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1LT8
Asym. Unit
Info
Asym.Unit (124 KB)
Biol.Unit 1 (234 KB)
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(1)
Title
:
REDUCED HOMO SAPIENS BETAINE-HOMOCYSTEINE S-METHYLTRANSFERASE IN COMPLEX WITH S-(DELTA-CARBOXYBUTYL)-L-HOMOCYSTEINE
Authors
:
J. C. Evans, D. P. Huddler, J. Jiracek, C. Castro, N. S. Millian, T. A. Garrow, M. L. Ludwig
Date
:
20 May 02 (Deposition) - 11 Sep 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Transferase, Homocysteine Metabolism, Homocysteinemia, Zinc, Thiol Alkyl Transfer
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. C. Evans, D. P. Huddler, J. Jiracek, C. Castro, N. S. Millian, T. A. Garrow, M. L. Ludwig
Betaine-Homocysteine Methyltransferase: Zinc In A Distorted Barrel.
Structure V. 10 1159 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: S-(D-CARBOXYBUTYL)-L-HOMOCYSTEINE (CBHa)
1b: S-(D-CARBOXYBUTYL)-L-HOMOCYSTEINE (CBHb)
2a: CITRIC ACID (CITa)
2b: CITRIC ACID (CITb)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CBH
2
Ligand/Ion
S-(D-CARBOXYBUTYL)-L-HOMOCYSTEINE
2
CIT
2
Ligand/Ion
CITRIC ACID
3
ZN
2
Ligand/Ion
ZINC ION
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:217 , CYS A:299 , CYS A:300 , CBH A:601
BINDING SITE FOR RESIDUE ZN A 501
2
AC2
SOFTWARE
CYS B:217 , CYS B:299 , CYS B:300 , CBH B:602
BINDING SITE FOR RESIDUE ZN B 502
3
AC3
SOFTWARE
GLY A:27 , GLY A:28 , PHE A:29 , VAL A:30 , TRP A:44 , PHE A:76 , TYR A:77 , GLU A:159 , TYR A:160 , ILE A:262 , PHE A:267 , CYS A:299 , CYS A:300 , ZN A:501 , HOH A:708 , HOH A:788 , HOH A:858 , HOH A:862 , HIS B:338
BINDING SITE FOR RESIDUE CBH A 601
4
AC4
SOFTWARE
HIS A:338 , GLY B:27 , GLY B:28 , PHE B:29 , VAL B:30 , TRP B:44 , GLN B:72 , PHE B:76 , TYR B:77 , GLU B:159 , TYR B:160 , PHE B:267 , CYS B:299 , CYS B:300 , ZN B:502 , HOH B:714 , HOH B:871 , HOH B:878
BINDING SITE FOR RESIDUE CBH B 602
5
AC5
SOFTWARE
ASP A:220 , HIS A:252 , ARG A:356 , GLY B:360 , PRO B:362 , TYR B:363 , LYS B:369 , HOH B:710
BINDING SITE FOR RESIDUE CIT A 701
6
AC6
SOFTWARE
GLY A:360 , PRO A:362 , TYR A:363 , LYS A:369 , HOH A:706 , ASP B:220 , HIS B:252 , ARG B:356 , HOH B:828
BINDING SITE FOR RESIDUE CIT B 702
[
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]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_061345 (G199S, chain A/B, )
2: VAR_015886 (Q239Q, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_061345
G
199
S
BHMT1_HUMAN
Polymorphism
59866108
A/B
G
199
S
2
UniProt
VAR_015886
R
239
Q
BHMT1_HUMAN
Polymorphism
3733890
A/B
Q
239
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: HCY (A:11-314,B:11-314)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HCY
PS50970
Homocysteine-binding domain profile.
BHMT1_HUMAN
11-314
2
A:11-314
B:11-314
[
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]
Exons
(8, 16)
Info
All Exons
Exon 1.1a (A:11-11 | B:11-11)
Exon 1.2b (A:12-56 | B:12-56)
Exon 1.3a (A:56-82 | B:56-79)
Exon 1.4a (A:96-159 | B:101-159)
Exon 1.5a (A:160-209 | B:160-209)
Exon 1.6a (A:209-270 | B:209-270)
Exon 1.7b (A:270-346 | B:270-346)
Exon 1.8c (A:346-371 | B:346-371)
View:
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All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2b
3: Boundary 1.2b/1.3a
4: Boundary 1.3a/1.4a
5: Boundary 1.4a/1.5a
6: Boundary 1.5a/1.6a
7: Boundary 1.6a/1.7b
8: Boundary 1.7b/1.8c
9: Boundary 1.8c/-
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
1.1a
ENST00000274353
1a
ENSE00001879035
chr5:
78407602-78407741
140
BHMT1_HUMAN
1-11
11
2
A:11-11
B:11-11
1
1
1.2b
ENST00000274353
2b
ENSE00000971690
chr5:
78411590-78411722
133
BHMT1_HUMAN
12-56
45
2
A:12-56
B:12-56
45
45
1.3a
ENST00000274353
3a
ENSE00000971691
chr5:
78415082-78415200
119
BHMT1_HUMAN
56-95
40
2
A:56-82
B:56-79
27
24
1.4a
ENST00000274353
4a
ENSE00000971692
chr5:
78416173-78416364
192
BHMT1_HUMAN
96-159
64
2
A:96-159
B:101-159
64
59
1.5a
ENST00000274353
5a
ENSE00000971693
chr5:
78417041-78417188
148
BHMT1_HUMAN
160-209
50
2
A:160-209
B:160-209
50
50
1.6a
ENST00000274353
6a
ENSE00000971694
chr5:
78421869-78422051
183
BHMT1_HUMAN
209-270
62
2
A:209-270
B:209-270
62
62
1.7b
ENST00000274353
7b
ENSE00001787224
chr5:
78423578-78423806
229
BHMT1_HUMAN
270-346
77
2
A:270-346
B:270-346
77
77
1.8c
ENST00000274353
8c
ENSE00001953069
chr5:
78426756-78428108
1353
BHMT1_HUMAN
346-406
61
2
A:346-371
B:346-371
26
26
[
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]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1lt8a_ (A:)
1b: SCOP_d1lt8b_ (B:)
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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
:
Homocysteine S-methyltransferase
(11)
Family
:
Homocysteine S-methyltransferase
(11)
Protein domain
:
Betaine-homocysteine S-methyltransferase
(3)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1lt8a_
A:
1b
d1lt8b_
B:
[
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]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1lt8B00 (B:11-371)
1b: CATH_1lt8A00 (A:11-371)
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(
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
[code=3.20.20.330, no name defined]
(11)
Human (Homo sapiens)
(2)
1a
1lt8B00
B:11-371
1b
1lt8A00
A:11-371
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_S_methyl_trans_1lt8B01 (B:17-316)
1b: PFAM_S_methyl_trans_1lt8B02 (B:17-316)
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(
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Organisms
(
)
(
)
Clan
:
no clan defined [family: S-methyl_trans]
(7)
Family
:
S-methyl_trans
(7)
Homo sapiens (Human)
(2)
1a
S-methyl_trans-1lt8B01
B:17-316
1b
S-methyl_trans-1lt8B02
B:17-316
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