Class 1 Oxidoreductases: EC 1

735 Pages·2013·3.2 MB·English

by  Professor Dietmar Schomburg, Dr. Ida Schomburg (auth.), Professor Dietmar Schomburg, Dr. Ida Schomburg (eds.)

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123
Springer Handbook of Enzymes
Supplement Volume S8

Dietmar Schomburg and
Ida Schomburg (Eds.)
Springer Handbook
of Enzymes
Supplement Volume S8
Class 1
Oxidoreductases
EC 1
coedited by Antje Chang
Second Edition
1 3
Professor Dietmar Schomburg TechnicalUniversityBraunschweig
e-mail: [email protected] Bioinformatics & Systems Biology
Langer Kamp 19b
Dr. Ida Schomburg 38106 Braunschweig
e-mail: [email protected] Germany
Dr. Antje Chang
e-mail: [email protected]
Library of Congress Control Number: 2013933107
ISBN 978-3-642-36264-4 ISBN (eBook) 978-3-642-36265-1
2nd Edition Springer Berlin Heidelberg New York
The first edition was published as the “Enzyme Handbook, edited by D. and
I.Schomburg”.
Thisworkissubjecttocopyright.Allrightsarereserved,whetherthewholeorpartofthematerialis
concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,
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LawofSeptember9,1965,initscurrentversion,andpermissionforusemustalwaysbeobtained
fromSpringer.ViolationsareliabletoprosecutionundertheGermanCopyrightLaw.
SpringerisapartofSpringerScience+BusinessMedia
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#Springer-VerlagBerlinHeidelberg2013
PrintedinGermany
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Preface
Today, as the full information about the genome is becoming available for a
rapidly increasing number of organisms and transcriptome and proteome
analysesarebeginningtoprovideuswithamuchwiderimageofproteinregu-
lationandfunction,itisobviousthattherearelimitationstoourabilitytoaccess
functionaldata for the geneproducts –theproteinsand,inparticular,foren-
zymes. Those data are inherently very difficult to collect, interpret and stan-
dardizeastheyarewidelydistributedamongjournalsfromdifferentfieldsand
areoftensubjectto experimentalconditions.Nevertheless asystematiccollec-
tionisessentialforourinterpretationofgenomeinformationandmoresofor
applicationsofthisknowledgeinthefieldsofmedicine,agriculture,etc.Progress
onenzymeimmobilisation,enzymeproduction,enzymeinhibition,coenzyme
regenerationandenzymeengineeringhasopenedupfascinatingnewfieldsfor
thepotentialapplicationofenzymesinawiderangeofdifferentareas.
ThedevelopmentoftheenzymedatainformationsystemBRENDAwasstartedin
1987 at the German National Research Centre for Biotechnology in Braun-
schweig(GBF),continuedattheUniversityofColognefrom1996to2007,and
then returned to Braunschweig, to the Technical University, Institute of Bio-
informatics & Systems Biology. The present book “Springer Handbookof En-
zymes”representstheprintedversionofthisdatabank.Theinformationsystem
hasbeendevelopedintoafullmetabolicdatabase.
The enzymes in this Handbook are arranged according to the Enzyme Com-
mission list of enzymes. Some 5,000 “different” enzymes are covered. Fre-
quently enzymes with very different properties are included under the same
EC-number.Althoughweintendtogivearepresentativeoverviewonthechar-
acteristicsandvariabilityofeachenzyme,theHandbookisnotacompendium.
Thereaderwillhavetogototheprimaryliteratureformoredetailedinforma-
tion.Naturallyit isnotpossibletocoverallthenumerousliteraturereferences
foreachenzyme(forsomeenzymesupto40,000)ifthedatarepresentationisto
beconciseasisintended.
Itshouldbementionedherethatthedatahavebeenextractedfromtheliterature
andcriticallyevaluatedbyqualifiedscientists.Ontheotherhand,theoriginal
authors’ nomenclatureforenzyme formsand subunits is retained. Inorder to
keepthetablesconcise,redundantinformationisavoidedasfaraspossible(e.g.
if K values are measured inthe presence of an obvious cosubstrate, only the
m
nameofthecosubstrateisgiveninparenthesesasacommentarywithoutrefer-
encetoitsspecificrole).
Theauthorsaregratefultothefollowingbiologistsandchemistsforinvaluable
helpinthecompilationofdata:CorneliaMunarettoandDr.AntjeChang.
Braunschweig
Autumn2012 DietmarSchomburg,IdaSchomburg
V

List of Abbreviations
A adenine
Ac acetyl
ADP adenosine5’-diphosphate
Ala alanine
All allose
Alt altrose
AMP adenosine5’-monophosphate
Ara arabinose
Arg arginine
Asn asparagine
Asp asparticacid
ATP adenosine5’-triphosphate
Bicine N,N’-bis(2-hydroxyethyl)glycine
C cytosine
cal calorie
CDP cytidine5’-diphosphate
CDTA trans-1,2-diaminocyclohexane-N,N,N,N-tetraaceticacid
CMP cytidine5’-monophosphate
CoA coenzymeA
CTP cytidine5’-triphosphate
Cys cysteine
d deoxy-
d- (andl-)prefixesindicatingconfiguration
DFP diisopropylfluorophosphate
DNA deoxyribonucleicacid
DPN diphosphopyridiniumnucleotide(nowNAD+)
DTNB 5,5’-dithiobis(2-nitrobenzoate)
DTT dithiothreitol(i.e.Cleland’sreagent)
EC numberofenzymeinEnzymeCommission’ssystem
E.coli Escherichiacoli
EDTA ethylenediaminetetraacetate
EGTA ethyleneglycolbis(-aminoethylether)tetraacetate
ER endoplasmicreticulum
Et ethyl
EXAFS extendedX-rayabsorptionfinestructure
FAD flavin-adeninedinucleotide
FMN flavinmononucleotide(riboflavin5’-monophosphate)
Fru fructose
Fuc fucose
G guanine
Gal galactose
VII
ListofAbbreviations
GDP guanosine5’-diphosphate
Glc glucose
GlcN glucosamine
GlcNAc N-acetylglucosamine
Gln glutamine
Glu glutamicacid
Gly glycine
GMP guanosine5’-monophosphate
GSH glutathione
GSSG oxidizedglutathione
GTP guanosine5’-triphosphate
Gul gulose
h hour
H4 tetrahydro
HEPES 4-(2-hydroxyethyl)-1-piperazineethanesulfonicacid
His histidine
HPLC highperformanceliquidchromatography
Hyl hydroxylysine
Hyp hydroxyproline
IAA iodoacetamide
IC50 50%inhibitoryconcentration
Ig immunoglobulin
Ile isoleucine
Ido idose
IDP inosine5’-diphosphate
IMP inosine5’-monophosphate
ITP inosine5’-triphosphate
K Michaelisconstant
m
l- (andd-)prefixesindicatingconfiguration
Leu leucine
Lys lysine
Lyx lyxose
M mol/l
mM millimol/l
m- meta-
Man mannose
MES 2-(N-morpholino)ethanesulfonate
Met methionine
min minute
MOPS 3-(N-morpholino)propanesulfonate
Mur muramicacid
MW molecularweight
NAD+ nicotinamide-adeninedinucleotide
NADH reducedNAD
NADP+ NADphosphate
NADPH reducedNADP
NAD(P)H indicateseitherNADHorNADPH
VIII
ListofAbbreviations
NBS N-bromosuccinimide
NDP nucleoside5’-diphosphate
NEM N-ethylmaleimide
Neu neuraminicacid
NMN nicotinamidemononucleotide
NMP nucleoside5’-monophosphate
NTP nucleoside5’-triphosphate
o- ortho-
Orn ornithine
p- para-
PBS phosphate-bufferedsaline
PCMB p-chloromercuribenzoate
PEP phosphoenolpyruvate
pH -log10[H+]
Ph phenyl
Phe phenylalanine
PHMB p-hydroxymercuribenzoate
PIXE proton-inducedX-rayemission
PMSF phenylmethane-sulfonylfluoride
p-NPP p-nitrophenylphosphate
Pro proline
(cid:2)
Q factorforthechangeinreactionratefora10 Ctemperatureincrease
10
Rha rhamnose
Rib ribose
RNA ribonucleicacid
mRNA messengerRNA
rRNA ribosomalRNA
tRNA transferRNA
Sar N-methylglycine(sarcosine)
SDS-PAGE sodiumdodecylsulfatepolyacrylamidegelelectrophoresis
Ser serine
T thymine
t timeforhalf-completionofreaction
H
Tal talose
TDP thymidine5’-diphosphate
TEA triethanolamine
Thr threonine
TLCK Na-p-tosyl-l-lysinechloromethylketone
T meltingtemperature
m
TMP thymidine5’-monophosphate
Tos- tosyl-(p-toluenesulfonyl-)
TPN triphosphopyridiniumnucleotide(nowNADP+)
Tris tris(hydroxymethyl)-aminomethane
Trp tryptophan
TTP thymidine5’-triphosphate
Tyr tyrosine
U uridine
IX