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2VLH
Biol. Unit 1
Info
Asym.Unit (174 KB)
Biol.Unit 1 (331 KB)
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(1)
Title
:
QUINONOID INTERMEDIATE OF CITROBACTER FREUNDII TYROSINE PHENOL-LYASE FORMED WITH METHIONINE
Authors
:
D. Milic, T. V. Demidkina, D. Matkovic-Calogovic, A. A. Antson
Date
:
14 Jan 08 (Deposition) - 19 Aug 08 (Release) - 02 Dec 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Plp-Dependent Enzyme, Quinonoid Intermediate, Lyase, Pyridoxal Phosphate, Tyrosine Degradation
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
D. Milic, T. V. Demidkina, N. G. Faleev, D. Matkovic-Calogovic, A. A. Antson
Insights Into The Catalytic Mechanism Of Tyrosine Phenol-Lyase From X-Ray Structures Of Quinonoid Intermediates.
J. Biol. Chem. V. 283 29206 2008
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Hetero Components
(4, 8)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
2a: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20... (P33a)
3a: TRIETHYLENE GLYCOL (PGEa)
4a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
5a: (2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5... (PM9a)
View:
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Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
P33
2
Ligand/Ion
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
3
PGE
2
Ligand/Ion
TRIETHYLENE GLYCOL
4
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
5
PM9
2
Ligand/Ion
(2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}-4-(METHYLSULFANYL)BUTANOIC ACID
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
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 , THR A:216 , ARG A:217 , SER A:254 , LYS A:257 , MET A:379 , ARG A:381 , ARG A:404 , PHE A:449 , HOH A:2425 , TYR B:71
BINDING SITE FOR RESIDUE PM9 A1457
2
AC2
SOFTWARE
GLY A:52 , ASN A:262 , HOH A:2083 , GLU B:69 , HOH B:2311
BINDING SITE FOR RESIDUE K A1458
3
AC3
SOFTWARE
GLN B:98 , GLY B:99 , ARG B:100 , GLU B:103 , PHE B:123 , THR B:126 , ASN B:185 , ASP B:214 , THR B:216 , ARG B:217 , SER B:254 , LYS B:257 , HOH B:2223 , HOH B:2458
BINDING SITE FOR RESIDUE PLP B1257
4
AC4
SOFTWARE
GLU A:69 , HOH A:2100 , HOH A:2299 , GLY B:52 , ASN B:262 , HOH B:2289
BINDING SITE FOR RESIDUE K B1458
5
AC5
SOFTWARE
LYS A:226 , GLU A:233 , TYR A:312 , HOH A:2426 , HOH A:2427
BINDING SITE FOR RESIDUE PGE A1459
6
AC6
SOFTWARE
MET A:1 , TYR A:3 , ASP A:418 , HOH A:2429 , TYR B:3 , TYR B:324 , TYR B:414 , ALA B:415 , ASP B:418 , VAL B:419 , ASP B:422 , HOH B:2415
BINDING SITE FOR RESIDUE P33 A1460
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SAPs(SNPs)/Variants
(0, 0)
Info
(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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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
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Exons
(0, 0)
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Note:
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_d2vlha_ (A:)
1b: SCOP_d2vlhb_ (B:)
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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
d2vlha_
A:
1b
d2vlhb_
B:
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2vlhA02 (A:58-310)
1b: CATH_2vlhB02 (B:58-310)
2a: CATH_2vlhA01 (A:1-57,A:311-455)
2b: CATH_2vlhB01 (B:1-57,B:311-455)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aspartate Aminotransferase; domain 2
(384)
Homologous Superfamily
:
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
(384)
Citrobacter freundii. Organism_taxid: 546.
(2)
1a
2vlhA02
A:58-310
1b
2vlhB02
B:58-310
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aspartate Aminotransferase, domain 1
(355)
Homologous Superfamily
:
Aspartate Aminotransferase, domain 1
(354)
Citrobacter freundii. Organism_taxid: 546.
(2)
2a
2vlhA01
A:1-57,A:311-455
2b
2vlhB01
B:1-57,B:311-455
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Pfam Domains
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