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Pathways & MoleculesM.A. Ott (CMBI)
Contents
Pathways and MoleculesM.A. Ott
• Enzymes and Metabolites
• Metabolic Pathways: Cholesterol Biosynthesis
• Metabolic Disorders
• BioMeta Database
Metabolite and Pathway Databases
Pathways and MoleculesM.A. Ott
http://www.genome.ad.jp/kegg/
http://www.brenda.uni-koeln.de/
http://www.expasy.org/tools/pathways/
http://www.empproject.com/
http://metacyc.org/
http://ecocyc.org/
http://www.ncgr.org/pathdb/
http://medicago.vbi.vt.edu/B-Net/
http://www.mol-net.de/biopath/
http://www.ergo-light.com/ERGO/
http://www.reactome.org/
http://www.chem.qmul.ac.uk/iubmb/enzyme/
Kyoto Encyclopedia of Genes and Genomes
BRENDA enzyme database
ExPASy biochemical pathway
EMP enzymology and metabolism data
MetaCyc metabolic pathways
EcoCyc E. coli genome and metabolism
PathDB biological pathways and networks
B-NET - Biochemical Network
BioPath C@ROL database
ERGO comprehensive genome analysis
Reactome biological processes
IUBMB enzymes
Metabolism and Friends
Pathways and MoleculesM.A. Ott
• Metabolism: The reactions in organisms
• Anabolism: Synthesis of larger biomolecules
from smaller ones
» Usually requires energy input
• Catabolism: Break down of larger molecules
into smaller ones
» Usually releases energy
Enzymes
Pathways and MoleculesM.A. Ott
• Virtually all metabolic reactions require enzymatic
catalysis
• Rate enhancement factor can be up to 1015
• Enzymes are highly reaction-specific, catalyzing
only one conversion
• Enzymes are substrate-specific, limiting their action
to only one compound or to related compounds
The Metabolic Network
Pathways and MoleculesM.A. Ott
Some Metabolites
Pathways and MoleculesM.A. Ott
• “Common” metabolites:
Water, NADH, ATP, Phosphate, …
• End products of pathways:
Vitamin B12, Urea, Penicillin, Ecdysone, …
• Intermediates in pathways:
Glucose-6-P, Lanosterol, Precorrins, Shikimate, …
O
O
O
O
O
O
O
O
O
O
O
H
H
H
OP
O
O O
Common Metabolites: ATP / ADP
Pathways and MoleculesM.A. Ott
RO
POH
O OHR
OH
N
N
ON
OHN
NH2
OPO
OH
O
PO
OH
O
P
OH
OH
O
OH
N
N
ON
OHN
NH2
OPO
OH
O
POH
OH
O
OH
2.7.1.10+ +
RO
POH
O OHR
OH
2.7.1.10
ATP ADP
Full structures:
Shorthand:
Common Metabolites: NADH / NAD+
Pathways and MoleculesM.A. Ott
Full structures:
Shorthand:
R1
O
R2 R
1
OH
R2H1.1.1.63
NADH, H+ NAD+
PO O
O OH
PO
OH O
O
OH
O
OH
N
OHOH
N+
N
N
N
NH2
ONH2
PO O
O OH
PO
OH O
O
OH
O
OH
N
OHOH
N
N
N
N
NH2
ONH2
H+
R1
OH
R2HR
1
O
R2
1.1.1.63+ ++
Common Metabolites
Pathways and MoleculesM.A. Ott
WaterAmmoniaPhosphateATP, ADPNADH, NAD+
NADPH, NADP+
FAD, FADH2FMN, FMNH2SAM, SAHCoenzyme AGlutamate/2-Oxoglutarate
PhosphorylationReduction/oxidationReduction/oxidation
Reduction/oxidationReduction/oxidationMethyl group transferAcyl group transferAmino/ketone group exchange
Cholesterol Biosynthesis: Outline
Pathways and MoleculesM.A. Ott
H
H
H
H
OH
C2
Acetate
C5
Isopentenyl-PP
C30
Lanosterol
C27
Cholesterol
C30
Squalene
C6
Mevalonate
C30
Lanosterol
C5
Isopentenyl-PPx 3
x 6
- CO2
- 2 CO2
- HCO2H
Cholesterol Biosynthesis from Squalene
Pathways and MoleculesM.A. Ott
H
H
H
H
OH
HH
H
OH
H
H
H
H
OH
CH3
HHO
H
O
H
HOH
H
H
HO
H
H
H
H
H
H
OH
Squalene
Cholesterol
Lanosterol
Zymosterol
Metabolic Disorders
Pathways and MoleculesM.A. Ott
• Inability to synthesize compounds:
Absence of important compounds
• Inability to degrade compounds:
Accumulation of undesired waste products
E.g., in phenylketonuria
Phenylketonuria (Error in Phenylalanine Catabolism)
Pathways and MoleculesM.A. Ott
NH2
OH
O
Phenylalanine
NH2
OH
O
OHTyrosine
O
OH
O
Phenylpyruvate
OH
OH
O
Phenyllactate
NADPH, H+ NADP+
Glutamate
2-Oxoglutarate
O2 H2O
BH4 BH2
The BioMeta Database
Pathways and MoleculesM.A. Ott
BioMeta Database Structure
Pathways and MoleculesM.A. Ott
BioMeta Database Structure
Pathways and MoleculesM.A. Ott
R# M# Role Stoich1 1 Substrate 11 2 Substrate 11 3 Product 11 4 Product 12 2 Substrate 12 3 Substrate 12 5 Product 12 6 Product 13 6 Substrate 23 7 Product 1
# CASREG1 1065-31-72 387-49-33 76-55-14 182-20-95 450-16-56 2754-97-27 233-04-8
# Revers1 Yes2 No3 No
Molecules
Reaction 1: Mol_1 + Mol_2 <-> Mol_3 + Mol_4
Reaction 2: Mol_2 + Mol_3 --> Mol_5 + Mol_6
Reaction 3: 2 Mol_6 --> Mol_7R-M Links
Reactions
Sample Database Query
Pathways and MoleculesM.A. Ott
OH
O
OH
O O
O
O
O
O2 H2O2
EC 1.2.3.4+
ec_nr | enzyme_name | rxn_id |rev| role |stoich| name
--------+-----------------+----------+---+------+------+------------
1.2.3.4 | oxalate oxidase | MR000247 | i | s | 1 | Oxalic acid
1.2.3.4 | oxalate oxidase | MR000247 | i | s | 1 | O2
1.2.3.4 | oxalate oxidase | MR000247 | i | p | 1 | H2O2
1.2.3.4 | oxalate oxidase | MR000247 | i | p | 2 | CO2
Molecular Structures and Reactions
Pathways and MoleculesM.A. Ott
NN
NNH
O
O
OH
OHOH
OH
POH OH
OH
OP OOH
OH
O O
OH OH
OH
Chiral
P OOH
OH
O
OH
OH
OH
NH
NH
NH2 NH
O
O
+ +
Reactions: balancing atoms & charges
adding direction/reversibility
Molecules: adding stereochemical configurations
“canonicalizing” tautomeric form
Alternative Pathways
Pathways and MoleculesM.A. Ott
O
O O
O
O
O
O
O O
O
O
O
O
O O
O
O
O
NADH, H+ NADH, H+
NAD+ NAD+
1.1.1.931.1.1.93
5.1.2.5
BioMeta Database
Pathways and MoleculesM.A. Ott
• Based on freely available data (KEGG Ligand database)
• Augmentation, completion and correction of
small-molecule information:
- Adding missing stereochemistry to structures
- Balancing atoms and charges in reactions
- Establishing the reversibility and direction of reactions
• Search for alternative pathways between metabolites
• Search for “missing” enzymes
BioMeta: Things Being Done
Pathways and MoleculesM.A. Ott
• Enhancing compound/reaction structures
• Establishing directionality/reversibility of reactions
• Distinguishing cofactors/“current”/“external”/ “common” metabolites from “real” metabolites
• Adding more compound data, e.g. pKa (curve)
• Building WWW interface
BioMeta: Things To Do
Pathways and MoleculesM.A. Ott
• Atom-to-atom correspondence (reaction mapping)
• Pathway search & generation
• Cellular localization
• Enzyme – species relations
Acknowledgements
Pathways and MoleculesM.A. Ott
Felix van Diggelen
Gert Vriend
CMBI
