EBI is an Outstation of the European Molecular Biology Laboratory. IntEnz Integrated relational Enzyme database 23 May 2015.

Slides:

Advertisements

Similar presentations

Enzyme Nomenclature & Classification

Advertisements

The EBI Enzyme Portal Cheminformatics and Metabolism Team.

EBI is an Outstation of the European Molecular Biology Laboratory. ChEBI: The story so far.

5 EBI is an Outstation of the European Molecular Biology Laboratory. Master title Molecular Interactions – the IntAct Database Sandra Orchard EMBL-EBI.

5 EBI is an Outstation of the European Molecular Biology Laboratory. Master title Molecular Interactions – the IntAct Database Sandra Orchard EMBL-EBI.

Other biological databases. Biological systems Taxonomic data Literature Protein folding and 3D structure Small molecules Pathways and networks Biological.

1 Enzymes Enzymes are biological catalysts. Recall that a catalyst speeds up the rate of a reaction by decreasing the activation energy needed for the.

Enzymes. What is an enzyme? globular protein which functions as a biological catalyst, speeding up reaction rate by lowering activation energy without.

Enzyme Structure, classification and mechanism of action

Biological Catalysts 21.2 Names and Classification of Enzymes 21.3 Enzymes as Catalysts 21.4 Factors Affecting Enzyme Activity Chapter 21 Enzymes.

ENZYME CLASSIFICATION EXERCISE (1) GLUCOSE + ATP  GLUCOSE-6-PHOSPHATE + ADP + H + (2) CH 3 CH 2 OH + NAD +  (CH3)CHO + NADH + H + (3) ATP + H 2 O  ADP.

EBI is an Outstation of the European Molecular Biology Laboratory. UniProt Jennifer McDowall, Ph.D. Senior InterPro Curator Protein Sequence Database:

MLAB 2401: Clinical Chemistry Keri Brophy-Martinez Enzymes: Overview.

Enzymatic Function Module (KEGG, MetaCyc, and EC Numbers)

Enzymes Definition Classification Chemistry Properties

Bioenergetic processes: biological oxidation.. Metabolism - the entire network of chemical reactions carried out by living cells. Metabolism also includes.

Introduction to metabolism: Compounds, Reactions, Enzymes and Pathways Kristian Axelsen, Alan Bridge Elisabeth Coudert & Anne Morgat SIB Swiss Institute.

1 II. Enzymes Proteins Organic catalysts that speed up the rate of a reaction, but are not used up Lower energy of activation Are specific in action, i.e.,

Enzymes Enzymes as Biological Catalysts

Chapter 3 Enzymes.

Cell Biology for Clinical Pharmacy Students MD102 Module II: Cell Functions (Lecture # 8 ) Dr. Ahmed Sherif Attia

Overview Enzymes are specialized proteins that function as catalysts to increase the rate of biochemical reactions. By interacting with substrates (reactant.

Biological Databases By : Lim Yun Ping E mail :

Enzymes: Basic concepts

ENZYMES BY DR. MARYJANE.

EBI is an Outstation of the European Molecular Biology Laboratory. ChEBI: The story so far Paula de Matos.

Introduction to Enzymes

Chapter 6.1 and 6.2: Introduction to Enzymes

1 Chapter 20 Enzymes and Vitamins 20.1 Enzymes Copyright © 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings.

Chp Chemistry 121 Winter 2009 LA Tech Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio State)

Enzymes are good catalysts

1 SURVEY OF BIOCHEMISTRY Enzyme Catalysis. 2 General Properties of Enzymes High reaction rates –10 6 to times faster than uncatalyzed reaction Mild.

1 Amino Acids, Proteins, and Enzymes Enzymes Enzyme Action Factors Affecting Enzyme Action Enzyme Inhibition.

Enzymes Biomolecules that catalyze chemical reactions - Increase reaction rates - Specific Oxidoreductases – catalyze redox reactions Transferases – transfer.

EBI is an Outstation of the European Molecular Biology Laboratory. Rhea Annotated reactions database 17 December 2015.

QUIZ 1.What is enzyme? 2.What is the function of enzyme? 3.What are the special characteristics of enzyme? 4.What kind of binding energy involve for the.

Chapter 16.6 & 16.7 Enzymes & Enzyme Actions

EBI is an Outstation of the European Molecular Biology Laboratory. Tutorial 5: ChEBI - On-line Submission and Curation.

1 Amino Acids, Proteins, and Enzymes Enzymes Enzyme Action Factors Affecting Enzyme Action Enzyme Inhibition.

Classification of enzymes. Units of enzyme activity.

Introduction to enzymes, enzyme catalyzed reactions and

Classification and Nomenclature of Enzymes

Aspirin Inhibits Cycloxygenase

Life Utilizes Energy PhototrophsChemotrophs HeterotrophAutotroph Energy Life Utilizes Matter.

Control of Metabolism Chapter 4. Topics 1.Overview of metabolic control at various level 2.Enzyme reactions and cofactors 3.Regulation of enzyme activities.

OncoTrack Bioinformatics Workshop Max Planck Institute for Molecular Genetics, Berlin Wednesday 6 th November 2013 TimeSubject 13:30-15:00 Introduction.

1 Enzymology INTRODUCTION 2006/09/18 Downloaded from

Catabolic and Anabolic Reactions  Metabolism: The sum of the chemical reactions in an organism.

Cheminformatics and Metabolism Team The EBI Enzyme Portal.

5 Microbial Metabolism.

Enzymes Enzymes as Biological Catalysts

Integrated relational Enzyme database

Enzymes Regulatory enzymes are usually the enzymes that are the rate-limiting, or committed step, in a pathway, meaning that after this step a particular.

20.2 Classification of Enzymes

Enzymes III Dr. Kevin Ahern.

Enzymes Enzymes can speed up a chemical reaction without being altered. Enzymes are biological catalysts. Each acts on a specific substance. The specificity.

Chapter Three: Enzymes

Clinical Enzymology Introduction.

Chapter 20 Enzymes and Vitamins

Bringing the Cyc to BioCyc

Identify the parts of the enzyme shown below:

Biomedical Importance of Enzymes Basic concepts about Enzymes Classification of Enzymes as per IUB.

4 th SEMESTER – BOTANY KARNATAKA UNIVERSITY, DHARWAD Modified from various internet resources by Dr. Jayakara Bhandary Associate Professor of Botany Government.

Chapter 16 Amino Acids, Proteins, and Enzymes

EC Numbers Are Everywhere

Annotation Presentation

Enzymes: Introduction

Classification of Enzymes

BIO103 Energy of Life HbR Dept. of Biology & Chemistry

Presentation transcript:

EBI is an Outstation of the European Molecular Biology Laboratory. IntEnz Integrated relational Enzyme database 23 May 2015

Enzymes Enzymes are proteins that catalyze chemical reactions. Very important as many processes in biological cells need enzymes.... As there are many enzymes in the world, a classification system was invented to help identify and name them... IntEnz23 May 20152

NC-IUBMB In the 1950’s the increasing amounts of known enzymes were causing confusion. No official nomenclature system for enzymes. The IUBMB created the International Commission on Enzymes in 1956 to deal with enzyme nomenclature Later replaced with the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) IntEnz23 May 20153

EC Numbers NC-IUBMB developed the Enzyme Classification number system (EC) Classification system is based on the reactions the enzymes catalyzed Classification:  Classes  Subclasses  Sub-subclasses  EC numbers (Enzyme Commission) Example EC IntEnz23 May 20154

EC Classification - Classes EC 1 – Oxidoreductases; catalyze oxidation/reduction reactions. EC 2 – Transferases; transfer a functional group e.g. Methyl group. EC 3 – Hydrolases; catalyse the hydrolysis of various bonds. EC 4 – Lyases; cleave various bonds by means other than hydrolysis and oxidation EC 5 – Isomerases; catalyse changes within one molecule. EC 6 – Ligases; joining of two molecules with concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. IntEnz23 May 20155

IntEnz23 May EC numbers lifecycle New Suggested Proposed Accepted Rejected Deleted Transferred Public Private

IntEnz ( IntEnz23 May 20157

IntEnz23 May What's in IntEnz Official Enzyme nomenclature from NC-IUBMB Data from ENZYME database (SIB)  Cofactors  Extra cross references: UniProtKB/Swiss-Prot, Prosite Extra cross references: CSA, GO Enzyme spotlights Two different views of the same data:  IntEnz  ENZYME

IntEnz23 May The (official) enzyme nomenclature Classification:  Classes  Subclasses  Sub-subclasses  EC numbers (Enzyme Commission) Nomenclature Reactions (as plain text) Comments Cross references: BRENDA, EXPASY, KEGG, ERGO, PDB, CAS registry Bibliographic references Maintained by NC-IUBMB

IntEnz Entry IntEnz23 May 2015 Classification system Accepted Name Reaction (Rhea) Cofactor (ChEBI) 10

IntEnz entry continued IntEnz23 May 2015 Citations UniProt Links 11

Simple Search Example IntEnz23 May

IntEnz23 May Simple search Search by EC number:    Search by compound:  Caffeine  CoA Search by enzyme name:  Oxalate oxidase  Agarase  3/4 collagenase Search by cross-reference:  Q42884  GO:

Advanced Search Example IntEnz23 May

IntEnz23 May Advanced search Search by reaction participant:  CoA  CoA-SH  CoASH  Coenzyme-A Search by cofactor:  CoA  magnesium manganese (any)  magnesium manganese (both)

IntEnz23 May Browsing IntEnz Browse the whole classification from the home page

Browsing via Enzyme entry IntEnz23 May 2015 Browse upwards from an enzyme entry 17

IntEnz23 May Downloading IntEnz IntEnzXML Individual enzymes/all of them ASCII format/XChars-enhanced format XSD available Query/format using XSLT enzyme.dat file Generated from IntEnz for SIB BioPAX level 2 A standard exchange format for biological pathway data Based in OWL (semantic web)

Rafael Alcántara (Developer, EBI) Kristian Axelsen (Curator, SIB) Paula de Matos (Coordinator, EBI) Anne Morgat (Curator, SIB) Christoph Steinbeck (Team leader, EBI) ftp://ftp.ebi.ac.uk/pub/databases/intenz IntEnz team and resources IntEnz23 May

IntEnz23 May Exercises!