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2R3V
Biol. Unit 3
Info
Asym.Unit (248 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (64 KB)
Biol.Unit 3 (64 KB)
Biol.Unit 4 (63 KB)
Biol.Unit 5 (124 KB)
Biol.Unit 6 (122 KB)
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(1)
Title
:
THE BIOCHEMICAL AND STRUCTURAL BASIS FOR FEEDBACK INHIBITION OF MEVALONATE KINASE AND ISOPRENOID METABOLISM
Authors
:
Z. Fu, N. E. Voynova, H. M. Miziorko, J. P. Kim
Date
:
30 Aug 07 (Deposition) - 24 Jun 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: A,B (1x)
Biol. Unit 6: C,D (1x)
Keywords
:
Mevalonate Kinase, Farnesyl Thiodiphophate, Atp-Binding, Cataract, Cholesterol Biosynthesis, Cytoplasm, Disease Mutation, Lipid Synthesis, Nucleotide-Binding, Peroxisome, Polymorphism, Steroid Biosynthesis, Sterol Biosynthesis, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Fu, N. E. Voynova, T. J. Herdendorf, H. M. Miziorko, J. J. Kim
Biochemical And Structural Basis For Feedback Inhibition Of Mevalonate Kinase And Isoprenoid Metabolism.
Biochemistry V. 47 3715 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(0, 0)
Info
All Hetero Components
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Sorry, no Info available
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Sites
(0, 0)
Info
All Sites
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Label:
Sorry, no Info available
[
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]
SAPs(SNPs)/Variants
(29, 29)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_010956 (H20N, chain C, )
02: VAR_004022 (H20P, chain C, )
03: VAR_029519 (H20Q, chain C, )
04: VAR_010957 (L39P, chain C, )
05: VAR_010958 (S52N, chain C, )
06: VAR_029520 (V132I, chain C, )
07: VAR_010959 (S135L, chain C, )
08: VAR_010960 (A148T, chain C, )
09: VAR_010961 (S150L, chain C, )
10: VAR_004023 (P167L, chain C, )
11: VAR_029521 (G171R, chain C, )
12: VAR_010962 (G202R, chain C, )
13: VAR_029522 (G211E, chain C, )
14: VAR_010963 (R215Q, chain C, )
15: VAR_010964 (T243I, chain C, )
16: VAR_029523 (V250I, chain C, )
17: VAR_010965 (L264F, chain C, )
18: VAR_010966 (L265P, chain C, )
19: VAR_029524 (L265R, chain C, )
20: VAR_004024 (I268T, chain C, )
21: VAR_004025 (N301T, chain C, )
22: VAR_010967 (G309S, chain C, )
23: VAR_009068 (V310M, chain C, )
24: VAR_010968 (G326R, chain C, )
25: VAR_004026 (A334T, chain C, )
26: VAR_029525 (G335S, chain C, )
27: VAR_029526 (T356M, chain C, )
28: VAR_029527 (G376V, chain C, )
29: VAR_004027 (V377I, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_010956
H
20
N
KIME_HUMAN
Disease (HIDS)
11544299
C
H
20
N
02
UniProt
VAR_004022
H
20
P
KIME_HUMAN
Disease (MEVA)
---
C
H
20
P
03
UniProt
VAR_029519
H
20
Q
KIME_HUMAN
Disease (HIDS)
---
C
H
20
Q
04
UniProt
VAR_010957
L
39
P
KIME_HUMAN
Disease (HIDS)
---
C
L
39
P
05
UniProt
VAR_010958
S
52
N
KIME_HUMAN
Polymorphism
7957619
C
S
52
N
06
UniProt
VAR_029520
V
132
I
KIME_HUMAN
Disease (HIDS)
---
C
V
132
I
07
UniProt
VAR_010959
S
135
L
KIME_HUMAN
Disease (HIDS)
---
C
S
135
L
08
UniProt
VAR_010960
A
148
T
KIME_HUMAN
Disease (HIDS)
---
C
A
148
T
09
UniProt
VAR_010961
S
150
L
KIME_HUMAN
Disease (HIDS)
---
C
S
150
L
10
UniProt
VAR_004023
P
167
L
KIME_HUMAN
Disease (HIDS)
---
C
P
167
L
11
UniProt
VAR_029521
G
171
R
KIME_HUMAN
Disease (HIDS)
---
C
G
171
R
12
UniProt
VAR_010962
G
202
R
KIME_HUMAN
Disease (HIDS)
---
C
G
202
R
13
UniProt
VAR_029522
G
211
E
KIME_HUMAN
Disease (HIDS)
---
C
G
211
E
14
UniProt
VAR_010963
R
215
Q
KIME_HUMAN
Disease (HIDS)
---
C
R
215
Q
15
UniProt
VAR_010964
T
243
I
KIME_HUMAN
Disease (MEVA)
---
C
T
243
I
16
UniProt
VAR_029523
V
250
I
KIME_HUMAN
Disease (HIDS)
---
C
V
250
I
17
UniProt
VAR_010965
L
264
F
KIME_HUMAN
Disease (MEVA)
---
C
L
264
F
18
UniProt
VAR_010966
L
265
P
KIME_HUMAN
Disease (MEVA)
---
C
L
265
P
19
UniProt
VAR_029524
L
265
R
KIME_HUMAN
Disease (HIDS)
---
C
L
265
R
20
UniProt
VAR_004024
I
268
T
KIME_HUMAN
Disease (MEVA)
---
C
I
268
T
21
UniProt
VAR_004025
N
301
T
KIME_HUMAN
Disease (MEVA)
28934896
C
N
301
T
22
UniProt
VAR_010967
G
309
S
KIME_HUMAN
Disease (HIDS)
---
C
G
309
S
23
UniProt
VAR_009068
V
310
M
KIME_HUMAN
Disease (MEVA)
---
C
V
310
M
24
UniProt
VAR_010968
G
326
R
KIME_HUMAN
Disease (HIDS)
---
C
G
326
R
25
UniProt
VAR_004026
A
334
T
KIME_HUMAN
Disease (MEVA)
---
C
A
334
T
26
UniProt
VAR_029525
G
335
S
KIME_HUMAN
Polymorphism
11614976
C
G
335
S
27
UniProt
VAR_029526
T
356
M
KIME_HUMAN
Polymorphism
---
C
T
356
M
28
UniProt
VAR_029527
G
376
V
KIME_HUMAN
Disease (HIDS)
---
C
G
376
V
29
UniProt
VAR_004027
V
377
I
KIME_HUMAN
Disease (HIDS)
28934897
C
V
377
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: GHMP_KINASES_ATP (C:137-148)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GHMP_KINASES_ATP
PS00627
GHMP kinases putative ATP-binding domain.
KIME_HUMAN
137-148
1
-
-
C:137-148
-
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2r3va2 (A:226-395)
1b: SCOP_d2r3vb2 (B:226-395)
1c: SCOP_d2r3vc2 (C:226-395)
1d: SCOP_d2r3vd2 (D:226-395)
2a: SCOP_d2r3va1 (A:2-225)
2b: SCOP_d2r3vb1 (B:2-225)
2c: SCOP_d2r3vc1 (C:2-225)
2d: SCOP_d2r3vd1 (D:2-225)
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(
)
(
)
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(
)
(
)
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(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
GHMP Kinase, C-terminal domain
(25)
Family
:
Mevalonate kinase
(5)
Protein domain
:
Mevalonate kinase
(5)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d2r3va2
A:226-395
1b
d2r3vb2
B:226-395
1c
d2r3vc2
C:226-395
1d
d2r3vd2
D:226-395
Fold
:
Ribosomal protein S5 domain 2-like
(306)
Superfamily
:
Ribosomal protein S5 domain 2-like
(306)
Family
:
GHMP Kinase, N-terminal domain
(19)
Protein domain
:
Mevalonate kinase
(5)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d2r3va1
A:2-225
2b
d2r3vb1
B:2-225
2c
d2r3vc1
C:2-225
2d
d2r3vd1
D:2-225
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2r3vA02 (A:227-374)
1b: CATH_2r3vB02 (B:227-374)
1c: CATH_2r3vC02 (C:227-374)
1d: CATH_2r3vD02 (D:227-374)
2a: CATH_2r3vB01 (B:2-226,B:375-395)
2b: CATH_2r3vD01 (D:2-226,D:375-395)
2c: CATH_2r3vA01 (A:2-226,A:375-395)
2d: CATH_2r3vC01 (C:2-226,C:375-395)
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.890, no name defined]
(18)
Human (Homo sapiens)
(2)
1a
2r3vA02
A:227-374
1b
2r3vB02
B:227-374
1c
2r3vC02
C:227-374
1d
2r3vD02
D:227-374
Topology
:
Ribosomal Protein S5; domain 2
(189)
Homologous Superfamily
:
[code=3.30.230.10, no name defined]
(170)
Human (Homo sapiens)
(6)
2a
2r3vB01
B:2-226,B:375-395
2b
2r3vD01
D:2-226,D:375-395
2c
2r3vA01
A:2-226,A:375-395
2d
2r3vC01
C:2-226,C:375-395
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_GHMP_kinases_N_2r3vD01 (D:130-212)
1b: PFAM_GHMP_kinases_N_2r3vD02 (D:130-212)
1c: PFAM_GHMP_kinases_N_2r3vD03 (D:130-212)
1d: PFAM_GHMP_kinases_N_2r3vD04 (D:130-212)
2a: PFAM_GHMP_kinases_C_2r3vD05 (D:290-366)
2b: PFAM_GHMP_kinases_C_2r3vD06 (D:290-366)
2c: PFAM_GHMP_kinases_C_2r3vD07 (D:290-366)
2d: PFAM_GHMP_kinases_C_2r3vD08 (D:290-366)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
S5
(103)
Family
:
GHMP_kinases_N
(23)
Homo sapiens (Human)
(2)
1a
GHMP_kinases_N-2r3vD01
D:130-212
1b
GHMP_kinases_N-2r3vD02
D:130-212
1c
GHMP_kinases_N-2r3vD03
D:130-212
1d
GHMP_kinases_N-2r3vD04
D:130-212
Clan
:
no clan defined [family: GHMP_kinases_C]
(13)
Family
:
GHMP_kinases_C
(13)
Homo sapiens (Human)
(2)
2a
GHMP_kinases_C-2r3vD05
D:290-366
2b
GHMP_kinases_C-2r3vD06
D:290-366
2c
GHMP_kinases_C-2r3vD07
D:290-366
2d
GHMP_kinases_C-2r3vD08
D:290-366
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Asymmetric Unit 1
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Asym.Unit (248 KB)
Header - Asym.Unit
Biol.Unit 1 (64 KB)
Header - Biol.Unit 1
Biol.Unit 2 (64 KB)
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Biol.Unit 3 (64 KB)
Header - Biol.Unit 3
Biol.Unit 4 (63 KB)
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