Table Of ContentSpringer Handbook of Enzymes
Supplement Volume S7
Dietmar Schomburg and
Ida Schomburg (Eds.)
Springer Handbook
of Enzymes
Supplement Volume S7
Class 4–6
Lyases, Isomerases, Ligases
EC 4–6
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: 2009927508
ISBN 978-3-540-85706-8 2nd Edition Springer Berlin Heidelberg New York
The first edition was published as the “Enzyme Handbook, edited by D. and
I.Schomburg”.
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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
andcriticallyevaluatedbyqualified scientists.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
Spring2009 DietmarSchomburg,IdaSchomburg
VII
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
IX
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
X
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
XI
ListofAbbreviations
U/mg mmol/(mg*min)
UDP uridine5’-diphosphate
UMP uridine5’-monophosphate
UTP uridine5’-triphosphate
Val valine
Xaa symbolforanaminoacidofunknownconstitutioninpeptideformula
XAS X-rayabsorptionspectroscopy
Xyl xylose
XII
Index of Recommended Enzyme Names
EC-No. RecommendedName Page
4.2.3.18 abietadienesynthase . . . . . . . . . . . . . . . . . . . . . . 276
6.4.1.6 acetonecarboxylase . . . . . . . . . . . . . . . . . . . . . . 657
4.2.1.112 acetylenehydratase. . . . . . . . . . . . . . . . . . . . . . . 118
4.1.1.78 acetylenedicarboxylatedecarboxylase. . . . . . . . . . . . . . . 1
6.3.1.10 adenosylcobinamide-phosphatesynthase . . . . . . . . . . . . . 592
6.3.5.10 adenosylcobyricacidsynthase(glutamine-hydrolysing) . . . . . . . 651
6.3.2.27 aerobactinsynthase . . . . . . . . . . . . . . . . . . . . . . 606
4.2.1.110 aldos-2-ulosedehydratase. . . . . . . . . . . . . . . . . . . . 111
4.99.1.5 aliphaticaldoximedehydratase. . . . . . . . . . . . . . . . . . 465
6.3.2.26 N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valinesynthase. . . . 600
6.3.2.28 L-amino-acida-ligase. . . . . . . . . . . . . . . . . . . . . . 609
4.1.3.38 aminodeoxychorismatelyase. . . . . . . . . . . . . . . . . . . 49
6.3.5.8 aminodeoxychorismatesynthase(transferredtoEC2.6.1.85) . . . . . 644
4.3.1.21 aminodeoxygluconateammonia-lyase(deleted,identicaltoEC4.3.1.9) 376
4.2.3.24 amorpha-4,11-dienesynthase . . . . . . . . . . . . . . . . . . 307
4.2.1.111 1,5-anhydro-D-fructosedehydratase. . . . . . . . . . . . . . . . 115
4.2.2.15 anhydrosialidase . . . . . . . . . . . . . . . . . . . . . . . . 131
4.2.3.9 aristolochenesynthase . . . . . . . . . . . . . . . . . . . . . 219
4.1.99.7 aristolochenesynthase(transferredtoEC4.2.3.9) . . . . . . . . . . 62
5.3.3.15 ascopyronetautomerase. . . . . . . . . . . . . . . . . . . . . 512
6.3.5.6 asparaginyl-tRNAsynthase(glutamine-hydrolysing) . . . . . . . . 628
6.3.1.12 D-aspartateligase . . . . . . . . . . . . . . . . . . . . . . . 597
6.1.1.23 aspartate-tRNAAsn ligase . . . . . . . . . . . . . . . . . . . . 562
4.1.99.11 benzylsuccinatesynthase . . . . . . . . . . . . . . . . . . . . 66
4.2.1.106 bile-acid7a-dehydratase . . . . . . . . . . . . . . . . . . . . 100
4.2.3.13 (+)-d-cadinenesynthase . . . . . . . . . . . . . . . . . . . . 250
5.3.99.8 capsanthin/capsorubinsynthase . . . . . . . . . . . . . . . . . 514
5.4.99.18 5-(carboxyamino)imidazoleribonucleotidemutase . . . . . . . . . 548
6.3.4.18 5-(carboxyamino)imidazoleribonucleotidesynthase . . . . . . . . 625
6.3.3.4 (carboxyethyl)arginineb-lactam-synthase . . . . . . . . . . . . . 622
4.2.3.8 casbenesynthase. . . . . . . . . . . . . . . . . . . . . . . . 215
4.2.2.19 chondroitinBlyase. . . . . . . . . . . . . . . . . . . . . . . 152
4.2.2.20 chondroitin-sulfate-ABCendolyase. . . . . . . . . . . . . . . . 159
4.2.2.21 chondroitin-sulfate-ABCexolyase . . . . . . . . . . . . . . . . 162
4.1.3.40 chorismatelyase . . . . . . . . . . . . . . . . . . . . . . . . 57
4.2.3.5 chorismatesynthase . . . . . . . . . . . . . . . . . . . . . . 202
6.6.1.2 cobaltochelatase . . . . . . . . . . . . . . . . . . . . . . . . 675
5.5.1.12 copalyldiphosphatesynthase . . . . . . . . . . . . . . . . . . 551
4.2.1.104 cyanase. . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
6.3.2.30 cyanophycinsynthase(L-arginine-adding). . . . . . . . . . . . . 616
6.3.2.29 cyanophycinsynthase(L-aspartate-adding) . . . . . . . . . . . . 610
4.2.1.100 cyclohexa-1,5-dienecarbonyl-CoAhydratase . . . . . . . . . . . . 80
4.2.1.102 cyclohexa-1,5-dienecarbonyl-CoAhydratase(transferredtoEC4.2.1.100) 86
4.2.1.103 cyclohexyl-isocyanidehydratase . . . . . . . . . . . . . . . . . 87
XIII
IndexofRecommendedEnzymeNames
4.4.1.25 L-cysteatesulfo-lyase . . . . . . . . . . . . . . . . . . . . . 413
4.3.3.4 deacetylipecosidesynthase. . . . . . . . . . . . . . . . . . . 381
4.3.3.3 deacetylisoipecosidesynthase. . . . . . . . . . . . . . . . . . 379
4.1.1.85 3-dehydro-L-gulonate-6-phosphatedecarboxylase . . . . . . . . . 22
4.2.3.4 3-dehydroquinatesynthase. . . . . . . . . . . . . . . . . . . 194
4.1.3.37 1-deoxy-D-xylulose5-phosphatesynthase(transferredtoEC2.2.1.7) 48
4.1.1.86 diaminobutyratedecarboxylase. . . . . . . . . . . . . . . . . 31
4.1.99.12 3,4-dihydroxy-2-butanone-4-phosphatesynthase . . . . . . . . . 70
4.3.1.22 3,4-dihydroxyphenylalaninereductivedeaminase . . . . . . . . . 377
4.1.1.84 D-dopachromedecarboxylase. . . . . . . . . . . . . . . . . . 18
4.2.1.108 ectoinesynthase . . . . . . . . . . . . . . . . . . . . . . . 104
4.2.3.10 (-)-endo-fencholsynthase . . . . . . . . . . . . . . . . . . . 227
5.5.1.13 ent-copalyldiphosphatesynthase . . . . . . . . . . . . . . . . 557
4.2.3.19 ent-kaurenesynthase . . . . . . . . . . . . . . . . . . . . . 281
4.3.1.20 erythro-3-hydroxyaspartateammonia-lyase. . . . . . . . . . . . 373
4.2.3.2 ethanolamine-phosphatephospho-lyase . . . . . . . . . . . . . 182
4.6.1.15 FAD-AMPlyase(cyclizing). . . . . . . . . . . . . . . . . . . 451
4.2.3.22 germacradienolsynthase. . . . . . . . . . . . . . . . . . . . 295
4.2.3.23 germacrene-Asynthase . . . . . . . . . . . . . . . . . . . . 301
4.2.2.14 glucuronanlyase . . . . . . . . . . . . . . . . . . . . . . . 127
6.3.1.11 glutamate-putrescineligase. . . . . . . . . . . . . . . . . . . 595
6.1.1.24 glutamate-tRNAGln ligase. . . . . . . . . . . . . . . . . . . . 572
6.3.5.7 glutaminyl-tRNAsynthase(glutamine-hydrolysing) . . . . . . . . 638
4.6.1.14 glycosylphosphatidylinositoldiacylglycerol-lyase . . . . . . . . . 441
6.3.5.9 hydrogenobyrinicacida,c-diamidesynthase(glutamine-hydrolysing) 645
4.1.3.39 4-hydroxy-2-oxovaleratealdolase . . . . . . . . . . . . . . . . 53
5.4.4.1 (hydroxyamino)benzenemutase . . . . . . . . . . . . . . . . 523
5.4.4.3 3-(hydroxyamino)phenolmutase . . . . . . . . . . . . . . . . 533
4.2.1.105 2-hydroxyisoflavanonedehydratase . . . . . . . . . . . . . . . 97
4.4.1.22 S-(hydroxymethyl)glutathionesynthase . . . . . . . . . . . . . 405
4.1.1.83 4-hydroxyphenylacetatedecarboxylase. . . . . . . . . . . . . . 15
4.1.1.80 4-hydroxyphenylpyruvatedecarboxylase. . . . . . . . . . . . . 6
4.2.99.19 2-hydroxypropyl-CoMlyase(transferredtoEC4.4.1.23). . . . . . . 329
4.4.1.23 2-hydroxypropyl-CoMlyase . . . . . . . . . . . . . . . . . . 407
4.99.1.6 indoleacetaldoximedehydratase. . . . . . . . . . . . . . . . . 473
4.2.2.17 inulinfructotransferase(DFA-I-forming). . . . . . . . . . . . . 141
4.2.2.18 inulinfructotransferase(DFA-III-forming) . . . . . . . . . . . . 145
5.4.4.2 isochorismatesynthase . . . . . . . . . . . . . . . . . . . . 526
5.1.1.17 isopenicillin-Nepimerase . . . . . . . . . . . . . . . . . . . 481
4.2.3.27 isoprenesynthase. . . . . . . . . . . . . . . . . . . . . . . 320
4.4.1.20 leukotriene-C synthase . . . . . . . . . . . . . . . . . . . . 388
4
4.2.2.16 levanfructotransferase(DFA-IV-forming) . . . . . . . . . . . . 134
4.2.3.16 (4S)-limonenesynthase . . . . . . . . . . . . . . . . . . . . 267
4.2.3.20 (R)-limonenesynthase. . . . . . . . . . . . . . . . . . . . . 288
4.1.99.10 (-)-(4S)-limonenesynthase(transferredtoEC4.2.3.16) . . . . . . . 65
4.2.3.25 S-linaloolsynthase . . . . . . . . . . . . . . . . . . . . . . 311
4.2.3.26 R-linaloolsynthase . . . . . . . . . . . . . . . . . . . . . . 317
6.1.1.25 lysine-tRNAPyl ligase . . . . . . . . . . . . . . . . . . . . . 578
6.6.1.1 magnesiumchelatase . . . . . . . . . . . . . . . . . . . . . 665
5.1.3.21 maltoseepimerase . . . . . . . . . . . . . . . . . . . . . . 495
4.6.1.12 2-C-methyl-D-erythritol2,4-cyclodiphosphatesynthase . . . . . . 415
4.2.3.3 methylglyoxalsynthase . . . . . . . . . . . . . . . . . . . . 185
4.2.1.109 methylthioribulose1-phosphatedehydratase . . . . . . . . . . . 109
XIV
