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1UPC
Asym. Unit
Info
Asym.Unit (528 KB)
Biol.Unit 1 (349 KB)
Biol.Unit 2 (349 KB)
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(1)
Title
:
CARBOXYETHYLARGININE SYNTHASE FROM STREPTOMYCES CLAVULIGERUS
Authors
:
M. E. C. Caines, J. M. Elkins, K. S. Hewitson, C. J. Schofield
Date
:
29 Sep 03 (Deposition) - 20 Nov 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F (2x)
Keywords
:
Synthase, Clavulanic Acid, Antibiotic, Lactamase, Flavoprotein, Thiamine Pyrophosphate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. E. C. Caines, J. M. Elkins, K. S. Hewitson, C. J. Schofield
Crystal Structure And Mechanistic Implications Of N2-(2-Carboxyethyl)Arginine Synthase, The First Enzyme In The Clavulanic Acid Biosynthesis Pathway
J. Biol. Chem. V. 279 5685 2004
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Hetero Components
(3, 24)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
3a: THIAMINE DIPHOSPHATE (TPPa)
3b: THIAMINE DIPHOSPHATE (TPPb)
3c: THIAMINE DIPHOSPHATE (TPPc)
3d: THIAMINE DIPHOSPHATE (TPPd)
3e: THIAMINE DIPHOSPHATE (TPPe)
3f: THIAMINE DIPHOSPHATE (TPPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
6
Ligand/Ion
MAGNESIUM ION
2
SO4
12
Ligand/Ion
SULFATE ION
3
TPP
6
Ligand/Ion
THIAMINE DIPHOSPHATE
[
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Sites
(24, 24)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:463 , ASN A:490 , THR A:492 , TPP A:600 , HOH A:2121
BINDING SITE FOR RESIDUE MG A 601
02
AC2
SOFTWARE
TYR A:271 , ARG A:414 , HIS A:415 , LEU A:495 , HOH A:2068 , HOH A:2106 , HOH A:2139 , HIS B:120 , GLN B:121
BINDING SITE FOR RESIDUE SO4 A 602
03
AC3
SOFTWARE
ASN A:490 , ASN A:560 , TYR A:561 , ASP A:562 , PHE A:563
BINDING SITE FOR RESIDUE SO4 A 603
04
AC4
SOFTWARE
ASP B:463 , ASN B:490 , THR B:492 , TPP B:600 , HOH B:2182
BINDING SITE FOR RESIDUE MG B 601
05
AC5
SOFTWARE
HIS A:120 , HOH A:2033 , TYR B:271 , ARG B:414 , HIS B:415 , LEU B:495 , HOH B:2086 , HOH B:2184 , HOH B:2185
BINDING SITE FOR RESIDUE SO4 B 602
06
AC6
SOFTWARE
ASN B:490 , ASN B:560 , TYR B:561 , ASP B:562 , PHE B:563
BINDING SITE FOR RESIDUE SO4 B 603
07
AC7
SOFTWARE
ASP C:463 , ASN C:490 , THR C:492 , TPP C:600 , HOH C:2105
BINDING SITE FOR RESIDUE MG C 601
08
AC8
SOFTWARE
TYR C:271 , ARG C:414 , HIS C:415 , HOH C:2067 , HOH C:2116 , HOH C:2118 , HIS D:120 , GLN D:121
BINDING SITE FOR RESIDUE SO4 C 602
09
AC9
SOFTWARE
ASN C:490 , ASN C:560 , TYR C:561 , ASP C:562
BINDING SITE FOR RESIDUE SO4 C 603
10
BC1
SOFTWARE
ASP D:463 , ASN D:490 , THR D:492 , TPP D:600 , HOH D:2144
BINDING SITE FOR RESIDUE MG D 601
11
BC2
SOFTWARE
HIS C:120 , GLN C:121 , TYR D:271 , ARG D:414 , HIS D:415 , LEU D:495 , HOH D:2096 , HOH D:2156 , HOH D:2157
BINDING SITE FOR RESIDUE SO4 D 602
12
BC3
SOFTWARE
ASN D:490 , ASN D:560 , TYR D:561 , ASP D:562
BINDING SITE FOR RESIDUE SO4 D 603
13
BC4
SOFTWARE
ASP E:463 , ASN E:490 , THR E:492 , TPP E:600 , HOH E:2110
BINDING SITE FOR RESIDUE MG E 601
14
BC5
SOFTWARE
TYR E:271 , ARG E:414 , HIS E:415 , LEU E:495 , HOH E:2076 , HIS F:120 , GLN F:121
BINDING SITE FOR RESIDUE SO4 E 602
15
BC6
SOFTWARE
ASN E:490 , ASN E:560 , TYR E:561 , ASP E:562
BINDING SITE FOR RESIDUE SO4 E 603
16
BC7
SOFTWARE
ASP F:463 , ASN F:490 , THR F:492 , TPP F:600 , HOH F:2126
BINDING SITE FOR RESIDUE MG F 601
17
BC8
SOFTWARE
HIS E:120 , GLN E:121 , TYR F:271 , ARG F:414 , HIS F:415 , LEU F:495 , HOH F:2064 , HOH F:2136
BINDING SITE FOR RESIDUE SO4 F 602
18
BC9
SOFTWARE
ASN F:490 , GLU F:497 , ASN F:560 , TYR F:561 , ASP F:562
BINDING SITE FOR RESIDUE SO4 F 603
19
CC1
SOFTWARE
ILE A:410 , GLY A:411 , PHE A:412 , PHE A:413 , SER A:436 , SER A:437 , PHE A:438 , GLY A:462 , ASP A:463 , GLY A:464 , GLY A:465 , ASN A:490 , THR A:492 , ASN A:493 , GLY A:494 , LEU A:495 , TYR A:561 , MG A:601 , HOH A:2121 , HOH A:2138 , HOH A:2139 , GLU B:57 , THR B:80 , ASN B:87
BINDING SITE FOR RESIDUE TPP A 600
20
CC2
SOFTWARE
GLU A:57 , THR A:80 , ASN A:87 , HOH A:2033 , ILE B:410 , GLY B:411 , PHE B:412 , PHE B:413 , SER B:436 , SER B:437 , PHE B:438 , GLY B:462 , ASP B:463 , GLY B:464 , GLY B:465 , ASN B:490 , THR B:492 , ASN B:493 , GLY B:494 , LEU B:495 , TYR B:561 , MG B:601 , HOH B:2182 , HOH B:2183
BINDING SITE FOR RESIDUE TPP B 600
21
CC3
SOFTWARE
ILE C:410 , GLY C:411 , PHE C:412 , PHE C:413 , SER C:436 , SER C:437 , PHE C:438 , GLY C:462 , ASP C:463 , GLY C:464 , GLY C:465 , ASN C:490 , THR C:492 , ASN C:493 , GLY C:494 , LEU C:495 , TYR C:561 , MG C:601 , HOH C:2105 , HOH C:2116 , HOH C:2117 , GLU D:57 , THR D:80 , ASN D:87
BINDING SITE FOR RESIDUE TPP C 600
22
CC4
SOFTWARE
GLU C:57 , THR C:80 , ASN C:87 , ILE D:410 , GLY D:411 , PHE D:412 , PHE D:413 , SER D:436 , SER D:437 , PHE D:438 , GLY D:462 , ASP D:463 , GLY D:464 , GLY D:465 , ASN D:490 , THR D:492 , ASN D:493 , GLY D:494 , LEU D:495 , TYR D:561 , MG D:601 , HOH D:2128 , HOH D:2144 , HOH D:2156
BINDING SITE FOR RESIDUE TPP D 600
23
CC5
SOFTWARE
ILE E:410 , PHE E:412 , PHE E:413 , SER E:436 , SER E:437 , PHE E:438 , GLY E:462 , ASP E:463 , GLY E:464 , GLY E:465 , ASN E:490 , THR E:492 , ASN E:493 , GLY E:494 , LEU E:495 , TYR E:561 , MG E:601 , HOH E:2110 , HOH E:2117 , GLU F:57 , THR F:80 , ASN F:87
BINDING SITE FOR RESIDUE TPP E 600
24
CC6
SOFTWARE
GLU E:57 , THR E:80 , ASN E:87 , ILE F:410 , PHE F:412 , PHE F:413 , SER F:436 , SER F:437 , PHE F:438 , GLY F:462 , ASP F:463 , GLY F:464 , GLY F:465 , ASN F:490 , THR F:492 , ASN F:493 , GLY F:494 , LEU F:495 , TYR F:561 , MG F:601 , HOH F:2126 , HOH F:2135
BINDING SITE FOR RESIDUE TPP F 600
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: TPP_ENZYMES (A:446-465,B:446-465,C:446-465,D:44...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TPP_ENZYMES
PS00187
Thiamine pyrophosphate enzymes signature.
CEAS_STRCL
446-465
6
A:446-465
B:446-465
C:446-465
D:446-465
E:446-465
F:446-465
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 18)
Info
All SCOP Domains
1a: SCOP_d1upca1 (A:198-374)
1b: SCOP_d1upcb1 (B:198-374)
1c: SCOP_d1upcc1 (C:198-374)
1d: SCOP_d1upcd1 (D:198-374)
1e: SCOP_d1upce1 (E:198-374)
1f: SCOP_d1upcf1 (F:198-374)
2a: SCOP_d1upca3 (A:375-572)
2b: SCOP_d1upcb3 (B:375-572)
2c: SCOP_d1upcc3 (C:375-572)
2d: SCOP_d1upcd3 (D:375-572)
2e: SCOP_d1upce3 (E:375-572)
2f: SCOP_d1upcf3 (F:375-572)
3a: SCOP_d1upca2 (A:12-197)
3b: SCOP_d1upcb2 (B:12-197)
3c: SCOP_d1upcc2 (C:12-197)
3d: SCOP_d1upcd2 (D:12-197)
3e: SCOP_d1upce2 (E:12-197)
3f: SCOP_d1upcf2 (F:12-197)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
DHS-like NAD/FAD-binding domain
(176)
Superfamily
:
DHS-like NAD/FAD-binding domain
(176)
Family
:
Pyruvate oxidase and decarboxylase, middle domain
(74)
Protein domain
:
Carboxyethylarginine synthase
(6)
Streptomyces clavuligerus [TaxId: 1901]
(6)
1a
d1upca1
A:198-374
1b
d1upcb1
B:198-374
1c
d1upcc1
C:198-374
1d
d1upcd1
D:198-374
1e
d1upce1
E:198-374
1f
d1upcf1
F:198-374
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
Pyruvate oxidase and decarboxylase PP module
(43)
Protein domain
:
Carboxyethylarginine synthase
(6)
Streptomyces clavuligerus [TaxId: 1901]
(6)
2a
d1upca3
A:375-572
2b
d1upcb3
B:375-572
2c
d1upcc3
C:375-572
2d
d1upcd3
D:375-572
2e
d1upce3
E:375-572
2f
d1upcf3
F:375-572
Family
:
Pyruvate oxidase and decarboxylase Pyr module
(43)
Protein domain
:
Carboxyethylarginine synthase
(6)
Streptomyces clavuligerus [TaxId: 1901]
(6)
3a
d1upca2
A:12-197
3b
d1upcb2
B:12-197
3c
d1upcc2
C:12-197
3d
d1upcd2
D:12-197
3e
d1upce2
E:12-197
3f
d1upcf2
F:12-197
[
close SCOP info
]
CATH Domains
(2, 18)
Info
all CATH domains
1a: CATH_1upcA03 (A:360-572)
1b: CATH_1upcA01 (A:12-195)
1c: CATH_1upcB01 (B:12-195)
1d: CATH_1upcD01 (D:12-195)
1e: CATH_1upcE01 (E:12-195)
1f: CATH_1upcF01 (F:12-195)
1g: CATH_1upcC01 (C:12-195)
1h: CATH_1upcB03 (B:360-572)
1i: CATH_1upcC03 (C:360-572)
1j: CATH_1upcD03 (D:360-572)
1k: CATH_1upcE03 (E:360-572)
1l: CATH_1upcF03 (F:360-572)
2a: CATH_1upcA02 (A:196-359)
2b: CATH_1upcB02 (B:196-359)
2c: CATH_1upcC02 (C:196-359)
2d: CATH_1upcD02 (D:196-359)
2e: CATH_1upcE02 (E:196-359)
2f: CATH_1upcF02 (F:196-359)
View:
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Streptomyces clavuligerus. Organism_taxid: 1901.
(3)
1a
1upcA03
A:360-572
1b
1upcA01
A:12-195
1c
1upcB01
B:12-195
1d
1upcD01
D:12-195
1e
1upcE01
E:12-195
1f
1upcF01
F:12-195
1g
1upcC01
C:12-195
1h
1upcB03
B:360-572
1i
1upcC03
C:360-572
1j
1upcD03
D:360-572
1k
1upcE03
E:360-572
1l
1upcF03
F:360-572
Homologous Superfamily
:
TPP-binding domain
(120)
Streptomyces clavuligerus. Organism_taxid: 1901.
(3)
2a
1upcA02
A:196-359
2b
1upcB02
B:196-359
2c
1upcC02
C:196-359
2d
1upcD02
D:196-359
2e
1upcE02
E:196-359
2f
1upcF02
F:196-359
[
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]
Pfam Domains
(0, 0)
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all PFAM domains
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