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1N2X
Asym. Unit
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Asym.Unit (107 KB)
Biol.Unit 1 (55 KB)
Biol.Unit 2 (49 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF TM0872, A PUTATIVE SAM-DEPENDENT METHYLTRANSFERASE, COMPLEXED WITH SAM
Authors
:
D. J. Miller, W. F. Anderson, Midwest Center For Structural Genomics (Mcsg)
Date
:
24 Oct 02 (Deposition) - 28 Jan 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Sam-Dependent Methyltransferase Fold, Protein-Sam Methyl Donor Complex, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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Reference
:
D. J. Miller, N. Ouellette, E. Evdokimova, A. Savchenko, A. Edwards, W. F. Anderson
Crystal Complexes Of A Predicted S-Adenosylmethionine-Dependent Methyltransferase Reveal A Typical Adomet Binding Domain And A Substrate Recognition Domain
Protein Sci. V. 12 1432 2003
(for further references see the
PDB file header
)
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
2a: S-ADENOSYLMETHIONINE (SAMa)
2b: S-ADENOSYLMETHIONINE (SAMb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
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No.
Name
Count
Type
Full Name
1
MSE
8
Mod. Amino Acid
SELENOMETHIONINE
2
SAM
2
Ligand/Ion
S-ADENOSYLMETHIONINE
3
SO4
2
Ligand/Ion
SULFATE ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:199 , LYS A:200 , ARG A:201
BINDING SITE FOR RESIDUE SO4 A 500
2
AC2
SOFTWARE
ARG B:199 , LYS B:200 , ARG B:201 , HOH B:511 , HOH B:552 , HOH B:592
BINDING SITE FOR RESIDUE SO4 B 501
3
AC3
SOFTWARE
HIS A:8 , CYS A:31 , THR A:32 , VAL A:33 , GLY A:34 , GLU A:35 , GLY A:36 , GLY A:37 , HIS A:38 , ASP A:55 , VAL A:56 , SER A:81 , TYR A:82 , ASP A:103 , LEU A:104 , GLY A:105 , GLN A:110 , MSE A:130 , ASN A:221 , ARG A:282 , HOH A:520 , HOH A:529 , HOH A:567 , HOH A:705 , HOH A:708
BINDING SITE FOR RESIDUE SAM A 401
4
AC4
SOFTWARE
HIS B:8 , THR B:32 , VAL B:33 , GLY B:34 , GLU B:35 , GLY B:36 , GLY B:37 , HIS B:38 , ASP B:55 , VAL B:56 , VAL B:60 , VAL B:80 , SER B:81 , TYR B:82 , ASP B:103 , GLY B:105 , VAL B:106 , GLN B:110 , MSE B:130 , ASN B:221
BINDING SITE FOR RESIDUE SAM B 402
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SAPs(SNPs)/Variants
(0, 0)
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PROSITE Patterns/Profiles
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1n2xa1 (A:115-215)
1b: SCOP_d1n2xb1 (B:115-215)
2a: SCOP_d1n2xa2 (A:8-114,A:216-294)
2b: SCOP_d1n2xb2 (B:8-114,B:216-292)
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Protein Domains
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Organisms
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)
Class
:
All alpha proteins
(14657)
Fold
:
SAM domain-like
(639)
Superfamily
:
Putative methyltransferase TM0872, insert domain
(3)
Family
:
Putative methyltransferase TM0872, insert domain
(3)
Protein domain
:
Putative methyltransferase TM0872, insert domain
(3)
Thermotoga maritima [TaxId: 2336]
(2)
1a
d1n2xa1
A:115-215
1b
d1n2xb1
B:115-215
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Superfamily
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Family
:
MraW-like putative methyltransferases
(3)
Protein domain
:
TM0872, methyltransferase domain
(3)
Thermotoga maritima [TaxId: 2336]
(2)
2a
d1n2xa2
A:8-114,A:216-294
2b
d1n2xb2
B:8-114,B:216-292
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1n2xA01 (A:8-113,A:219-294)
1b: CATH_1n2xB01 (B:8-113,B:219-292)
2a: CATH_1n2xA02 (A:114-218)
2b: CATH_1n2xB02 (B:114-218)
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Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Vaccinia Virus protein VP39
(378)
Thermotoga maritima. Organism_taxid: 2336.
(5)
1a
1n2xA01
A:8-113,A:219-294
1b
1n2xB01
B:8-113,B:219-292
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
[code=1.10.150.170, no name defined]
(3)
Thermotoga maritima. Organism_taxid: 2336.
(2)
2a
1n2xA02
A:114-218
2b
1n2xB02
B:114-218
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Methyltransf_5_1n2xB01 (B:8-292)
1b: PFAM_Methyltransf_5_1n2xB02 (B:8-292)
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Clan
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NADP_Rossmann
(1239)
Family
:
Methyltransf_5
(3)
Thermotoga maritima
(2)
1a
Methyltransf_5-1n2xB01
B:8-292
1b
Methyltransf_5-1n2xB02
B:8-292
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Show PDB file:
Asym.Unit (107 KB)
Header - Asym.Unit
Biol.Unit 1 (55 KB)
Header - Biol.Unit 1
Biol.Unit 2 (49 KB)
Header - Biol.Unit 2
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