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Clasificarea enzimelor
Shewale – Enzyme everywere - 1996
Enzyme classification
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Baze de date generale
Baze de date specifice
Baze de date pentru enzime
General databases
Database for special enzymes classes
Available enzyme databases
Enzyme Commission / International Union for Biochemistry and
Molecular Biology (IUBMB)
Comisia de Enzimologie /Uniunea Internațională de Biochimie și
Biologie Moleculară (IUBMB)
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http://www.enzyme-database.org/
Bazele de date generale
ExplorEnz
General enzyme databases
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Bazele de date generale
General enzyme databases
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Bazele de date generale
General enzyme databases
Raportare de enzime necatalogate → a sugereza modificări
To report not classified enzymes → requesting changes
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Bazele de date generale
ExplorEnz
General enzyme databases
Conținutul din ExplorEnz apare și pe pagina de web a
IUBMB / secțiunea nomenclatura enzimelor
The content of the ExplorEnz is also displayed on
IUBMB webpage on Enzyme Nomenclature
https://www.chem.qmul.ac.uk/iubmb/enzyme/
o rules for naming enzymes
o nomenclature of biochemical molecules
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Bazele de date generale
UniProt https://www.uniprot.org
SIB-ENZYME conectează nomenclatura cu secvența (UNIPROT)
SIB-ENZYME connects the nomenclature with sequence (UNIPROT)
General enzyme databases
SIB Swiss Institute of Bioinformatics
Compresive catalog of protein sequence/ functional annotation
It has four components
UniProt Knowledgebase (UniProtKB)
UniProt Archive (UniParc)
UniProt Reference Clusters (UniRef)
UniProt Metagenomic and Environmental Sequences
(UniMES)
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Bazele de date generale
https://enzyme.expasy.org/
General enzyme databases
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Bazele de date generale
http://www.ebi.ac.uk/intenz/
IntEnz – Integrated relational Enzyme database (nomenclatura)
General enzyme databases
Contain enzyme data – enzyme name / reaction – NC- IUBMB
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Bazele de date generale
IntEnz General enzyme databases
Some enzyme data
ChEBI
ChEBI – dictionary of Chemical
Compound of Biological Interest
Hosted by EBI
European Bioinformatics Institute
ChEBI provide links to protein
sequences (UniProt)
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Baze de date pentru enzime
http://www.brenda-enzymes.org/index.php
BRENDA
Enzyme-Fuctional databases
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o clasificare și nomenclatură
Baze de date pentru enzime
BRENDA - gamă largă de
proprietăți enzimatice
o reacții și specificitate
(substrate naturale/artificiale)
Enzyme-Fuctional databases
o classification și nomenclature
BRENDA – full range of
enzyme properties
o reactions și specificiy
(natural / artificial substrates)
Inhibitori, cofactori,
ioni metalici, activatori
Inhibitors, cofactors,
metal ions, activators
o Posedă un dictionar pentru
liganzi Chemical Identifier
(INChI)
o Equipped with a thesaurus for
ligand names
Chemical Identifier (INChI)
o Compuși care
interacționează (grafic)
o Compounds interacting
(graphical representations)
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Baze de date pentru enzime
BRENDA - gamă largă de
proprietăți enzimatice
o izolarea și prepararea
organism, tesut sau
localizare celulară
o fiecare intrare
referințe bibliografice
Enzyme-Fuctional databases
o structura enzimelor
o parametri funcționali
o informații legate de
organismul din care provin
TaxTree explorer
o Functional parameters
o organism-related
informations
TaxTree explorer
BRENDA – full range of
enzyme properties
o isolation and preparation
source of enzyme
organism, the tissue,
subcellular localization
o enzyme structure
o Each entry linked with
literature refereces
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Baze de date pentru enzime
o aplicații și inginerie
o enzimele - responsabile
pentru anumite boli
Enzyme-Fuctional databases
o application and engineering
o Enzyme – disease relationships
Două baze complementare
AMENDA
FRENDA
Two supplements to BRENDA
AMENDA
(Automatic Mining of ENzyme DAta)
FRENDA
(Full Reference ENzyme DAta)
Extrase din PubMed
Abstacte
Extracted from PubMed abstract
(US National Library of Medicine)
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Baze de date pentru enzime
KEGG - gamă largă de proprietăți enzimatice
Enzyme-Fuctional databases
KEGG (Kyoto Encyclopedia of Gene and Genomes)
Informații despre enzime - parte a bazei de date LIGAND
Enzyme information is stored as a part of the LIGAND database
Conține Consisting of
compusi compound
medicamente drug
glicani glycan
reactii reaction
Interactiuni reactanti Rpair (reactant
pair alignment)
enzime enzymes
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Baze de date pentru enzime
Enzyme-Fuctional databases
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Baze de date pentru enzime
Enzyme-Fuctional databases
KEGG – mentinuta de
Kanehisa Laboratories in the Bioinformatics Center of Kyoto
și de Human Genom Center of the University of Tokyo
KEGG – developed and mantained by
Kanehisa Laboratories in the Bioinformatics Center
of Kyoto and the Human Genom Center of the
University of Tokyo
Date
Nomenclatura
Substrate
Produsi
Reactii
Nume de gene
Structura metaboliti
Diagrame reactie
Căi metabolice
Data comprise
Nomenclature
Substrates
Products
Reactions
Gene names
Chemical structure of metabolites
Reactions diagrams
Metabolic pathways
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Baze de date specializate pentru unele enzime
Special Enzyme Databases
MEROPS (https://www.ebi.ac.uk/merops/)
Baza de date pentru peptidaze
(proteaze, proteinaze sau
enzime proteolitice)
Resourse for peptidase
(proteases, proteinases or
proteolytic enzymes)
ClasificareaCompararea secvențelor
(proteolitic / de legare inhibitor)
The ClassificationSequence comparisons
Domains (peptidase / inhibitor
unit)
O proteină a cărei secvență
este cunoscută și care este
caracterizată biochimicreprezentativă
A proteine that has been
sequenced and characterized
biochemically Representative (“holotype”)
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Baze de date specializate pentru unele enzime
Special Enzyme Databases
MEROPS (https://www.ebi.ac.uk/merops/)
Secvențele
Variante ale secv.
reprezentativeSpecii proteice
All sequences
Variants of holotype“Protein species”
Secvențele proteice
asemănătoare statisticFamilie
The sequences of statistically
related protein species“Family”
Familia
3D asemănătoare
str. primară situs activ similarăascendent comun → Clan
Family
similar 3D structure
active site residues same ordercommon ancestor → “Clan”
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Baze de date specializate pentru unele enzime
Special Enzyme Databases
MEROPS (https://www.ebi.ac.uk/merops/)
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Baze de date specializate pentru unele enzime
Special Enzyme Databases
MEROPS
Descrierea specificității
pentru substratPeptidaze cu > 10 scindări
O prezentare a preferințelor
si de clivare
The substrate specificity Any peptidase with > 10 cleavages
A display – the amino acids
preferred at its substrate binding
sites
Aminoacizii
Verde polari
Rosu acizi
Albastru bazici
Negri nepolari
Amino acids
green polar
red acidic
blu basic
black hydrophobic
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Baze de date cu enzime specializate
MEROPS – specificitate de clivare cleavage specificity
aminopeptidase A
(Homo sapiens)
Ectoenzimă
degradează
angiotensina II
Dostal, D.E. Baker, K. M.
Circulation Research.
1999;85:643-650
Special Enzyme Databases
Ectoenzyme
degrades
angiotensin II
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Baze de date cu enzime specializate
MEROPS
substrate
cu relevanță fiziologică (P)
sau nu (N)
substrate sintetice (S)
Special Enzyme Databases
MEROPS
artificial (S) substrate
pathologicaly relevant (P)
or not (N)
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Baze de date pentru enzime
Baze de date cu enzime specializate
MetaCyc (https://metacyc.org)
Special Enzyme Databases
metabolismul
moleculelor
de dimensiuni mici
conține căi metabolice
(microbiane sau
vegetale)
dovedite experimental
informații - enzimele ce
asistă anumite reacții
Enzyme-Fuctional databases
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Baze de date pentru enzime
Baze de date cu enzime specializate
MetaCyc – căutare după cod
Special Enzyme Databases
Enzyme-Fuctional databases
Search by EC number / names
orz
barley (Hordeum vulgare)
Enzima-marker pt dezvoltarea
embrionară a semințelor de grâu
(în decursul germinației)
The enzyme serves as a marker
of embryonic development
in germinating wheat grains
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Baze de date pentru enzime
Baze de date cu enzime specializate
MetaCyc
Special Enzyme Databases
Enzyme-Fuctional databases
Diagramă grafică
a reacției
A graphycal
reaction diagram
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Baze de date pentru enzime
Baze de date cu enzime specializate
REBASE (http://rebase.neb.com/rebase/rebadvsearch.html)
Special Enzyme Databases
Enzyme-Fuctional databases
enzimele de restricție
ADN metiltransferazele
proteinele înrudite Procesele biologice de restricție-
modificare
restriction enzymes
DNA methyl transferases
related proteinsRestriction-modification process
Informații bibliografice situsurilor de recunoaștere
de legare
disponibilitatea comercială
sensibilitatea la metilare,
cristalizarea
secvențelor acestora
Referenced informationrecognition and cleavage sites
commercial availability
methylation sensitivity
crystal data
sequence data
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Baze de date pentru enzime
Baze de date cu enzime specializate
REBASE
Special Enzyme Databases
Enzyme-Fuctional databases
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Baze de date pentru enzime
Baze de date cu enzime specializate
REBASE
Enzyme-Fuctional databases
Special Enzyme Databases
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Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
REBASE
Date cinetice Kinetic data
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http://www.cazy.org/CAZY – Carbohydrate-Active enZYme Database
Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
familii de “module” enzimatice
legare carbohidrațilorFormare/modificare/clivare
legături glicozidice
Glicozil transferaze
Formare de di-, oligo- sau
polizaharide
Families of structurally related
catalytic and carbohydrate-
binding modulesDegrade/modify/create new glycosidic
bonds
Glycosyl transferase (EC 2.4.a.b.)
https://www.sbhsciences.com/
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CAZY
Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
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CAZY
Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
Alte clase
de enzime Liaze
esteraze
Enzime active la
carbohidrați
identificarea in genom
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Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
CAZYpedia http://www.cazypedia.org/
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http://bioinf.man.ac.uk/phosphabase/index.html
PhosphaBase (PhB) – baza de date pentru fosfataze
Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
T. Igawa, International journal of urology, 2017
DOI:10.1111/iju.13197aria
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Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
resorufin-based substrates
protein tyrosine phosphatase (PTP)
activity in vitro and in living cells
acidic and neutral pH.
Substrate pe bază de resorufin
protein tirozin fosfataze (PTP)
activitatea in vitro și in vivo
pH acid / neutru
Biswa et. al, Chemical Communication, 14, 2017
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PhosphaBase (PhB) – baza de date pentru fosfataze
Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
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DEPOD – baza de date pentru fosfataze umane
http://depod.bioss.uni-freiburg.de/
Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databasesSpecial Enzyme Databases
The human EPhOsphorylation Dtabase
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DEPOD
Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
Substrate experimentale
testate
Proteic and nonproteic
substrates
Metabolic
Pathway
KEGG
Cai
metabolice
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http://www0.nih.go.jp/mirror/Kinases/
PKR – the Protein Kinase Resource (old)
Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
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3000 de gene pentru kinaze
genomul uman
Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
3,000 protein kinase genes
in human genomes
Funcțiile
Evoluțiile
diversitatea
Factori
comportarea
celulară
“kinome”
function
evolutiondi
versity
key
controlers
cell
behavior
kinome
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https://randr.nist.gov/enzyme/Default.aspx
TECRDB
The Thermodynamics of Enzyme-catalyzed Reactions Database
Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
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TECRDB
Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
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TECRDB
Baze de date pentru enzime
Baze de date cu enzime specializate
Enzyme-Fuctional databases
Special Enzyme Databases
cod
EC
metoda
tamponul
reactia
Enzima
cofactorul
ID
EC
method
buffer
reaction
enzyme
cofactor
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Baze de date pentru enzime
http://enzymefunction.org/projects
EFI (Enzyme Function Initiative)
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Scindarea legaturilor peptidice din lanturile proteinelor (enzimelor)
2. Caracterizarea enzimei3.2. Determinarea structurii primare
Proteaza Natura legaturii peptidice clivate
N-terminal -----XYZ----------C-terminal
X Y Z
Tripsina
Clostripaina
Chimotripsina
Elastaza
Papaina
Endoproteaza Glu-C
Pepsina
-
-
-
-
Phe
-
-
Lys, Arg
Arg
Trp, Tyr, Phe
Leu, Met, Ala
Lys
Glu, Asp
Phe
-
-
-
-
Leu si Trp
-
Phe, Trp, Tyr
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CLASA Caracteristici inhibitor exemple functia
Serin proteaze situsul activ fluorofosfat tripsina digestia
H57, D102, S195 trombina coagulare sange
plasmina scindare cheaguri
subtilisina digestia
Cistein proteaze situsul activ iodoacetat papaina digestia
C25, H159, N175 strept. proteinaza digestia
catepsin B digestia
Acid proteaze pH optim acid diazocetone pepsina digestia
D32, D215 chimozina coagulare lapte
Metaloproteaze Zn2+, E270 o-phenanthroline carboxipeptidazele digestia
Zn2+, Ca2+ o-phenanthroline termolizina digestia
E143, H231
Scindarea legaturilor peptidice din lanturile proteinelor (enzimelor)
2. Caracterizarea enzimei3.2. Determinarea structurii primare
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Tripsina-scindeaza la legaturile peptidice Lys/Arg
3. Caracterizarea enzimei3.2. Determinarea structurii primare
Exemplu de proteaze
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Scindarea metioninei
3. Caracterizarea enzimei3.2. Determinarea structurii primare
Scindare chimica
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Enzima
puraReactii de
clivare
Etapa 1 Amestec de
fragmenteSepararea
fragmentelor
Etapa 2 Fragmente
purificate
Etapa 3
secventierea
Set de
secvente
individuale
Etapa 4
-clivarea
alternativa;
-separarea si
secventiereaSecventa
completa
2. Caracterizarea enzimei2.2. Determinarea structurii primare
Amestec
complexProteoliza
PeptideSepararea
fragmentelor
HPLC Fragmente
purificate
LC-MS/MS
Izolare
peptidaFragmentare
(Spectru de masa)
Tripsina
Baza de date
Secvente
Complete
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3. Caracterizarea enzimei3.2. Determinarea structurii primare
Pehr Edman
1972-secventa
fibrinogenului
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Structura
primara
Mw
Localizare AA
Identificarea de parti functionale
Fosfolipaza A2 ALWQF
interacțiuni cu substratul nepolar
Stabilirea unor relatii de evolutie
3. Caracterizarea enzimei3.2. Determinarea structurii primare
Determinarea pI
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Structuri 3D determinate experimental http://www.rcsb.org/pdb/
Baze de date pentru proteine/enzime
http://www.expasy.org/proteomics
http://www.uniprot.org/ (pir.georgetown.edu)
http://www.nextprot.org/ Proteine umane
http://string-db.org/ Interactiuni dintre proteine
NCBI http://www.ncbi.nlm.nih.gov/pubmed
Cea mai mare baza de date
5 milioane proteine
Expert Protein Analysis System ExPASy