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1D4F
Asym. Unit
Info
Asym.Unit (288 KB)
Biol.Unit 1 (279 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSYLHOMOCYSTEINE HYDROLASE
Authors
:
J. Komoto, Y. Huang, F. Takusagawa, T. Gomi, H. Ogawa, Y. Takata, M. Fujioka
Date
:
22 Jun 00 (Deposition) - 17 Jan 01 (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
:
S-Adenosylhomocysteine Hydrolase, Adohcyase, Adohcy, Mutagenesis, X-Ray Crystal Structure, Enzyme Structure
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Komoto, Y. Huang, T. Gomi, H. Ogawa, Y. Takata, M. Fujioka, F. Takusagawa
Effects Of Site-Directed Mutagenesis On Structure And Function Of Recombinant Rat Liver S-Adenosylhomocysteine Hydrolase. Crystal Structure Of D244E Mutant Enzyme.
J. Biol. Chem. V. 275 32147 2000
(for further references see the
PDB file header
)
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: ADENOSINE (ADNa)
1b: ADENOSINE (ADNb)
1c: ADENOSINE (ADNc)
1d: ADENOSINE (ADNd)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
2d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
ADN
4
Ligand/Ion
ADENOSINE
2
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:156 , THR A:157 , THR A:158 , ASN A:190 , GLY A:219 , GLY A:221 , ASP A:222 , VAL A:223 , GLU A:242 , ILE A:243 , ASN A:247 , THR A:275 , CYS A:277 , ILE A:280 , ILE A:298 , HIS A:300 , LEU A:343 , ASN A:345 , HIS A:352 , ADN A:601 , LEU B:408 , GLN B:412 , TYR B:429
BINDING SITE FOR RESIDUE NAD A 501
2
AC2
SOFTWARE
HIS A:54 , THR A:56 , GLU A:58 , THR A:59 , ASP A:130 , GLU A:155 , THR A:156 , LYS A:185 , ASP A:189 , HIS A:300 , LEU A:343 , LEU A:346 , MET A:350 , GLY A:351 , HIS A:352 , MET A:357 , PHE A:361 , NAD A:501
BINDING SITE FOR RESIDUE ADN A 601
3
AC3
SOFTWARE
LEU A:408 , GLN A:412 , TYR A:429 , THR B:156 , THR B:157 , THR B:158 , ASN B:190 , GLY B:219 , ASP B:222 , VAL B:223 , THR B:241 , GLU B:242 , ILE B:243 , ASN B:247 , THR B:275 , CYS B:277 , ILE B:280 , ILE B:298 , HIS B:300 , LEU B:343 , ASN B:345 , HIS B:352 , ADN B:602
BINDING SITE FOR RESIDUE NAD B 502
4
AC4
SOFTWARE
LEU B:53 , HIS B:54 , THR B:56 , GLU B:58 , THR B:59 , ASP B:130 , GLU B:155 , THR B:156 , LYS B:185 , ASP B:189 , HIS B:300 , LEU B:343 , MET B:350 , HIS B:352 , MET B:357 , PHE B:361 , NAD B:502
BINDING SITE FOR RESIDUE ADN B 602
5
AC5
SOFTWARE
THR C:156 , THR C:157 , THR C:158 , ASN C:190 , ASP C:222 , VAL C:223 , GLU C:242 , ILE C:243 , GLU C:244 , ASN C:247 , THR C:274 , THR C:275 , CYS C:277 , ILE C:280 , ILE C:298 , HIS C:300 , LEU C:343 , ASN C:345 , HIS C:352 , ADN C:603 , LEU D:408 , GLN D:412 , TYR D:429
BINDING SITE FOR RESIDUE NAD C 503
6
AC6
SOFTWARE
LEU C:53 , HIS C:54 , THR C:56 , GLU C:58 , ASP C:130 , GLU C:155 , THR C:156 , LYS C:185 , ASP C:189 , HIS C:300 , HIS C:352 , MET C:357 , PHE C:361 , NAD C:503
BINDING SITE FOR RESIDUE ADN C 603
7
AC7
SOFTWARE
LEU C:408 , GLN C:412 , TYR C:429 , THR D:156 , THR D:157 , THR D:158 , ASN D:190 , ASP D:222 , VAL D:223 , GLU D:242 , ILE D:243 , GLU D:244 , ASN D:247 , THR D:275 , CYS D:277 , ILE D:280 , ILE D:298 , HIS D:300 , ASN D:345 , HIS D:352 , ADN D:604 , HOH D:671
BINDING SITE FOR RESIDUE NAD D 504
8
AC8
SOFTWARE
HIS D:54 , THR D:56 , GLU D:58 , THR D:59 , ASP D:130 , GLU D:155 , THR D:156 , LYS D:185 , ASP D:189 , HIS D:300 , LEU D:343 , HIS D:352 , MET D:357 , NAD D:504
BINDING SITE FOR RESIDUE ADN D 604
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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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:77-91,C:77-91,D:77-91)
2: ADOHCYASE_2 (A:212-228,B:212-228,C:212-228,D:21...)
;
View:
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Label:
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:77-91
C:77-91
D:77-91
2
ADOHCYASE_2
PS00739
S-adenosyl-L-homocysteine hydrolase signature 2.
SAHH_RAT
213-229
4
A:212-228
B:212-228
C:212-228
D:212-228
[
close PROSITE info
]
Exons
(10, 40)
Info
All Exons
Exon 1.1 (A:2-9 | B:2-9 | C:2-9 | D:2-9)
Exon 1.2 (A:9-72 | B:9-72 | C:9-72 | D:9-72)
Exon 1.3 (A:73-98 | B:73-98 | C:73-98 | D:73...)
Exon 1.4 (A:98-148 | B:98-148 | C:98-148 | D...)
Exon 1.5 (A:148-185 | B:148-185 | C:148-185 ...)
Exon 1.6 (A:186-255 | B:186-255 | C:186-255 ...)
Exon 1.7 (A:255-284 | B:255-284 | C:255-284 ...)
Exon 1.8 (A:284-323 | B:284-323 | C:284-323 ...)
Exon 1.9 (A:324-388 | B:324-388 | C:324-388 ...)
Exon 1.10 (A:389-431 | B:389-431 | C:389-431 ...)
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:
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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:2-9
B:2-9
C:2-9
D:2-9
8
8
8
8
1.2
ENSRNOT00000024310
2
ENSRNOE00000170967
chr3:
145553987-145553797
191
SAHH_RAT
10-73
64
4
A:9-72
B:9-72
C:9-72
D:9-72
64
64
64
64
1.3
ENSRNOT00000024310
3
ENSRNOE00000294915
chr3:
145552338-145552263
76
SAHH_RAT
74-99
26
4
A:73-98
B:73-98
C:73-98
D:73-98
26
26
26
26
1.4
ENSRNOT00000024310
4
ENSRNOE00000171132
chr3:
145550643-145550494
150
SAHH_RAT
99-149
51
4
A:98-148
B:98-148
C:98-148
D:98-148
51
51
51
51
1.5
ENSRNOT00000024310
5
ENSRNOE00000323260
chr3:
145549883-145549771
113
SAHH_RAT
149-186
38
4
A:148-185
B:148-185
C:148-185
D:148-185
38
38
38
38
1.6
ENSRNOT00000024310
6
ENSRNOE00000171339
chr3:
145549377-145549170
208
SAHH_RAT
187-256
70
4
A:186-255
B:186-255
C:186-255
D:186-255
70
70
70
70
1.7
ENSRNOT00000024310
7
ENSRNOE00000171520
chr3:
145549090-145549003
88
SAHH_RAT
256-285
30
4
A:255-284
B:255-284
C:255-284
D:255-284
30
30
30
30
1.8
ENSRNOT00000024310
8
ENSRNOE00000171706
chr3:
145548909-145548792
118
SAHH_RAT
285-324
40
4
A:284-323
B:284-323
C:284-323
D:284-323
40
40
40
40
1.9
ENSRNOT00000024310
9
ENSRNOE00000171914
chr3:
145547384-145547190
195
SAHH_RAT
325-389
65
4
A:324-388
B:324-388
C:324-388
D:324-388
65
65
65
65
1.10
ENSRNOT00000024310
10
ENSRNOE00000172116
chr3:
145545669-145544834
836
SAHH_RAT
390-432
43
4
A:389-431
B:389-431
C:389-431
D:389-431
43
43
43
43
[
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]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1d4fa2 (A:2-189,A:353-431)
1b: SCOP_d1d4fb2 (B:2-189,B:353-431)
1c: SCOP_d1d4fc2 (C:2-189,C:353-431)
1d: SCOP_d1d4fd2 (D:2-189,D:353-431)
2a: SCOP_d1d4fa1 (A:190-352)
2b: SCOP_d1d4fb1 (B:190-352)
2c: SCOP_d1d4fc1 (C:190-352)
2d: SCOP_d1d4fd1 (D:190-352)
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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
d1d4fa2
A:2-189,A:353-431
1b
d1d4fb2
B:2-189,B:353-431
1c
d1d4fc2
C:2-189,C:353-431
1d
d1d4fd2
D:2-189,D:353-431
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
d1d4fa1
A:190-352
2b
d1d4fb1
B:190-352
2c
d1d4fc1
C:190-352
2d
d1d4fd1
D:190-352
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1d4fA01 (A:2-191,A:352-403)
1b: CATH_1d4fB01 (B:2-191,B:352-403)
1c: CATH_1d4fC01 (C:2-191,C:352-403)
1d: CATH_1d4fD01 (D:2-191,D:352-403)
2a: CATH_1d4fA02 (A:192-351)
2b: CATH_1d4fB02 (B:192-351)
2c: CATH_1d4fC02 (C:192-351)
2d: CATH_1d4fD02 (D:192-351)
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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
1d4fA01
A:2-191,A:352-403
1b
1d4fB01
B:2-191,B:352-403
1c
1d4fC01
C:2-191,C:352-403
1d
1d4fD01
D:2-191,D:352-403
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Norway rat (Rattus norvegicus)
(18)
2a
1d4fA02
A:192-351
2b
1d4fB02
B:192-351
2c
1d4fC02
C:192-351
2d
1d4fD02
D:192-351
[
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Pfam Domains
(0, 0)
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all PFAM domains
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