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2YCT
Biol. Unit 1
Info
Asym.Unit (321 KB)
Biol.Unit 1 (625 KB)
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(1)
Title
:
TYROSINE PHENOL-LYASE FROM CITROBACTER FREUNDII IN COMPLEX WITH PYRIDINE N-OXIDE AND THE QUINONOID INTERMEDIATE FORMED WITH L-ALANINE
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
:
2.25
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Lyase, Pyridoxal 5'-Phosphate Dependent Enzyme, Beta-Elimination
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
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
(5, 16)
Info
All Hetero Components
1a: PYRIDINE-N-OXIDE (9POa)
1b: PYRIDINE-N-OXIDE (9POb)
1c: PYRIDINE-N-OXIDE (9POc)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
3a: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20... (P33a)
4a: (2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5... (PLIa)
5a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
5b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
6a: PHOSPHATE ION (PO4a)
View:
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Label:
No.
Name
Count
Type
Full Name
1
9PO
6
Ligand/Ion
PYRIDINE-N-OXIDE
2
K
-1
Ligand/Ion
POTASSIUM ION
3
P33
2
Ligand/Ion
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
4
PLI
2
Ligand/Ion
(2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}PROPANOIC ACID
5
PLP
4
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
6
PO4
2
Ligand/Ion
PHOSPHATE ION
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Sites
(10, 10)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:98 , GLY A:99 , ARG A:100 , GLU A:103 , PHE A:123 , THR A:125 , ASN A:185 , ASP A:214 , ARG A:217 , SER A:254 , LYS A:257 , PO4 A:1461 , HOH A:2241 , HOH A:2372
BINDING SITE FOR RESIDUE PLP A1257
02
AC2
SOFTWARE
GLN B:98 , GLY B:99 , ARG B:100 , GLU B:103 , PHE B:123 , ASN B:185 , ASP B:214 , ARG B:217 , SER B:254 , LYS B:257 , HOH B:2256 , HOH B:2257
BINDING SITE FOR RESIDUE PLP B1257
03
AC3
SOFTWARE
THR A:49 , SER A:51 , GLN A:98 , GLY A:99 , ARG A:100 , GLU A:103 , PHE A:123 , THR A:125 , ASN A:185 , ASP A:214 , THR A:216 , ARG A:217 , SER A:254 , LYS A:257 , MET A:379 , ARG A:404 , 9PO A:1459 , HOH A:2241 , HOH A:2372
BINDING SITE FOR RESIDUE PLI A1457
04
AC4
SOFTWARE
GLY A:52 , ASN A:262 , HOH A:2069 , GLU B:69 , HOH B:2282
BINDING SITE FOR RESIDUE K A1458
05
AC5
SOFTWARE
ARG A:100 , PHE A:123 , THR A:124 , ARG A:381 , PHE A:448 , PHE A:449 , PLI A:1457 , PO4 A:1461 , HOH A:2241 , TYR B:71
BINDING SITE FOR RESIDUE 9PO A1459
06
AC6
SOFTWARE
SER A:12 , TRP A:61 , MET A:65 , HOH A:2373 , SER B:12 , TRP B:61 , MET B:65
BINDING SITE FOR RESIDUE 9PO A1460
07
AC7
SOFTWARE
THR A:49 , PHE A:123 , ASN A:185 , ARG A:217 , LYS A:257 , ARG A:381 , ARG A:404 , PLP A:1257 , 9PO A:1459
BINDING SITE FOR RESIDUE PO4 A1461
08
AC8
SOFTWARE
GLU A:69 , HOH A:2088 , HOH A:2259 , GLY B:52 , ASN B:262 , HOH B:2255
BINDING SITE FOR RESIDUE K B1457
09
AC9
SOFTWARE
TYR A:3 , TYR A:324 , TYR A:414 , ASP A:418 , TYR B:3 , TYR B:324 , TYR B:414 , ALA B:415 , ASP B:418 , HOH B:2376 , HOH B:2416 , HOH B:2417
BINDING SITE FOR RESIDUE P33 B1458
10
BC1
SOFTWARE
ALA B:148 , GLY B:149 , ILE B:336 , ASP B:348 , LEU B:400 , HOH B:2418
BINDING SITE FOR RESIDUE 9PO B1459
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: BETA_ELIM_LYASE (A:247-265,B:247-265)
;
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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
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Exons
(0, 0)
Info
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2ycta_ (A:)
1b: SCOP_d2yctb_ (B:)
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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
d2ycta_
A:
1b
d2yctb_
B:
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CATH Domains
(0, 0)
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Pfam Domains
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Asym.Unit (321 KB)
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