27 th September 2017 wwwuniprotorg The two sides of UniProtKB curated by experts data from scientific papers annotation of sequence features collates isoforms in one entry annotation from rule systems incl expertcurated rules ID: 917262
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Slide1
Enzymes in UniProtKB
Webinar
27th September 2017
Slide2www.uniprot.org
Slide3The two sides of UniProtKB
curated by experts
data from scientific papers
annotation of sequence features
collates isoforms in one entry
annotation from rule systems (incl. expert-curated rules)
mapped experimental sequence features (3D structures)
isoforms are kept separate
Slide4Specific information for enzymes
pathway
kinetics
cofactor
Enzyme regulation
Catalytic activity
Slide5Specific information for enzymes
EC number
Slide6Specific information for enzymes
Cofactor binding sites
Substrate binding sites
Catalytic site
Slide7Catalytic activity and EC number
EC (E
nzyme Commission) number Provide a classification for enzymatic reactionsCatalytic activity: description of the reaction
EC 2.7.11.1
class
s
ub-class
sub-subclass
http://www.ebi.ac.uk/intenz/
EC 1.-.-.- oxidoreductases
EC
2.-.-.- transferases
EC
3.-.-.- hydrolases
EC
4.-.-.-
lyases
EC
5.-.-.- isomerases
EC
6.-.-.- ligases
5%
Slide8Catalytic activity and EC number
Complete EC number
Partial EC number
No catalytic activity -> Function
Experimental evidence
Slide9Cofactor
non-protein substance required for a protein to be catalytically activeInorganic: metal atoms zinc, iron,
etc.Organic: vitaminsmapped to ChEBI identifiers
Slide10Biophysicochemical properties
Information about enzyme biophysical
and chemical propertieskinetic dataMichaelis-Menten constant (KM) and maximal velocity (Vmax).Physiological substratesoptimum pH for enzyme activityoptimal
temperature for enzyme
activity
Slide11Enzyme regulation
Describe components which regulate the enzyme activity:natural and
synthetic productsallostericpost-translational modification (ex. phosphorylation)
Slide12Pathway
describes the metabolic pathway(s) associated with a protein
Slide13Additional information
Function: more substrates, contextPost translational modification (phosphorylation, cleavage etc.)
Slide14Active site
indicates the residues directly involved in catalysisif known, we provide the exact role (ex.
nucleophile etc..)
Slide15Substrate/cofactor binding sites
Slide16Feature viewer: summary of sequence features
Slide17Feature viewer: summary of sequence features
Slide18Feature viewer: summary of sequence features
Slide19Search
Free text
Advanced search -> combining search in various fields
Slide20Example 1: Search for acetyltransferases using EC number
Acetyltransferase -> EC 2.3.2.-
Slide21Results
Slide22Example 2: metalloproteases and diseases
How many metalloproteases that uses zinc as a cofactor are related to
a disease?
Slide23How can I see the disease(s) in which they are involved?
Results
Customizing columns
Slide24Customizing result page columns
Slide25Slide26Cross-references to external resources
information related to enzymes and found in data collections other than UniProtKB
Slide27Cross-references to external
resources
Enzymatic reaction
Enzyme families
Pathways
Slide28EBI-Enzyme Portal
http://www.ebi.ac.uk/enzymeportal/
Slide29Finding help
http://www.uniprot.org/help/advanced_search
http://www.uniprot.org/help/catalytic_activityhttp://www.uniprot.org/help/act_sitehttp://www.uniprot.org/help/biophysicochemical_propertieshttp://
www.uniprot.org/help/cofactor
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Slide30PIs
:
Alex Bateman, Cathy Wu, Ioannis Xenarios
Key staff
:
Alan Bridge (
Content),
Cecilia
Arighi
(Curation
), Darren
Natale
(Content
),
Hongzhan Huang (Development), Lydie Bougueleret (Co-direction), Manuela
Pruess (Coordination), Maria Martin (Development), Michele Magrane (Curation), Nicole Redaschi (Development), Peter McGarvey (Content), Sandra Orchard (Content), Sylvain Poux (Curation)Content/Curation: Aleksandra Shypitsyna, Alistair MacDougall, Andre Stutz, Andrea Auchincloss, Anne Estreicher, Anne Morgat
, Arnaud
Gos
,
Barbara
Palka
,
Bernd
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, Brigitte
Boeckmann
,
C
. R.
Vinayaka
,
Catherine
Rivoire
, Chantal
Hulo
, Christian
Sigrist
, Cristina
Casals
Casas, Damien
Lieberherr
,
Daniel Gonzalez, Elena
Speretta
,
Elisabeth
Coudert
,
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Boutet, Florence Jungo, George Georghiou, Ghislaine Argoud-Puy, Guillaume Keller, Hema Bye-A-Jee, Ivo Pedruzzi, John S. Garavelli, Karen Ross, Kate Warner, Kati Laiho, Klemens Pichler
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Yeh
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Aimo
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Gruaz
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Penelope
Garmiri
,
Philippe
Lemercier
,
Qinghua
Wang,
Ramona
Britto
, Rossana
Zaru
,
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Pilbout
,
Shyamala
Sundaram
, Ursula
Hinz
,
Yvonne
Lussi
Development:
Alan
Da
Silva,
Alexandr
Ignatchenko
, Alexandre
Renaux
, Andrew Nightingale,
Arnaud
Kerhornou
, Beatrice
Cuche
,
Benoit Bely,
Borisas
Bursteinas
,
Chuming
Chen,
Delphine
Baratin
,
Dushyanth Jyothi,
Edouard
De
Castro,
Edward Turner,
Elisabeth
Gasteiger
,
Emanuele
Alpi
,
Guoying
Qi, Hermann
Zellner
,
Jerven
Bolleman
,
Jian Zhang,
Jie
Luo, Joseph
Onwubiko
, Leonardo Gonzales,
Leslie
Arminski
,
Leyla
Garcia
Castro, Mark Bingley,
Monica
Pozzato
,
Parit
Bansal,
Rabie
Saidi
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Sangya
Pundir
, Sara
Benmohhamed
,
Sebastien Gehant, Teresa Batista Neto, Thierry Lombardot, Tony Sawford, Tony Wardell, Tunca Dogan, Vicente Lara, Vishal Joshi, Vladimir Volynkin, Wudong Liu, Xavier Martin, Xavier Watkins, Yongxing Chen, Yuqi Wan
European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
SIB Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
UniProt
Team
Protein Information Resource (PIR), Washington DC and Delaware, USA
Slide31UniProt funding
UniProt
is supported by the National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI) and National Institute of General Medical Sciences (NIGMS) grant U41HG007822.
Additional support for the
EMBL-EBI
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, the
British Heart Foundation (BHF
) (RG/13/5/30112), the
Parkinson's Disease United Kingdom (PDUK)
GO grant G-1307, and the NIH
GO grant U41HG02273.
UniProt activities at the
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