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1KY4
Asym. Unit
Info
Asym.Unit (274 KB)
Biol.Unit 1 (268 KB)
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(1)
Title
:
S-ADENOSYLHOMOCYSTEINE HYDROLASE REFINED WITH NONCRYSTALLOGRAPHIC RESTRAINTS
Authors
:
Y. Takata, F. Takusagawa
Date
:
03 Feb 02 (Deposition) - 25 Sep 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Hydrolase, S-Adenosylhomocysteine
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Takata, T. Yamada, Y. Huang, J. Komoto, T. Gomi, H. Ogawa, M. Fujioka, F. Takusagawa
Catalytic Mechanism Of S-Adenosylhomocysteine Hydrolase. Site-Directed Mutagenesis Of Asp-130, Lys-185, Asp-189, And Asn-190.
J. Biol. Chem. V. 277 22670 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:189 , ASN A:190 , GLY A:219 , GLY A:221 , ASP A:222 , VAL A:223 , THR A:241 , GLU A:242 , ILE A:243 , ASP A:244 , ASN A:247 , THR A:274 , THR A:275 , GLY A:276 , ILE A:280 , ILE A:298 , GLY A:299 , HIS A:300 , LEU A:343 , ASN A:345 , HIS A:352 , HOH A:5040 , HOH A:5337 , GLN B:1412 , LYS B:1425 , TYR B:1429
BINDING SITE FOR RESIDUE NAD A 432
2
AC2
SOFTWARE
GLN A:412 , LYS A:425 , TYR A:429 , ASP B:1189 , ASN B:1190 , GLY B:1219 , GLY B:1221 , ASP B:1222 , VAL B:1223 , THR B:1241 , GLU B:1242 , ILE B:1243 , ASP B:1244 , ASN B:1247 , THR B:1274 , THR B:1275 , GLY B:1276 , ILE B:1280 , ILE B:1298 , GLY B:1299 , HIS B:1300 , LEU B:1343 , ASN B:1345 , HIS B:1352 , HOH B:5125 , HOH B:5145
BINDING SITE FOR RESIDUE NAD B 1432
3
AC3
SOFTWARE
ASP C:2189 , ASN C:2190 , GLY C:2219 , GLY C:2221 , ASP C:2222 , VAL C:2223 , THR C:2241 , GLU C:2242 , ILE C:2243 , ASP C:2244 , ASN C:2247 , THR C:2274 , THR C:2275 , GLY C:2276 , ILE C:2280 , ILE C:2298 , GLY C:2299 , HIS C:2300 , LEU C:2343 , ASN C:2345 , HIS C:2352 , HOH C:5041 , GLN D:3412 , LYS D:3425 , TYR D:3429
BINDING SITE FOR RESIDUE NAD C 2432
4
AC4
SOFTWARE
GLN C:2412 , LYS C:2425 , TYR C:2429 , ASP D:3189 , ASN D:3190 , GLY D:3219 , GLY D:3221 , ASP D:3222 , VAL D:3223 , THR D:3241 , GLU D:3242 , ILE D:3243 , ASP D:3244 , ASN D:3247 , THR D:3274 , THR D:3275 , GLY D:3276 , ILE D:3280 , ILE D:3298 , GLY D:3299 , HIS D:3300 , LEU D:3343 , ASN D:3345 , HIS D:3352 , HOH D:5216
BINDING SITE FOR RESIDUE NAD D 3432
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ADOHCYASE_1 (A:77-91,B:1077-1091,C:2077-2091,D:...)
2: ADOHCYASE_2 (A:212-228,B:1212-1228,C:2212-2228,...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADOHCYASE_1
PS00738
S-adenosyl-L-homocysteine hydrolase signature 1.
SAHH_RAT
78-92
4
A:77-91
B:1077-1091
C:2077-2091
D:3077-3091
2
ADOHCYASE_2
PS00739
S-adenosyl-L-homocysteine hydrolase signature 2.
SAHH_RAT
213-229
4
A:212-228
B:1212-1228
C:2212-2228
D:3212-3228
[
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Exons
(10, 40)
Info
All Exons
Exon 1.1 (A:4-9 | B:1004-1009 | C:2004-2009 ...)
Exon 1.2 (A:9-72 | B:1009-1072 | C:2009-2072...)
Exon 1.3 (A:73-98 | B:1073-1098 | C:2073-209...)
Exon 1.4 (A:98-148 | B:1098-1148 | C:2098-21...)
Exon 1.5 (A:148-185 | B:1148-1185 | C:2148-2...)
Exon 1.6 (A:186-255 | B:1186-1255 | C:2186-2...)
Exon 1.7 (A:255-284 | B:1255-1284 | C:2255-2...)
Exon 1.8 (A:284-323 | B:1284-1323 | C:2284-2...)
Exon 1.9 (A:324-388 | B:1324-1388 | C:2324-2...)
Exon 1.10 (A:389-431 | B:1389-1431 | C:2389-2...)
View:
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All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10
11: Boundary 1.10/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENSRNOT00000024310
1
ENSRNOE00000170864
chr3:
145560052-145560005
48
SAHH_RAT
1-10
10
4
A:4-9
B:1004-1009
C:2004-2009
D:3004-3009
6
6
6
6
1.2
ENSRNOT00000024310
2
ENSRNOE00000170967
chr3:
145553987-145553797
191
SAHH_RAT
10-73
64
4
A:9-72
B:1009-1072
C:2009-2072
D:3009-3072
64
64
64
64
1.3
ENSRNOT00000024310
3
ENSRNOE00000294915
chr3:
145552338-145552263
76
SAHH_RAT
74-99
26
4
A:73-98
B:1073-1098
C:2073-2098
D:3073-3098
26
26
26
26
1.4
ENSRNOT00000024310
4
ENSRNOE00000171132
chr3:
145550643-145550494
150
SAHH_RAT
99-149
51
4
A:98-148
B:1098-1148
C:2098-2148
D:3098-3148
51
51
51
51
1.5
ENSRNOT00000024310
5
ENSRNOE00000323260
chr3:
145549883-145549771
113
SAHH_RAT
149-186
38
4
A:148-185
B:1148-1185
C:2148-2185
D:3148-3185
38
38
38
38
1.6
ENSRNOT00000024310
6
ENSRNOE00000171339
chr3:
145549377-145549170
208
SAHH_RAT
187-256
70
4
A:186-255
B:1186-1255
C:2186-2255
D:3186-3255
70
70
70
70
1.7
ENSRNOT00000024310
7
ENSRNOE00000171520
chr3:
145549090-145549003
88
SAHH_RAT
256-285
30
4
A:255-284
B:1255-1284
C:2255-2284
D:3255-3284
30
30
30
30
1.8
ENSRNOT00000024310
8
ENSRNOE00000171706
chr3:
145548909-145548792
118
SAHH_RAT
285-324
40
4
A:284-323
B:1284-1323
C:2284-2323
D:3284-3323
40
40
40
40
1.9
ENSRNOT00000024310
9
ENSRNOE00000171914
chr3:
145547384-145547190
195
SAHH_RAT
325-389
65
4
A:324-388
B:1324-1388
C:2324-2388
D:3324-3388
65
65
65
65
1.10
ENSRNOT00000024310
10
ENSRNOE00000172116
chr3:
145545669-145544834
836
SAHH_RAT
390-432
43
4
A:389-431
B:1389-1431
C:2389-2431
D:3389-3431
43
43
43
43
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1ky4a2 (A:4-189,A:353-431)
1b: SCOP_d1ky4b2 (B:1004-1189,B:1353-1431)
1c: SCOP_d1ky4c2 (C:2004-2189,C:2353-2431)
1d: SCOP_d1ky4d2 (D:3004-3189,D:3353-3431)
2a: SCOP_d1ky4a1 (A:190-352)
2b: SCOP_d1ky4b1 (B:1190-1352)
2c: SCOP_d1ky4c1 (C:2190-2352)
2d: SCOP_d1ky4d1 (D:3190-3352)
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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
:
Flavodoxin-like
(1057)
Superfamily
:
Formate/glycerate dehydrogenase catalytic domain-like
(49)
Family
:
S-adenosylhomocystein hydrolase
(10)
Protein domain
:
S-adenosylhomocystein hydrolase
(10)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(7)
1a
d1ky4a2
A:4-189,A:353-431
1b
d1ky4b2
B:1004-1189,B:1353-1431
1c
d1ky4c2
C:2004-2189,C:2353-2431
1d
d1ky4d2
D:3004-3189,D:3353-3431
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Formate/glycerate dehydrogenases, NAD-domain
(49)
Protein domain
:
S-adenosylhomocystein hydrolase
(10)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(7)
2a
d1ky4a1
A:190-352
2b
d1ky4b1
B:1190-1352
2c
d1ky4c1
C:2190-2352
2d
d1ky4d1
D:3190-3352
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1ky4A01 (A:4-191,A:352-403)
1b: CATH_1ky4B01 (B:1004-1191,B:1352-1403)
1c: CATH_1ky4C01 (C:2004-2191,C:2352-2403)
1d: CATH_1ky4D01 (D:3004-3191,D:3352-3403)
2a: CATH_1ky4A02 (A:192-351)
2b: CATH_1ky4B02 (B:1192-1351)
2c: CATH_1ky4C02 (C:2192-2351)
2d: CATH_1ky4D02 (D:3192-3351)
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(
)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1480, no name defined]
(11)
Norway rat (Rattus norvegicus)
(7)
1a
1ky4A01
A:4-191,A:352-403
1b
1ky4B01
B:1004-1191,B:1352-1403
1c
1ky4C01
C:2004-2191,C:2352-2403
1d
1ky4D01
D:3004-3191,D:3352-3403
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Norway rat (Rattus norvegicus)
(18)
2a
1ky4A02
A:192-351
2b
1ky4B02
B:1192-1351
2c
1ky4C02
C:2192-2351
2d
1ky4D02
D:3192-3351
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_AdoHcyase_1ky4D01 (D:3004-3430)
1b: PFAM_AdoHcyase_1ky4D02 (D:3004-3430)
1c: PFAM_AdoHcyase_1ky4D03 (D:3004-3430)
1d: PFAM_AdoHcyase_1ky4D04 (D:3004-3430)
2a: PFAM_AdoHcyase_NAD_1ky4D05 (D:3190-3351)
2b: PFAM_AdoHcyase_NAD_1ky4D06 (D:3190-3351)
2c: PFAM_AdoHcyase_NAD_1ky4D07 (D:3190-3351)
2d: PFAM_AdoHcyase_NAD_1ky4D08 (D:3190-3351)
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Organisms
(
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(
)
Clan
:
Form_Glyc_dh
(56)
Family
:
AdoHcyase
(11)
Rattus norvegicus (Rat)
(3)
1a
AdoHcyase-1ky4D01
D:3004-3430
1b
AdoHcyase-1ky4D02
D:3004-3430
1c
AdoHcyase-1ky4D03
D:3004-3430
1d
AdoHcyase-1ky4D04
D:3004-3430
Clan
:
NADP_Rossmann
(1239)
Family
:
AdoHcyase_NAD
(11)
Rattus norvegicus (Rat)
(3)
2a
AdoHcyase_NAD-1ky4D05
D:3190-3351
2b
AdoHcyase_NAD-1ky4D06
D:3190-3351
2c
AdoHcyase_NAD-1ky4D07
D:3190-3351
2d
AdoHcyase_NAD-1ky4D08
D:3190-3351
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Asym.Unit (274 KB)
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