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1RG9
Asym. Unit
Info
Asym.Unit (247 KB)
Biol.Unit 1 (240 KB)
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(1)
Title
:
S-ADENOSYLMETHIONINE SYNTHETASE COMPLEXED WITH SAM AND PPNP
Authors
:
J. Komoto, T. Yamada, Y. Takata, G. D. Markham, F. Takusagawa
Date
:
11 Nov 03 (Deposition) - 02 Mar 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
S-Adenosylmethionine Synthetase; Methionine Adenosyltransferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Komoto, T. Yamada, Y. Takata, G. D. Markham, F. Takusagawa
Crystal Structure Of The S-Adenosylmethionine Synthetase Ternary Complex: A Novel Catalytic Mechanism Of S-Adenosylmethionine Synthesis From Atp And Met.
Biochemistry V. 43 1821 2004
(for further references see the
PDB file header
)
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Hetero Components
(4, 20)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
3a: (DIPHOSPHONO)AMINOPHOSPHONIC ACID (PPKa)
3b: (DIPHOSPHONO)AMINOPHOSPHONIC ACID (PPKb)
3c: (DIPHOSPHONO)AMINOPHOSPHONIC ACID (PPKc)
3d: (DIPHOSPHONO)AMINOPHOSPHONIC ACID (PPKd)
4a: S-ADENOSYLMETHIONINE (SAMa)
4b: S-ADENOSYLMETHIONINE (SAMb)
4c: S-ADENOSYLMETHIONINE (SAMc)
4d: S-ADENOSYLMETHIONINE (SAMd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
4
Ligand/Ion
POTASSIUM ION
2
MG
8
Ligand/Ion
MAGNESIUM ION
3
PPK
4
Ligand/Ion
(DIPHOSPHONO)AMINOPHOSPHONIC ACID
4
SAM
4
Ligand/Ion
S-ADENOSYLMETHIONINE
[
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Sites
(20, 20)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:238 , CYS A:239 , PPK A:384 , GLU B:42
BINDING SITE FOR RESIDUE K A 386
02
AC2
SOFTWARE
GLU A:8 , LYS A:165 , PPK A:384
BINDING SITE FOR RESIDUE MG A 387
03
AC3
SOFTWARE
ASP A:16 , PPK A:384
BINDING SITE FOR RESIDUE MG A 388
04
AC4
SOFTWARE
GLU A:42 , ASP B:238 , CYS B:239 , PPK B:484
BINDING SITE FOR RESIDUE K B 486
05
AC5
SOFTWARE
GLU B:8 , LYS B:165 , PPK B:484
BINDING SITE FOR RESIDUE MG B 487
06
AC6
SOFTWARE
ASP B:16 , PPK B:484
BINDING SITE FOR RESIDUE MG B 488
07
AC7
SOFTWARE
ASP C:238 , CYS C:239 , PPK C:584 , GLU D:42
BINDING SITE FOR RESIDUE K C 586
08
AC8
SOFTWARE
LYS C:165 , PPK C:584 , ASP D:118 , ASP D:271
BINDING SITE FOR RESIDUE MG D 587
09
AC9
SOFTWARE
ASP C:16 , PPK C:584
BINDING SITE FOR RESIDUE MG C 588
10
BC1
SOFTWARE
GLU C:42 , ASP D:238 , CYS D:239 , PPK D:684
BINDING SITE FOR RESIDUE K D 686
11
BC2
SOFTWARE
ASP C:271 , LYS D:165 , PPK D:684
BINDING SITE FOR RESIDUE MG C 687
12
BC3
SOFTWARE
ASP D:16 , PPK D:684
BINDING SITE FOR RESIDUE MG D 688
13
BC4
SOFTWARE
HIS A:14 , PRO A:15 , ASP A:163 , LYS A:165 , SER A:186 , ARG A:229 , PHE A:230 , ASP A:238 , PPK A:384 , HOH A:389 , HOH A:390 , HOH A:391 , HOH A:392 , ALA B:40 , GLU B:55 , GLN B:98 , ASP B:101 , ILE B:102 , GLY B:117 , ASP B:118 , LYS B:269 , ILE B:302
BINDING SITE FOR RESIDUE SAM A 385
14
BC5
SOFTWARE
ALA A:40 , GLU A:55 , GLN A:98 , ASP A:101 , ILE A:102 , GLY A:117 , ASP A:118 , LYS A:269 , ILE A:302 , HOH A:393 , HIS B:14 , PRO B:15 , ASP B:163 , LYS B:165 , SER B:186 , THR B:227 , ARG B:229 , PHE B:230 , ASP B:238 , PPK B:484 , HOH B:500
BINDING SITE FOR RESIDUE SAM B 485
15
BC6
SOFTWARE
HIS C:14 , PRO C:15 , ASP C:163 , LYS C:165 , THR C:227 , ARG C:229 , PHE C:230 , ASP C:238 , PPK C:584 , HOH C:700 , HOH C:702 , HOH C:711 , HOH C:716 , ALA D:40 , GLU D:55 , GLN D:98 , ASP D:101 , ILE D:102 , GLY D:117 , ASP D:118 , LYS D:269 , ILE D:302
BINDING SITE FOR RESIDUE SAM C 585
16
BC7
SOFTWARE
ALA C:40 , GLU C:55 , GLN C:98 , ASP C:101 , ILE C:102 , GLY C:117 , ASP C:118 , LYS C:269 , ILE C:302 , HOH C:900 , HOH C:902 , HIS D:14 , ASP D:163 , LYS D:165 , THR D:227 , ARG D:229 , PHE D:230 , ASP D:238 , PPK D:684 , HOH D:916
BINDING SITE FOR RESIDUE SAM C 685
17
BC8
SOFTWARE
HIS A:14 , ASP A:16 , LYS A:165 , ASP A:238 , ARG A:244 , LYS A:245 , SAM A:385 , K A:386 , MG A:387 , MG A:388 , ASP B:118 , GLY B:259 , GLY B:260 , ALA B:261 , LYS B:265 , ASP B:271
BINDING SITE FOR RESIDUE PPK A 384
18
BC9
SOFTWARE
ASP A:118 , GLY A:259 , GLY A:260 , ALA A:261 , LYS A:265 , ASP A:271 , HIS B:14 , ASP B:16 , LYS B:165 , ASP B:238 , ARG B:244 , LYS B:245 , SAM B:485 , K B:486 , MG B:487 , MG B:488
BINDING SITE FOR RESIDUE PPK B 484
19
CC1
SOFTWARE
HIS C:14 , ASP C:16 , LYS C:165 , ASP C:238 , ARG C:244 , LYS C:245 , SAM C:585 , K C:586 , MG C:588 , ASP D:118 , GLY D:259 , GLY D:260 , ALA D:261 , LYS D:265 , ASP D:271 , MG D:587
BINDING SITE FOR RESIDUE PPK C 584
20
CC2
SOFTWARE
ASP C:118 , GLY C:259 , GLY C:260 , ALA C:261 , LYS C:265 , ASP C:271 , SAM C:685 , MG C:687 , HIS D:14 , ASP D:16 , LYS D:165 , ARG D:244 , LYS D:245 , K D:686 , MG D:688 , HOH D:930
BINDING SITE FOR RESIDUE PPK D 684
[
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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: ADOMET_SYNTHASE_1 (A:115-125,B:115-125,C:115-125,D:11...)
2: ADOMET_SYNTHASE_2 (A:258-266,B:258-266,C:258-266,D:25...)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADOMET_SYNTHASE_1
PS00376
S-adenosylmethionine synthase signature 1.
METK_ECOLI
116-126
4
A:115-125
B:115-125
C:115-125
D:115-125
2
ADOMET_SYNTHASE_2
PS00377
S-adenosylmethionine synthase signature 2.
METK_ECOLI
259-267
4
A:258-266
B:258-266
C:258-266
D:258-266
[
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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.
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1rg9a1 (A:1-102)
1b: SCOP_d1rg9a2 (A:103-231)
1c: SCOP_d1rg9a3 (A:232-383)
1d: SCOP_d1rg9b1 (B:1-102)
1e: SCOP_d1rg9b2 (B:103-231)
1f: SCOP_d1rg9b3 (B:232-383)
1g: SCOP_d1rg9c1 (C:1-102)
1h: SCOP_d1rg9c2 (C:103-231)
1i: SCOP_d1rg9c3 (C:232-383)
1j: SCOP_d1rg9d1 (D:1-102)
1k: SCOP_d1rg9d2 (D:103-231)
1l: SCOP_d1rg9d3 (D:232-383)
View:
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)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
S-adenosylmethionine synthetase
(23)
Superfamily
:
S-adenosylmethionine synthetase
(23)
Family
:
S-adenosylmethionine synthetase
(15)
Protein domain
:
S-adenosylmethionine synthetase
(15)
Escherichia coli [TaxId: 562]
(9)
1a
d1rg9a1
A:1-102
1b
d1rg9a2
A:103-231
1c
d1rg9a3
A:232-383
1d
d1rg9b1
B:1-102
1e
d1rg9b2
B:103-231
1f
d1rg9b3
B:232-383
1g
d1rg9c1
C:1-102
1h
d1rg9c2
C:103-231
1i
d1rg9c3
C:232-383
1j
d1rg9d1
D:1-102
1k
d1rg9d2
D:103-231
1l
d1rg9d3
D:232-383
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1rg9A03 (A:1-9,A:136-232)
1b: CATH_1rg9A02 (A:10-101,A:233-269)
1c: CATH_1rg9B02 (B:10-101,B:233-269)
1d: CATH_1rg9C02 (C:10-101,C:233-269)
1e: CATH_1rg9D02 (D:10-101,D:233-269)
1f: CATH_1rg9A01 (A:108-135,A:270-382)
1g: CATH_1rg9B01 (B:108-135,B:270-382)
1h: CATH_1rg9C01 (C:108-135,C:270-382)
1i: CATH_1rg9D01 (D:108-135,D:270-382)
1j: CATH_1rg9B03 (B:1-9,B:136-232)
1k: CATH_1rg9C03 (C:1-9,C:136-232)
1l: CATH_1rg9D03 (D:1-9,D:136-232)
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)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
GMP Synthetase; Chain A, domain 3
(192)
Homologous Superfamily
:
[code=3.30.300.10, no name defined]
(22)
Escherichia coli. Organism_taxid: 562.
(2)
1a
1rg9A03
A:1-9,A:136-232
1b
1rg9A02
A:10-101,A:233-269
1c
1rg9B02
B:10-101,B:233-269
1d
1rg9C02
C:10-101,C:233-269
1e
1rg9D02
D:10-101,D:233-269
1f
1rg9A01
A:108-135,A:270-382
1g
1rg9B01
B:108-135,B:270-382
1h
1rg9C01
C:108-135,C:270-382
1i
1rg9D01
D:108-135,D:270-382
1j
1rg9B03
B:1-9,B:136-232
1k
1rg9C03
C:1-9,C:136-232
1l
1rg9D03
D:1-9,D:136-232
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_S_AdoMet_synt_C_1rg9D01 (D:232-369)
1b: PFAM_S_AdoMet_synt_C_1rg9D02 (D:232-369)
1c: PFAM_S_AdoMet_synt_C_1rg9D03 (D:232-369)
1d: PFAM_S_AdoMet_synt_C_1rg9D04 (D:232-369)
2a: PFAM_S_AdoMet_synt_M_1rg9D05 (D:112-230)
2b: PFAM_S_AdoMet_synt_M_1rg9D06 (D:112-230)
2c: PFAM_S_AdoMet_synt_M_1rg9D07 (D:112-230)
2d: PFAM_S_AdoMet_synt_M_1rg9D08 (D:112-230)
3a: PFAM_S_AdoMet_synt_N_1rg9D09 (D:1-100)
3b: PFAM_S_AdoMet_synt_N_1rg9D10 (D:1-100)
3c: PFAM_S_AdoMet_synt_N_1rg9D11 (D:1-100)
3d: PFAM_S_AdoMet_synt_N_1rg9D12 (D:1-100)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: S-AdoMet_synt_C]
(16)
Family
:
S-AdoMet_synt_C
(16)
Escherichia coli (strain K12)
(7)
1a
S-AdoMet_synt_C-1rg9D01
D:232-369
1b
S-AdoMet_synt_C-1rg9D02
D:232-369
1c
S-AdoMet_synt_C-1rg9D03
D:232-369
1d
S-AdoMet_synt_C-1rg9D04
D:232-369
Clan
:
no clan defined [family: S-AdoMet_synt_M]
(16)
Family
:
S-AdoMet_synt_M
(16)
Escherichia coli (strain K12)
(7)
2a
S-AdoMet_synt_M-1rg9D05
D:112-230
2b
S-AdoMet_synt_M-1rg9D06
D:112-230
2c
S-AdoMet_synt_M-1rg9D07
D:112-230
2d
S-AdoMet_synt_M-1rg9D08
D:112-230
Clan
:
no clan defined [family: S-AdoMet_synt_N]
(16)
Family
:
S-AdoMet_synt_N
(16)
Escherichia coli (strain K12)
(7)
3a
S-AdoMet_synt_N-1rg9D09
D:1-100
3b
S-AdoMet_synt_N-1rg9D10
D:1-100
3c
S-AdoMet_synt_N-1rg9D11
D:1-100
3d
S-AdoMet_synt_N-1rg9D12
D:1-100
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