g1fF00
F:9-225
1f
3g1fG00
G:9-225
1g
3g1fM00
M:9-225
1h
3g1fB00
B:10-225
1i
3g1fH00
H:10-225
1j
3g1fK00
K:10-225
1k
3g1fL00
L:10-225
1l
3g1fD00
D:11-225
1m
3g1fI00
I:14-225
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (447 KB)
Header - Asym.Unit
Biol.Unit 1 (75 KB)
Header - Biol.Unit 1
Biol.Unit 2 (74 KB)
Header - Biol.Unit 2
Biol.Unit 3 (73 KB)
Header - Biol.Unit 3
Biol.Unit 4 (73 KB)
Header - Biol.Unit 4
Biol.Unit 5 (74 KB)
Header - Biol.Unit 5
Biol.Unit 6 (73 KB)
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Biol.Unit 7 (75 KB)
Header - Biol.Unit 7
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