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2YCP
Asym. Unit
Info
Asym.Unit (639 KB)
Biol.Unit 1 (628 KB)
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(1)
Title
:
F448H MUTANT OF TYROSINE PHENOL-LYASE FROM CITROBACTER FREUNDII IN COMPLEX WITH QUINONOID INTERMEDIATE FORMED WITH 3-FLUORO-L-TYROSINE
Authors
:
D. Milic, T. V. Demidkina, N. G. Faleev, R. S. Phillips, D. Matkovic-Cal A. A. Antson
Date
:
16 Mar 11 (Deposition) - 14 Sep 11 (Release) - 26 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Lyase, Pyridoxal 5'-Phosphate Dependent Enzyme, Beta-Elimination
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Milic, T. V. Demidkina, N. G. Faleev, R. S. Phillips, D. Matkovic-Calogovic, A. A. Antson
Crystallographic Snapshots Of Tyrosine Phenol-Lyase Show That Substrate Strain Plays A Role In C-C Bond Cleavage
J. Am. Chem. Soc. V. 133 16468 2011
[
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Hetero Components
(8, 32)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
2a: 1,2-ETHANEDIOL (EDOa)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
3c: POTASSIUM ION (Kc)
3d: POTASSIUM ION (Kd)
4a: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20... (P33a)
4b: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20... (P33b)
5a: (2E)-3-(3-FLUORO-4-HYDROXYPHENYL)-... (P61a)
5b: (2E)-3-(3-FLUORO-4-HYDROXYPHENYL)-... (P61b)
5c: (2E)-3-(3-FLUORO-4-HYDROXYPHENYL)-... (P61c)
5d: (2E)-3-(3-FLUORO-4-HYDROXYPHENYL)-... (P61d)
6a: DI(HYDROXYETHYL)ETHER (PEGa)
6b: DI(HYDROXYETHYL)ETHER (PEGb)
7a: TETRAETHYLENE GLYCOL (PG4a)
7b: TETRAETHYLENE GLYCOL (PG4b)
7c: TETRAETHYLENE GLYCOL (PG4c)
7d: TETRAETHYLENE GLYCOL (PG4d)
7e: TETRAETHYLENE GLYCOL (PG4e)
8a: TRIETHYLENE GLYCOL (PGEa)
8b: TRIETHYLENE GLYCOL (PGEb)
8c: TRIETHYLENE GLYCOL (PGEc)
8d: TRIETHYLENE GLYCOL (PGEd)
8e: TRIETHYLENE GLYCOL (PGEe)
8f: TRIETHYLENE GLYCOL (PGEf)
8g: TRIETHYLENE GLYCOL (PGEg)
8h: TRIETHYLENE GLYCOL (PGEh)
8i: TRIETHYLENE GLYCOL (PGEi)
8j: TRIETHYLENE GLYCOL (PGEj)
8k: TRIETHYLENE GLYCOL (PGEk)
8l: TRIETHYLENE GLYCOL (PGEl)
8m: TRIETHYLENE GLYCOL (PGEm)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
1
Ligand/Ion
PENTAETHYLENE GLYCOL
2
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
3
K
4
Ligand/Ion
POTASSIUM ION
4
P33
2
Ligand/Ion
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
5
P61
4
Ligand/Ion
(2E)-3-(3-FLUORO-4-HYDROXYPHENYL)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}PROPANOICACID
6
PEG
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
7
PG4
5
Ligand/Ion
TETRAETHYLENE GLYCOL
8
PGE
13
Ligand/Ion
TRIETHYLENE GLYCOL
[
close Hetero Component info
]
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: 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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:36 , THR A:49 , GLN A:98 , GLY A:99 , ARG A:100 , GLU A:103 , PHE A:123 , THR A:124 , THR A:125 , ASN A:185 , ASP A:214 , ARG A:217 , SER A:254 , LYS A:257 , MET A:379 , ARG A:381 , ARG A:404 , HIS A:448 , PHE A:449 , HOH A:2095
BINDING SITE FOR RESIDUE P61 A 600
02
AC2
SOFTWARE
ASP A:139 , LYS A:162 , LYS A:165 , GLU A:169 , LYS A:170 , HOH A:2476
BINDING SITE FOR RESIDUE PGE A1457
03
AC3
SOFTWARE
LYS A:226 , GLU A:227 , GLU A:233 , HOH A:2477 , HOH A:2478
BINDING SITE FOR RESIDUE PGE A1458
04
AC4
SOFTWARE
GLU A:313 , HOH A:2481 , VAL D:16 , SER D:17 , HOH D:2023
BINDING SITE FOR RESIDUE PGE A1459
05
AC5
SOFTWARE
LYS A:444 , PGE A:1461 , SER B:277
BINDING SITE FOR RESIDUE PG4 A1460
06
AC6
SOFTWARE
GLU A:442 , LYS A:444 , PG4 A:1460 , HOH A:2483
BINDING SITE FOR RESIDUE PGE A1461
07
AC7
SOFTWARE
GLY A:52 , ASN A:262 , HOH A:2094 , GLU B:69 , HOH B:2321
BINDING SITE FOR RESIDUE K A1462
08
AC8
SOFTWARE
GLU A:69 , HOH A:2332 , GLY B:52 , ASN B:262 , HOH B:2095
BINDING SITE FOR RESIDUE K A1463
09
AC9
SOFTWARE
VAL A:16 , SER A:17 , MET A:18 , TYR A:44 , HOH A:2484 , GLN D:311 , GLU D:313
BINDING SITE FOR RESIDUE PG4 A1464
10
BC1
SOFTWARE
PHE B:36 , THR B:49 , GLN B:98 , GLY B:99 , ARG B:100 , GLU B:103 , PHE B:123 , THR B:124 , ASN B:185 , ASP B:214 , ARG B:217 , SER B:254 , LYS B:257 , MET B:379 , ARG B:381 , ARG B:404 , HIS B:448 , PHE B:449 , HOH B:2236 , HOH B:2442
BINDING SITE FOR RESIDUE P61 B 600
11
BC2
SOFTWARE
ASP B:139 , LYS B:162 , GLU B:169 , HOH B:2225 , HOH B:2443
BINDING SITE FOR RESIDUE PG4 B1457
12
BC3
SOFTWARE
LYS B:226 , GLU B:233 , TYR B:312 , GLU B:313
BINDING SITE FOR RESIDUE PGE B1458
13
BC4
SOFTWARE
SER A:277 , LYS B:444 , EDO B:1460 , HOH B:2445
BINDING SITE FOR RESIDUE PG4 B1459
14
BC5
SOFTWARE
GLU B:442 , PG4 B:1459 , HOH B:2446
BINDING SITE FOR RESIDUE EDO B1460
15
BC6
SOFTWARE
LYS B:59 , MET B:66 , HOH B:2104 , HOH B:2447 , HOH B:2449 , LYS D:59 , MET D:66
BINDING SITE FOR RESIDUE PGE B1461
16
BC7
SOFTWARE
VAL B:16 , MET B:18 , HOH B:2450 , GLU C:313
BINDING SITE FOR RESIDUE 1PE B1462
17
BC8
SOFTWARE
PHE C:36 , THR C:49 , GLN C:98 , GLY C:99 , ARG C:100 , GLU C:103 , PHE C:123 , THR C:124 , ASN C:185 , ASP C:214 , ARG C:217 , SER C:254 , LYS C:257 , MET C:379 , ARG C:381 , ARG C:404 , HIS C:448 , PHE C:449 , HOH C:2235 , HOH C:2472
BINDING SITE FOR RESIDUE P61 C 600
18
BC9
SOFTWARE
MET B:1 , TYR B:3 , TYR B:324 , TYR B:414 , ASP B:422 , HOH B:2413 , MET C:1 , TYR C:3 , ASP C:422 , HOH C:2426
BINDING SITE FOR RESIDUE P33 C1457
19
CC1
SOFTWARE
GLN B:311 , GLU B:313 , VAL C:16 , SER C:17 , TYR C:44
BINDING SITE FOR RESIDUE PGE C1458
20
CC2
SOFTWARE
VAL C:138 , ASP C:139 , LYS C:165 , LEU C:166 , GLU C:169 , LYS C:170 , HOH C:2474
BINDING SITE FOR RESIDUE PGE C1459
21
CC3
SOFTWARE
LYS C:226 , TYR C:312 , HOH C:2278 , HOH C:2476 , HOH C:2477
BINDING SITE FOR RESIDUE PGE C1460
22
CC4
SOFTWARE
LYS C:444 , HOH C:2480 , SER D:277 , GLU D:280
BINDING SITE FOR RESIDUE PGE C1461
23
CC5
SOFTWARE
GLU C:442 , HOH C:2481
BINDING SITE FOR RESIDUE PEG C1462
24
CC6
SOFTWARE
GLY C:52 , ASN C:262 , GLU D:69 , HOH D:2098 , HOH D:2305
BINDING SITE FOR RESIDUE K C1463
25
CC7
SOFTWARE
GLU C:69 , HOH C:2325 , GLY D:52 , ASN D:262 , HOH D:2079
BINDING SITE FOR RESIDUE K C1464
26
CC8
SOFTWARE
PHE D:36 , THR D:49 , GLN D:98 , GLY D:99 , ARG D:100 , GLU D:103 , PHE D:123 , THR D:124 , ASN D:185 , ASP D:214 , THR D:216 , ARG D:217 , SER D:254 , LYS D:257 , MET D:379 , ARG D:381 , ARG D:404 , HIS D:448 , PHE D:449 , HOH D:2080
BINDING SITE FOR RESIDUE P61 D 600
27
CC9
SOFTWARE
MET A:1 , TYR A:3 , TYR A:324 , TYR A:414 , ALA A:415 , ASP A:422 , HOH A:2435 , MET D:1 , TYR D:3 , TYR D:324 , TYR D:414 , ASP D:422
BINDING SITE FOR RESIDUE P33 D1457
28
DC1
SOFTWARE
TYR D:116 , ASP D:139 , LYS D:162 , LYS D:165 , LEU D:166 , GLU D:169 , LYS D:170 , HOH D:2442
BINDING SITE FOR RESIDUE PGE D1458
29
DC2
SOFTWARE
GLU D:233 , HOH D:2244 , HOH D:2259
BINDING SITE FOR RESIDUE PGE D1459
30
DC3
SOFTWARE
SER C:277 , GLU C:280 , LYS D:444
BINDING SITE FOR RESIDUE PG4 D1460
31
DC4
SOFTWARE
GLU D:442 , LYS D:444
BINDING SITE FOR RESIDUE PGE D1461
32
DC5
SOFTWARE
LEU D:109 , ILE D:111 , LYS D:112
BINDING SITE FOR RESIDUE PEG D1462
[
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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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: BETA_ELIM_LYASE (A:247-265,B:247-265,C:247-265,D:24...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BETA_ELIM_LYASE
PS00853
Beta-eliminating lyases pyridoxal-phosphate attachment site.
TPL_CITFR
247-265
4
A:247-265
B:247-265
C:247-265
D:247-265
[
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2ycpa_ (A:)
1b: SCOP_d2ycpb_ (B:)
1c: SCOP_d2ycpc_ (C:)
1d: SCOP_d2ycpd_ (D:)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
Beta-eliminating lyases
(16)
Protein domain
:
automated matches
(8)
Citrobacter freundii [TaxId: 546]
(8)
1a
d2ycpa_
A:
1b
d2ycpb_
B:
1c
d2ycpc_
C:
1d
d2ycpd_
D:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
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Sorry, no Info available
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