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2YWC
Asym. Unit
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Asym.Unit (316 KB)
Biol.Unit 1 (158 KB)
Biol.Unit 2 (156 KB)
Biol.Unit 3 (308 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GMP SYNTHETASE FROM THERMUS THERMOPHILUS IN COMPLEX WITH XMP
Authors
:
S. Baba, M. Kanagawa, S. Kuramitsu, S. Yokoyama, G. Sampei, G. Kawai, Ri Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
20 Apr 07 (Deposition) - 23 Oct 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Gmp Synthetase, Xmp Binding, Atp Binding, Purine Nucleotide Biosynthetic Pathway, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase
(Keyword Search:
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Reference
:
S. Baba, M. Kanagawa, H. Yanai, T. Ishii, S. Kuramitsu, S. Yokoyama, G. Sampei, G. Kawai
Crystal Structure Of Gmp Synthetase From Thermus Thermophilus
To Be Published
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Hetero Components
(2, 24)
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)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
1o: SELENOMETHIONINE (MSEo)
1p: SELENOMETHIONINE (MSEp)
1q: SELENOMETHIONINE (MSEq)
1r: SELENOMETHIONINE (MSEr)
1s: SELENOMETHIONINE (MSEs)
1t: SELENOMETHIONINE (MSEt)
2a: XANTHOSINE-5'-MONOPHOSPHATE (XMPa)
2b: XANTHOSINE-5'-MONOPHOSPHATE (XMPb)
2c: XANTHOSINE-5'-MONOPHOSPHATE (XMPc)
2d: XANTHOSINE-5'-MONOPHOSPHATE (XMPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
20
Mod. Amino Acid
SELENOMETHIONINE
2
XMP
4
Ligand/Ion
XANTHOSINE-5'-MONOPHOSPHATE
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:288 , PRO A:382 , GLY A:383 , PRO A:384 , GLN A:424 , LYS A:495 , THR A:499 , ILE A:500 , GLU A:501 , HOH A:773 , HOH A:784 , HOH A:807
BINDING SITE FOR RESIDUE XMP A 701
2
AC2
SOFTWARE
ARG B:288 , PRO B:382 , GLY B:383 , PRO B:384 , GLN B:424 , PHE B:458 , LYS B:495 , THR B:499 , ILE B:500 , GLU B:501 , HOH B:748
BINDING SITE FOR RESIDUE XMP B 702
3
AC3
SOFTWARE
ARG C:288 , PRO C:382 , GLY C:383 , PRO C:384 , GLN C:424 , PHE C:458 , LYS C:495 , THR C:499 , ILE C:500 , GLU C:501
BINDING SITE FOR RESIDUE XMP C 703
4
AC4
SOFTWARE
ARG D:288 , PRO D:382 , GLY D:383 , PRO D:384 , GLN D:424 , PHE D:458 , LYS D:495 , THR D:499 , ILE D:500 , GLU D:501
BINDING SITE FOR RESIDUE XMP D 704
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GMPS_ATP_PPASE (A:190-378,B:190-378,C:190-378,D:19...)
;
View:
Select:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GMPS_ATP_PPASE
PS51553
GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile.
GUAA_THET8
190-378
4
A:190-378
B:190-378
C:190-378
D:190-378
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 12)
Info
All SCOP Domains
1a: SCOP_d2ywca3 (A:383-503)
1b: SCOP_d2ywcb3 (B:383-503)
1c: SCOP_d2ywcc3 (C:383-503)
1d: SCOP_d2ywcd3 (D:383-503)
2a: SCOP_d2ywca2 (A:190-382)
2b: SCOP_d2ywcb2 (B:190-382)
2c: SCOP_d2ywcc2 (C:190-382)
2d: SCOP_d2ywcd2 (D:190-382)
3a: SCOP_d2ywca1 (A:1-189)
3b: SCOP_d2ywcb1 (B:1-189)
3c: SCOP_d2ywcc1 (C:1-189)
3d: SCOP_d2ywcd1 (D:1-189)
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)
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)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Alpha-lytic protease prodomain-like
(115)
Superfamily
:
GMP synthetase C-terminal dimerisation domain
(6)
Family
:
GMP synthetase C-terminal dimerisation domain
(3)
Protein domain
:
GMP synthetase C-terminal dimerisation domain
(3)
Thermus thermophilus HB8 [TaxId: 300852]
(2)
1a
d2ywca3
A:383-503
1b
d2ywcb3
B:383-503
1c
d2ywcc3
C:383-503
1d
d2ywcd3
D:383-503
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Adenine nucleotide alpha hydrolase-like
(440)
Superfamily
:
Adenine nucleotide alpha hydrolases-like
(110)
Family
:
N-type ATP pyrophosphatases
(44)
Protein domain
:
GMP synthetase, central domain
(3)
Thermus thermophilus HB8 [TaxId: 300852]
(2)
2a
d2ywca2
A:190-382
2b
d2ywcb2
B:190-382
2c
d2ywcc2
C:190-382
2d
d2ywcd2
D:190-382
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Class I glutamine amidotransferase-like
(173)
Family
:
Class I glutamine amidotransferases (GAT)
(48)
Protein domain
:
GMP synthetase
(3)
Thermus thermophilus HB8 [TaxId: 300852]
(2)
3a
d2ywca1
A:1-189
3b
d2ywcb1
B:1-189
3c
d2ywcc1
C:1-189
3d
d2ywcd1
D:1-189
[
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CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_2ywcD03 (D:395-502)
1b: CATH_2ywcA03 (A:395-502)
1c: CATH_2ywcB03 (B:395-502)
1d: CATH_2ywcC03 (C:395-502)
2a: CATH_2ywcA01 (A:2-188)
2b: CATH_2ywcB01 (B:2-188)
2c: CATH_2ywcC01 (C:2-188)
2d: CATH_2ywcD01 (D:2-188)
3a: CATH_2ywcA02 (A:189-378)
3b: CATH_2ywcB02 (B:189-378)
3c: CATH_2ywcC02 (C:189-378)
3d: CATH_2ywcD02 (D:189-378)
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)
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)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(2)
1a
2ywcD03
D:395-502
1b
2ywcA03
A:395-502
1c
2ywcB03
B:395-502
1d
2ywcC03
C:395-502
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.880, no name defined]
(97)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(3)
2a
2ywcA01
A:2-188
2b
2ywcB01
B:2-188
2c
2ywcC01
C:2-188
2d
2ywcD01
D:2-188
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
(328)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(2)
3a
2ywcA02
A:189-378
3b
2ywcB02
B:189-378
3c
2ywcC02
C:189-378
3d
2ywcD02
D:189-378
[
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]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_GATase_2ywcD01 (D:3-184)
1b: PFAM_GATase_2ywcD02 (D:3-184)
1c: PFAM_GATase_2ywcD03 (D:3-184)
1d: PFAM_GATase_2ywcD04 (D:3-184)
2a: PFAM_GMP_synt_C_2ywcD05 (D:410-502)
2b: PFAM_GMP_synt_C_2ywcD06 (D:410-502)
2c: PFAM_GMP_synt_C_2ywcD07 (D:410-502)
2d: PFAM_GMP_synt_C_2ywcD08 (D:410-502)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
Glutaminase_I
(73)
Family
:
GATase
(26)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(6)
1a
GATase-2ywcD01
D:3-184
1b
GATase-2ywcD02
D:3-184
1c
GATase-2ywcD03
D:3-184
1d
GATase-2ywcD04
D:3-184
Clan
:
no clan defined [family: GMP_synt_C]
(3)
Family
:
GMP_synt_C
(3)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(2)
2a
GMP_synt_C-2ywcD05
D:410-502
2b
GMP_synt_C-2ywcD06
D:410-502
2c
GMP_synt_C-2ywcD07
D:410-502
2d
GMP_synt_C-2ywcD08
D:410-502
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