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1AO0
Asym. Unit
Info
Asym.Unit (299 KB)
Biol.Unit 1 (289 KB)
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(1)
Title
:
GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE FROM B. SUBTILIS COMPLEXED WITH ADP AND GMP
Authors
:
D. R. Tomchick, J. L. Smith
Date
:
15 Jul 97 (Deposition) - 12 Nov 97 (Release) - 24 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Transferase, Glutamine Amidotransferase, Prtase, Purine Biosynthesis, Phosphoribosyltransferase, Glycosyltransferase, Tglutamine Amidotransferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Chen, D. R. Tomchick, D. Wolle, P. Hu, J. L. Smith, R. L. Switzer, H. Zalkin
Mechanism Of The Synergistic End-Product Regulation Of Bacillus Subtilis Glutamine Phosphoribosylpyrophosphate Amidotransferase By Nucleotides.
Biochemistry V. 36 10718 1997
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 16)
Info
All Hetero Components
1a: GUANOSINE-5'-MONOPHOSPHATE (5GPa)
1b: GUANOSINE-5'-MONOPHOSPHATE (5GPb)
1c: GUANOSINE-5'-MONOPHOSPHATE (5GPc)
1d: GUANOSINE-5'-MONOPHOSPHATE (5GPd)
2a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
2b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
2c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
2d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: IRON/SULFUR CLUSTER (SF4a)
4b: IRON/SULFUR CLUSTER (SF4b)
4c: IRON/SULFUR CLUSTER (SF4c)
4d: IRON/SULFUR CLUSTER (SF4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5GP
4
Ligand/Ion
GUANOSINE-5'-MONOPHOSPHATE
2
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
SF4
4
Ligand/Ion
IRON/SULFUR CLUSTER
[
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Sites
(32, 32)
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: AMA (UNKNOWN)
11: AMB (UNKNOWN)
12: AMC (UNKNOWN)
13: AMD (UNKNOWN)
14: BC1 (SOFTWARE)
15: BC2 (SOFTWARE)
16: BC3 (SOFTWARE)
17: BC4 (SOFTWARE)
18: BC5 (SOFTWARE)
19: BC6 (SOFTWARE)
20: BC7 (SOFTWARE)
21: MGA (UNKNOWN)
22: MGB (UNKNOWN)
23: MGC (UNKNOWN)
24: MGD (UNKNOWN)
25: NTA (UNKNOWN)
26: NTB (UNKNOWN)
27: NTC (UNKNOWN)
28: NTD (UNKNOWN)
29: PRA (UNKNOWN)
30: PRB (UNKNOWN)
31: PRC (UNKNOWN)
32: PRD (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:283 , ASP A:345 , ASP A:346 , 5GP A:467 , HOH A:470
BINDING SITE FOR RESIDUE MG A 469
02
AC2
SOFTWARE
SER B:283 , ASP B:345 , ASP B:346 , 5GP B:467 , HOH B:470
BINDING SITE FOR RESIDUE MG B 469
03
AC3
SOFTWARE
SER C:283 , ASP C:345 , ASP C:346 , 5GP C:467 , HOH C:470
BINDING SITE FOR RESIDUE MG C 469
04
AC4
SOFTWARE
SER D:283 , ASP D:345 , ASP D:346 , 5GP D:467 , HOH D:470
BINDING SITE FOR RESIDUE MG D 469
05
AC5
SOFTWARE
CYS A:236 , SER A:237 , MET A:238 , CYS A:382 , CYS A:437 , ALA A:439 , CYS A:440
BINDING SITE FOR RESIDUE SF4 A 466
06
AC6
SOFTWARE
MET A:238 , TYR A:242 , SER A:283 , ASP A:345 , ASP A:346 , SER A:347 , VAL A:349 , ARG A:350 , GLY A:351 , THR A:352 , THR A:353 , ASP A:387 , ADP A:468 , MG A:469 , HOH A:470
BINDING SITE FOR RESIDUE 5GP A 467
07
AC7
SOFTWARE
HIS A:25 , TYR A:242 , SER A:244 , ARG A:245 , PRO A:246 , ARG A:259 , PRO A:281 , ASP A:282 , SER A:283 , LYS A:305 , 5GP A:467 , ILE B:304 , LYS B:305 , ARG B:307
BINDING SITE FOR RESIDUE ADP A 468
08
AC8
SOFTWARE
CYS B:236 , SER B:237 , MET B:238 , CYS B:382 , CYS B:437 , ALA B:439 , CYS B:440
BINDING SITE FOR RESIDUE SF4 B 466
09
AC9
SOFTWARE
MET B:238 , TYR B:242 , SER B:283 , ASP B:345 , ASP B:346 , SER B:347 , VAL B:349 , ARG B:350 , GLY B:351 , THR B:352 , THR B:353 , ASP B:387 , ADP B:468 , MG B:469 , HOH B:470
BINDING SITE FOR RESIDUE 5GP B 467
10
AMA
UNKNOWN
ADP A:468
ALLOSTERIC NUCLEOTIDE BINDING SITE AT INTERFACE OF A AND B MONOMERS, NEAR MOLECULAR TWO-FOLD AXIS, IDENTIFIED BY BINDING OF ADP.
11
AMB
UNKNOWN
ADP B:468
ALLOSTERIC NUCLEOTIDE BINDING SITE AT INTERFACE OF A AND B MONOMERS, NEAR MOLECULAR TWO-FOLD AXIS, IDENTIFIED BY BINDING OF ADP.
12
AMC
UNKNOWN
ADP C:468
ALLOSTERIC NUCLEOTIDE BINDING SITE AT INTERFACE OF C AND D MONOMERS, NEAR MOLECULAR TWO-FOLD AXIS, IDENTIFIED BY BINDING OF ADP.
13
AMD
UNKNOWN
ADP D:468
ALLOSTERIC NUCLEOTIDE BINDING SITE AT INTERFACE OF C AND D MONOMERS, NEAR MOLECULAR TWO-FOLD AXIS, IDENTIFIED BY BINDING OF ADP.
14
BC1
SOFTWARE
ILE A:304 , LYS A:305 , ARG A:307 , TYR B:242 , SER B:244 , ARG B:245 , PRO B:246 , ARG B:259 , PRO B:281 , ASP B:282 , SER B:283 , LYS B:305 , 5GP B:467
BINDING SITE FOR RESIDUE ADP B 468
15
BC2
SOFTWARE
CYS C:236 , SER C:237 , MET C:238 , CYS C:382 , TYR C:384 , CYS C:437 , ALA C:439 , CYS C:440
BINDING SITE FOR RESIDUE SF4 C 466
16
BC3
SOFTWARE
MET C:238 , TYR C:242 , SER C:283 , ASP C:345 , ASP C:346 , SER C:347 , VAL C:349 , ARG C:350 , GLY C:351 , THR C:352 , THR C:353 , ASP C:387 , ADP C:468 , MG C:469 , HOH C:470
BINDING SITE FOR RESIDUE 5GP C 467
17
BC4
SOFTWARE
TYR C:242 , SER C:244 , ARG C:245 , PRO C:246 , ARG C:259 , PRO C:281 , ASP C:282 , SER C:283 , LYS C:305 , 5GP C:467 , ILE D:304 , LYS D:305 , ARG D:307
BINDING SITE FOR RESIDUE ADP C 468
18
BC5
SOFTWARE
CYS D:236 , SER D:237 , MET D:238 , CYS D:382 , TYR D:384 , CYS D:437 , ALA D:439 , CYS D:440
BINDING SITE FOR RESIDUE SF4 D 466
19
BC6
SOFTWARE
MET D:238 , TYR D:242 , SER D:283 , ASP D:345 , ASP D:346 , SER D:347 , VAL D:349 , ARG D:350 , GLY D:351 , THR D:352 , THR D:353 , ASP D:387 , ADP D:468 , MG D:469 , HOH D:470
BINDING SITE FOR RESIDUE 5GP D 467
20
BC7
SOFTWARE
ILE C:304 , LYS C:305 , ARG C:307 , TYR D:242 , SER D:244 , ARG D:245 , PRO D:246 , ARG D:259 , PRO D:281 , ASP D:282 , SER D:283 , LYS D:305 , 5GP D:467
BINDING SITE FOR RESIDUE ADP D 468
21
MGA
UNKNOWN
MG A:469
MG2+ ION BINDING SITE. THE MG2+ ION IS OCTAHEDRALLY COORDINATED BY THE OXYGENS OF THREE AMINO ACID SIDE CHAINS, THE TWO RIBOSE HYDROXYL OXYGENS OF THE GMP INHIBITOR, AND A WATER.
22
MGB
UNKNOWN
MG B:469
MG2+ ION BINDING SITE. THE MG2+ ION IS OCTAHEDRALLY COORDINATED BY THE OXYGENS OF THREE AMINO ACID SIDE CHAINS, THE TWO RIBOSE HYDROXYL OXYGENS OF THE GMP INHIBITOR, AND A WATER.
23
MGC
UNKNOWN
MG C:469
MG2+ ION BINDING SITE. THE MG2+ ION IS OCTAHEDRALLY COORDINATED BY THE OXYGENS OF THREE AMINO ACID SIDE CHAINS, THE TWO RIBOSE HYDROXYL OXYGENS OF THE GMP INHIBITOR, AND A WATER.
24
MGD
UNKNOWN
MG D:469
MG2+ ION BINDING SITE. THE MG2+ ION IS OCTAHEDRALLY COORDINATED BY THE OXYGENS OF THREE AMINO ACID SIDE CHAINS, THE TWO RIBOSE HYDROXYL OXYGENS OF THE GMP INHIBITOR, AND A WATER.
25
NTA
UNKNOWN
CYS A:1
NTN TYPE GLUTAMINE AMIDOTRANSFERASE CATALYTIC RESIDUE. THIS SITE BELONGS TO THE NTN SUPERFAMILY, WHICH ARE THOUGHT TO UTILIZE THE ALPHA-AMINO GROUP OF THE N-TERMINAL RESIDUE AS A PROTON DONOR, AND THE SIDE CHAIN OF THIS RESIDUE AS A NUCLEOPHILE IN CATALYSIS OF A HYDROLYTIC REACTION.
26
NTB
UNKNOWN
CYS B:1
NTN TYPE GLUTAMINE AMIDOTRANSFERASE CATALYTIC RESIDUE. THIS SITE BELONGS TO THE NTN SUPERFAMILY, WHICH ARE THOUGHT TO UTILIZE THE ALPHA-AMINO GROUP OF THE N-TERMINAL RESIDUE AS A PROTON DONOR, AND THE SIDE CHAIN OF THIS RESIDUE AS A NUCLEOPHILE IN CATALYSIS OF A HYDROLYTIC REACTION.
27
NTC
UNKNOWN
CYS C:1
NTN TYPE GLUTAMINE AMIDOTRANSFERASE CATALYTIC RESIDUE. THIS SITE BELONGS TO THE NTN SUPERFAMILY, WHICH ARE THOUGHT TO UTILIZE THE ALPHA-AMINO GROUP OF THE N-TERMINAL RESIDUE AS A PROTON DONOR, AND THE SIDE CHAIN OF THIS RESIDUE AS A NUCLEOPHILE IN CATALYSIS OF A HYDROLYTIC REACTION.
28
NTD
UNKNOWN
CYS D:1
NTN TYPE GLUTAMINE AMIDOTRANSFERASE CATALYTIC RESIDUE. THIS SITE BELONGS TO THE NTN SUPERFAMILY, WHICH ARE THOUGHT TO UTILIZE THE ALPHA-AMINO GROUP OF THE N-TERMINAL RESIDUE AS A PROTON DONOR, AND THE SIDE CHAIN OF THIS RESIDUE AS A NUCLEOPHILE IN CATALYSIS OF A HYDROLYTIC REACTION.
29
PRA
UNKNOWN
5GP A:467
DUAL SITE: BINDING SITE FOR SUBSTRATE PRPP IN THIS AND OTHER MEMBERS OF THE TYPE I PHOSPHORIBOSYLTRANSFERASE (PRTASE)FAMILY OF ENZYMES, AND NUCLEOTIDE INHIBITOR (IN THIS CASE, 5GP) BINDING SITE.
30
PRB
UNKNOWN
5GP B:467
DUAL SITE: BINDING SITE FOR SUBSTRATE PRPP IN THIS AND OTHER MEMBERS OF THE TYPE I PHOSPHORIBOSYLTRANSFERASE (PRTASE)FAMILY OF ENZYMES, AND NUCLEOTIDE INHIBITOR (IN THIS CASE, 5GP) BINDING SITE.
31
PRC
UNKNOWN
5GP C:467
DUAL SITE: BINDING SITE FOR SUBSTRATE PRPP IN THIS AND OTHER MEMBERS OF THE TYPE I PHOSPHORIBOSYLTRANSFERASE (PRTASE)FAMILY OF ENZYMES, AND NUCLEOTIDE INHIBITOR (IN THIS CASE, 5GP) BINDING SITE.
32
PRD
UNKNOWN
5GP D:467
DUAL SITE: BINDING SITE FOR SUBSTRATE PRPP IN THIS AND OTHER MEMBERS OF THE TYPE I PHOSPHORIBOSYLTRANSFERASE (PRTASE)FAMILY OF ENZYMES, AND NUCLEOTIDE INHIBITOR (IN THIS CASE, 5GP) BINDING SITE.
[
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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
(2, 8)
Info
All PROSITE Patterns/Profiles
1: GATASE_TYPE_2 (A:1-220,B:1-220,C:1-220,D:1-220)
2: PUR_PYR_PR_TRANSFER (A:341-353,B:341-353,C:341-353,D:34...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GATASE_TYPE_2
PS51278
Glutamine amidotransferase type 2 domain profile.
PUR1_BACSU
12-231
4
A:1-220
B:1-220
C:1-220
D:1-220
2
PUR_PYR_PR_TRANSFER
PS00103
Purine/pyrimidine phosphoribosyl transferases signature.
PUR1_BACSU
352-364
4
A:341-353
B:341-353
C:341-353
D:341-353
[
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1ao0a2 (A:1-234)
1b: SCOP_d1ao0b2 (B:1-234)
1c: SCOP_d1ao0c2 (C:1-234)
1d: SCOP_d1ao0d2 (D:1-234)
2a: SCOP_d1ao0a1 (A:235-459)
2b: SCOP_d1ao0b1 (B:235-459)
2c: SCOP_d1ao0c1 (C:235-459)
2d: SCOP_d1ao0d1 (D:235-459)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ntn hydrolase-like
(356)
Superfamily
:
N-terminal nucleophile aminohydrolases (Ntn hydrolases)
(352)
Family
:
Class II glutamine amidotransferases
(27)
Protein domain
:
Glutamine PRPP amidotransferase, N-terminal domain
(7)
Bacillus subtilis [TaxId: 1423]
(2)
1a
d1ao0a2
A:1-234
1b
d1ao0b2
B:1-234
1c
d1ao0c2
C:1-234
1d
d1ao0d2
D:1-234
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PRTase-like
(145)
Superfamily
:
PRTase-like
(145)
Family
:
Phosphoribosyltransferases (PRTases)
(100)
Protein domain
:
Glutamine PRPP amidotransferase, C-terminal domain
(7)
Bacillus subtilis [TaxId: 1423]
(2)
2a
d1ao0a1
A:235-459
2b
d1ao0b1
B:235-459
2c
d1ao0c1
C:235-459
2d
d1ao0d1
D:235-459
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1ao0A02 (A:260-305,A:328-379,A:391-424)
1b: CATH_1ao0B02 (B:260-305,B:328-379,B:391-424)
1c: CATH_1ao0C02 (C:260-305,C:328-379,C:391-424)
1d: CATH_1ao0D02 (D:260-305,D:328-379,D:391-424)
2a: CATH_1ao0A01 (A:1-259,A:380-390,A:425-458)
2b: CATH_1ao0B01 (B:1-259,B:380-390,B:425-458)
2c: CATH_1ao0C01 (C:1-259,C:380-390,C:425-458)
2d: CATH_1ao0D01 (D:1-259,D:380-390,D:425-458)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.2020, no name defined]
(117)
Bacillus subtilis. Organism_taxid: 1423.
(8)
1a
1ao0A02
A:260-305,A:328-379,A:391-424
1b
1ao0B02
B:260-305,B:328-379,B:391-424
1c
1ao0C02
C:260-305,C:328-379,C:391-424
1d
1ao0D02
D:260-305,D:328-379,D:391-424
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
(128)
Homologous Superfamily
:
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
(124)
Bacillus subtilis. Organism_taxid: 1423.
(2)
2a
1ao0A01
A:1-259,A:380-390,A:425-458
2b
1ao0B01
B:1-259,B:380-390,B:425-458
2c
1ao0C01
C:1-259,C:380-390,C:425-458
2d
1ao0D01
D:1-259,D:380-390,D:425-458
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Pfam Domains
(0, 0)
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all PFAM domains
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