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1S4D
Biol. Unit 4
Info
Asym.Unit (485 KB)
Biol.Unit 1 (87 KB)
Biol.Unit 2 (86 KB)
Biol.Unit 3 (85 KB)
Biol.Unit 4 (88 KB)
Biol.Unit 5 (85 KB)
Biol.Unit 6 (82 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF THE S-ADENOSYL-L-METHIONINE DEPENDENT UROPORPHYRINOGEN-III C-METHYLTRANSFERASE SUMT
Authors
:
J. Vevodova, R. M. Graham, E. Raux, H. L. Schubert, D. I. Roper, A. A. Brin A. I. Scott, C. A. Roessner, N. P. J. Stamford, M. E. Stroupe, E. D. Getzo M. J. Warren, K. S. Wilson
Date
:
16 Jan 04 (Deposition) - 30 Nov 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,D,E,F,G,H,I,J,K,L,M
Biol. Unit 1: A,B (1x)
Biol. Unit 2: D,E (1x)
Biol. Unit 3: F,G (1x)
Biol. Unit 4: H,I (1x)
Biol. Unit 5: J,K (1x)
Biol. Unit 6: L,M (1x)
Keywords
:
Tetrapyrrole Biosynthesis, Cobalamin, Sam, Sah, Uroporphyrinogen-Iii Methyltransferase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Vevodova, R. M. Graham, E. Raux, H. L. Schubert, D. I. Roper, A. A. Brindley, A. I. Scott, C. A. Roessner, N. P. J. Stamford, M. E. Stroupe, E. D. Getzoff, M. J. Warren, K. S. Wilson
Structure/Function Studies On A S-Adenosyl-L-Methionine-Dependent Uroporphyrinogen Iii C Methyltransferase (Sumt), A Key Regulatory Enzyme Of Tetrapyrrole Biosynthesis
J. Mol. Biol. V. 344 419 2004
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
1l: GLYCEROL (GOLl)
1m: GLYCEROL (GOLm)
1n: GLYCEROL (GOLn)
1o: GLYCEROL (GOLo)
1p: GLYCEROL (GOLp)
1q: GLYCEROL (GOLq)
1r: GLYCEROL (GOLr)
1s: GLYCEROL (GOLs)
1t: GLYCEROL (GOLt)
1u: GLYCEROL (GOLu)
1v: GLYCEROL (GOLv)
1w: GLYCEROL (GOLw)
1x: GLYCEROL (GOLx)
1y: GLYCEROL (GOLy)
1z: GLYCEROL (GOLz)
2a: S-ADENOSYL-L-HOMOCYSTEINE (SAHa)
2b: S-ADENOSYL-L-HOMOCYSTEINE (SAHb)
2c: S-ADENOSYL-L-HOMOCYSTEINE (SAHc)
2d: S-ADENOSYL-L-HOMOCYSTEINE (SAHd)
2e: S-ADENOSYL-L-HOMOCYSTEINE (SAHe)
2f: S-ADENOSYL-L-HOMOCYSTEINE (SAHf)
2g: S-ADENOSYL-L-HOMOCYSTEINE (SAHg)
2h: S-ADENOSYL-L-HOMOCYSTEINE (SAHh)
2i: S-ADENOSYL-L-HOMOCYSTEINE (SAHi)
2j: S-ADENOSYL-L-HOMOCYSTEINE (SAHj)
2k: S-ADENOSYL-L-HOMOCYSTEINE (SAHk)
2l: S-ADENOSYL-L-HOMOCYSTEINE (SAHl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
SAH
2
Ligand/Ion
S-ADENOSYL-L-HOMOCYSTEINE
[
close Hetero Component info
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Sites
(6, 6)
Info
All Sites
1: AC7 (SOFTWARE)
2: AC8 (SOFTWARE)
3: CC9 (SOFTWARE)
4: DC1 (SOFTWARE)
5: DC2 (SOFTWARE)
6: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC7
SOFTWARE
PRO H:24 , GLY H:100 , GLY H:101 , ASP H:102 , VAL H:105 , PHE H:106 , THR H:130 , ALA H:131 , TYR H:183 , MET H:184 , VAL H:210 , ASN H:212 , ALA H:213 , PRO H:240 , ALA H:241 , ILE H:242 , HOH H:4503 , HOH H:4524
BINDING SITE FOR RESIDUE SAH H 4501
2
AC8
SOFTWARE
PRO I:24 , LEU I:49 , GLY I:100 , GLY I:101 , ASP I:102 , VAL I:105 , PHE I:106 , THR I:130 , ALA I:131 , TYR I:183 , MET I:184 , VAL I:210 , ASN I:212 , ALA I:213 , ALA I:241 , ILE I:242
BINDING SITE FOR RESIDUE SAH I 4511
3
CC9
SOFTWARE
ASP H:102 , PRO H:127 , GLY H:128 , THR H:130 , GLY I:128 , ILE I:129 , THR I:130 , ILE I:133 , GLY I:134 , HOH I:4541
BINDING SITE FOR RESIDUE GOL I 4002
4
DC1
SOFTWARE
MET H:184 , ALA H:185 , MET H:186 , LYS H:187
BINDING SITE FOR RESIDUE GOL H 4003
5
DC2
SOFTWARE
HIS I:158 , MET I:184 , ALA I:185 , MET I:186 , LYS I:187
BINDING SITE FOR RESIDUE GOL I 4011
6
DC3
SOFTWARE
THR H:144 , HIS H:145 , ARG H:146 , PHE I:106 , ARG I:108 , GLY I:110 , GLU I:111
BINDING SITE FOR RESIDUE GOL H 4012
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: SUMT_1 (H:20-34,I:20-34)
2: SUMT_2 (H:95-128,I:95-128)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SUMT_1
PS00839
Uroporphyrin-III C-methyltransferase signature 1.
SUMT_PSEDE
20-34
2
-
-
-
-
-
-
H:20-34
I:20-34
-
-
-
-
2
SUMT_2
PS00840
Uroporphyrin-III C-methyltransferase signature 2.
SUMT_PSEDE
95-128
2
-
-
-
-
-
-
H:95-128
I:95-128
-
-
-
-
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
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
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1s4da_ (A:)
1b: SCOP_d1s4db_ (B:)
1c: SCOP_d1s4dl_ (L:)
1d: SCOP_d1s4dm_ (M:)
1e: SCOP_d1s4dd_ (D:)
1f: SCOP_d1s4de_ (E:)
1g: SCOP_d1s4df_ (F:)
1h: SCOP_d1s4dg_ (G:)
1i: SCOP_d1s4dh_ (H:)
1j: SCOP_d1s4di_ (I:)
1k: SCOP_d1s4dj_ (J:)
1l: SCOP_d1s4dk_ (K:)
View:
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)
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)
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(
)
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(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Tetrapyrrole methylase
(104)
Superfamily
:
Tetrapyrrole methylase
(104)
Family
:
Tetrapyrrole methylase
(96)
Protein domain
:
Uroporphyrin-III C-methyltransferase (SUMT, UROM, CobA)
(2)
Pseudomonas denitrificans [TaxId: 43306]
(1)
1a
d1s4da_
A:
1b
d1s4db_
B:
1c
d1s4dl_
L:
1d
d1s4dm_
M:
1e
d1s4dd_
D:
1f
d1s4de_
E:
1g
d1s4df_
F:
1h
d1s4dg_
G:
1i
d1s4dh_
H:
1j
d1s4di_
I:
1k
d1s4dj_
J:
1l
d1s4dk_
K:
[
close SCOP info
]
CATH Domains
(2, 24)
Info
all CATH domains
1a: CATH_1s4dE02 (E:130-270)
1b: CATH_1s4dI02 (I:130-269)
1c: CATH_1s4dL02 (L:131-260)
1d: CATH_1s4dJ02 (J:131-268)
1e: CATH_1s4dB02 (B:130-267)
1f: CATH_1s4dG02 (G:130-267)
1g: CATH_1s4dH02 (H:130-271)
1h: CATH_1s4dA02 (A:130-270)
1i: CATH_1s4dF02 (F:130-269)
1j: CATH_1s4dK02 (K:130-263)
1k: CATH_1s4dM02 (M:130-269)
1l: CATH_1s4dD02 (D:131-263)
2a: CATH_1s4dD01 (D:7-130)
2b: CATH_1s4dM01 (M:10-129)
2c: CATH_1s4dB01 (B:4-129)
2d: CATH_1s4dE01 (E:4-129)
2e: CATH_1s4dF01 (F:7-129)
2f: CATH_1s4dJ01 (J:6-130)
2g: CATH_1s4dA01 (A:6-129)
2h: CATH_1s4dG01 (G:8-129)
2i: CATH_1s4dL01 (L:7-130)
2j: CATH_1s4dH01 (H:6-129)
2k: CATH_1s4dK01 (K:5-129)
2l: CATH_1s4dI01 (I:4-129)
View:
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(
)
(
)
Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
(97)
Homologous Superfamily
:
Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
(97)
Pseudomonas denitrificans. Organism_taxid: 43306.
(1)
1a
1s4dE02
E:130-270
1b
1s4dI02
I:130-269
1c
1s4dL02
L:131-260
1d
1s4dJ02
J:131-268
1e
1s4dB02
B:130-267
1f
1s4dG02
G:130-267
1g
1s4dH02
H:130-271
1h
1s4dA02
A:130-270
1i
1s4dF02
F:130-269
1j
1s4dK02
K:130-263
1k
1s4dM02
M:130-269
1l
1s4dD02
D:131-263
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Cobalt-precorrin-4 Transmethylase; domain 1
(96)
Homologous Superfamily
:
Cobalt-precorrin-4 Transmethylase; Domain 1
(96)
Pseudomonas denitrificans. Organism_taxid: 43306.
(1)
2a
1s4dD01
D:7-130
2b
1s4dM01
M:10-129
2c
1s4dB01
B:4-129
2d
1s4dE01
E:4-129
2e
1s4dF01
F:7-129
2f
1s4dJ01
J:6-130
2g
1s4dA01
A:6-129
2h
1s4dG01
G:8-129
2i
1s4dL01
L:7-130
2j
1s4dH01
H:6-129
2k
1s4dK01
K:5-129
2l
1s4dI01
I:4-129
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_TP_methylase_1s4dM01 (M:16-229)
1b: PFAM_TP_methylase_1s4dM02 (M:16-229)
1c: PFAM_TP_methylase_1s4dM03 (M:16-229)
1d: PFAM_TP_methylase_1s4dM04 (M:16-229)
1e: PFAM_TP_methylase_1s4dM05 (M:16-229)
1f: PFAM_TP_methylase_1s4dM06 (M:16-229)
1g: PFAM_TP_methylase_1s4dM07 (M:16-229)
1h: PFAM_TP_methylase_1s4dM08 (M:16-229)
1i: PFAM_TP_methylase_1s4dM09 (M:16-229)
1j: PFAM_TP_methylase_1s4dM10 (M:16-229)
1k: PFAM_TP_methylase_1s4dM11 (M:16-229)
1l: PFAM_TP_methylase_1s4dM12 (M:16-229)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: TP_methylase]
(35)
Family
:
TP_methylase
(35)
Pseudomonas denitrificans
(1)
1a
TP_methylase-1s4dM01
M:16-229
1b
TP_methylase-1s4dM02
M:16-229
1c
TP_methylase-1s4dM03
M:16-229
1d
TP_methylase-1s4dM04
M:16-229
1e
TP_methylase-1s4dM05
M:16-229
1f
TP_methylase-1s4dM06
M:16-229
1g
TP_methylase-1s4dM07
M:16-229
1h
TP_methylase-1s4dM08
M:16-229
1i
TP_methylase-1s4dM09
M:16-229
1j
TP_methylase-1s4dM10
M:16-229
1k
TP_methylase-1s4dM11
M:16-229
1l
TP_methylase-1s4dM12
M:16-229
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Asym.Unit (485 KB)
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