Enzyme Handbook

1037 Pages·1991·14.081 MB·English

by  Dietmar Schomburg, Margit Salzmann (auth.)

ISBN 978-3-642-48963-1 ISBN 978-3-642-76729-6 (e Book)
DOI 10.1007/978-3-642-76729-6
Preface
Recent progress in enzyme immobilisation, enzyme production, coenzyme
regeneration and enzyme engineering has opened up fascinating new fields
for the potential application of enzymes in a large range of different areas. As
more progress in research and application of enzymes has been made the
more apparent has become the Iack of an up-to-date overview of enzyme
molecular properties. The need for such a data bankwas also expressed by
the EC-task force "Biotechnology and Information". Therefore we started the
development of an enzyme data information system as part of protein-design
activities at GBF. The present book "Enzyme Handbook" represents the
printed version of this data bank. ln future it is also planned to make a com
puter searchable version available.
The enzymes in the Handbook are arranged according to the 1984 Enzyme
Commission Iist of enzymes and later supplements. Some 3000 "different" en
zymes are covered. Frequently very different enzymes are included under the
same E. C. number. Although we intended to give a representative overview
on the molecular variability of each enzyme, the Handbook is not a com
pendium. The readerwill have to go to the primary Iiterature for more detailed
information. Naturally it is not possible to cover all numerous, up to 40 000,
Iiterature references for each enzyme if data representation is to be concise
as is intended.
The authors are grateful to the following bioligists and chemists for invalu
able help in the compilation of data, expecially Cornelia Munaretto, Dr. lda
Schomburg, Dr. Sabine Vogei-Ziebolz, Uwe Hirschgänger, Inka Siegmund and
Roland Vogt. Mrs. C. Munaretto and Dr. I. Schamburg are also thanked for
the correction of the final manuscript.
Braunschweig Margit Salzmann
June, 1990 Dietmar Schamburg
V
BRENDA-Enzyme Data for Research and Production
Enzymes are used in all parts of the living world for catalysis of innumerable
biochemical reactions. lt has been known for some time that they represent
potentially highly interesting catalysts for chemical research and production
because of their high efficiency, stereospecifity, and their regio- and
enantioselectivity. Enormous progress has been made in recent years in en
zyme immobilisation, stabilisation, coenzyme regeneration etc., while gene
technology has made possible the production of large quantities of otherwise
inaccessible enzymes. Enzyme-design methods and recent work on enzyme
behaviour in organic solvents have opened further possibilities for their use in
new application areas. ln addition to the chemical industry their use in the
food industry and environmental technology is worthy of mention.
A number of problems still have to be overcome before enzymes take their
place besides the other commonly used catalysts in the chemical laboratory,
productions and in the awareness of the ehernist and the general public. So
the current industrial use of enzymes is more or less limited to proteases and
carbohydrases, i. e. hydrolytic enzymes. Other synthetically important reac
tions such as the forming of C-C bonds are rarely achieved enzymatically at
present. ln addition to the real problems (price, too high selectivity etc.) reser
vatians on the part of the chemists prohibit decisions about their potential
use.
This is mainly caused by the undeniable fact that information about en
zymes is not as easily obtained as that about other synthetic means and
catalysts. Results of enzyme research are often published in journals which
are rarely read by most chemists and are often not available in organic
chemistry libraries. The published data on molecular weight, stability etc. can
be contradictory, the use of a number of different names for the same en
zyme is common, and the systematic classification of the enzyme is usually
unsatisfactory.
The apparently simple question:
"/s there an enzyme, that catalyzes the enantiose/ective replacement of an
hydrogen atom in an r:x-position to an aromatic ring and is stable in a water
solution with a certain pH-value and a given temperature?"
can often only be answered after intensive work in a library or the use Iitera
ture data bases. A rational choice between several potential enzyme
catalyzed reaction paths is imposible in a reasonable time. When planning
research projects in the area of enzyme design, information about potential
enzymes and use of the correct initial enzymeisalso essential.
ln addition to the above types of chemical problem, systematic biochemical
investigations are central to the wide interest in enzymes, therefore a great
deal of information can be gained from establishment of a comprehensive
collection of enzyme data.
VII
BRENDA-Enzyme Data for Research and Production
ln the GBF research programme, enzyme technology has always played a
significant role. This is documented by innovative contributions in the field of
cofactor regeneration, enzyme production by genetic engineering and down
stream processing after fermentation.
·The area has gained new significance from the activities in protein design
where the central theme is protein structure determination and biocomputing.
lt soon became evident that the next logical step was the development of
an enzyme data bank which could be undertaken by the group for molecular
structure research. We hope that publication of this comprehensive, critical
Iiterature evaluation will be of wide interest to external users and, in this way,
we hope the GBF has provided a further important contribution to the in
formation infrastructure in biotechnology.
Braunschweig Joachim Klein
June, 1990 GBF, Scientific Director
VIII
List of Abbreviations
A adenosine E. coli Escherichia coli
Ac acetyl EDTA ethylene
ADP adenosine 5'- d iaminetetraacetate
diphosphate EGTA ethylene glycol bis
Ala alanine (ß-aminoethyl ether)
All allose tetraacetate
Alt altrose ER endoplasmic reticulum
AMP adenosine 5'- Et ethyl
monophosphate EXAFS extended X-ray
Ara arabinose absorption fine
Arg arginine structure
Asn asparagine FAD flavin-adenine
Asp aspartic acid dinucleotide
ATP adenosine 5'- FMN flavin mononucleotide
triphosphate (riboflavin 5'-
c
cytidine monophosphate)
cal calories Fru fructose
COP cytidine 5'-diphosphate Fuc fucose
CDTA trans-1 ,2- G guanosine
diaminocyclohexane- Ga I galactose
N, N, N, N-tetra -acetic GDP guanosine 5'-
acid diphosphate
CMP cytidine 5'- Glc glucose
monophosphate GieN glucosamine
CoA coenzymeA GlcNAc N-acetylglucosamine
CTP cytidine 5'-triphosphate Gin glutamine
Cys cysteine Glu glutamic acid
d deoxy- Gly glycine
D- GMP guanosine 5'-
and L- prefixes indicating con- monophosphate
figuration GSH glutathione
DFP diisopropyl GTP guanosine 5'-
fluorophosphate triphosphate
DNA deoxyribonucleic acid Gul gulose
DPN diphosphopyridinium H4 tetrahydro
nucleotide (now NAD) His histidine
DTNB 5,5'-dithiobis (2- HPLC high pressureliquid
nitrobenzoate) chromatography
DTT dithiothreitol (i.e. Hyl hydroxylysine
Cleland's reagent) Hyp hydroxyproline
EC number of enzymein IAA iodoacetamide
Enzyme Commis- lg immunoglobulin
sion's system lle isoleueine
IX
List of Abbreviations
ldo idose NMN nicotinamide
IOP inosine 5'-diphosphate mononucleotide
IMP inosine NMP nucleoside
5'-monophosphate 5' -monophosphate
ITP inosine 5'-triphosphate NTP nucleoside
Km concentration of 5'-triphosphate
substrate giving half 0- ortho-
maximum velocity Orn ornithine
(Michaelis constant) p- para-
L- see 0- PCMB p-chloro-
Leu leueine mercuribenzoate
Lys Iysine PEP phosphoenolpyruvate
Lyx lyxose pH -log10 [H]
M gm molecule (1 mole) Ph phenyl
per litre Phe phenylalanine
m- meta- PI XE proton-ind uced
Man mannose X-ray emission
MES 2-( N-morpholino )ethane PMSF phenylmethane-
sulfonate sulfonylfluoride
Met methionine Pro proline
mM 10-3 Mole temperature coefficient
010
Mur muramic acid for a reaction
MW molecular weight Rha rhamnose
NAO nicotinamide-adenine Rib ribose
dinucleotide (state of RNA ribonucleic acid
oxidation mRNA messenger RNA
unspecified) rRNA ribosomal RNA
NAO+ nicotinamide-adenine tRNA transfer RNA
dinucleotide (oxidized Sar N-methylglycine
form) (sarcosine)
NAOH reduced NAO SOS-PAGE sodium dodecyl sulphate
(=
NAOP NAO phosphate sodium lauryl sul-
(state of oxidation phate)-
unspecified) polyacrylamide
NAOP+ NAOP (oxidized form) gel electrophoresis
NAO(P)+ indicates either NAo+ T ribosylthymine
orNAOP+ Ser serine
NAOPH reduced NAOP ty, time for half-completion
NAO(P)H indicates either NAOH of reaction
orNAOPH Tal talose
NOP nucleoside TOP ribosylthymine
5'-diphosphate 5'-diphosphate
NEM N-ethylmaleimide Thr threonine
Neu Neuraminic acid TMP ribosylthymine
nm nanometre (10-9 metre) 5'-monophosphate
X
List of Abbreviations
Tos- tosyl- UDP uridine 5'-diphosphate
(p-toluenesu lfonyl-) UMP uridine
TPN triphosphopyridinium 5'-monophosphate
nucleotide UTP uridine 5'-triphosphate
(nowNADP) Val valine
Tris tris(hydroxymethyl)- Xaa symbol for an amino
aminomethane acid of unknown con-
Trp tryptophan stitution in peptide
TTP ribosylthymine formula
5'-triphosphate XAS X-ray absorption
Tyr tyrosine spectroscopy
u uridine Xyl xylose
U/mg J..Lmol/(mg*min)
XI
Index
(Aiphabetical order of Enzyme names)
EC-No. Name EC-No. Name
3.4.24.8 Achromobacter iophagus 3.4.11.15 Aminopeptidase
collagenase (c obalt-activated)
3.4.21.50 Achromobacter proteinase I 3.4.11.14 Aminopeptidase (human liver)
3.4.21.10 Acrosin 3.4.99.3 Angiotensinase
3.4.22.14 Actinidin 3.6.1.5 Apyrase
3.4.19.1 Acylamino-acid-releasing 3.4.11.6 Arginineaminopeptidase
enzyme 3.4.99.32 Armillaria mellea neutral
3.4.17.7 Acylmuramoyl-alanine proteinase
carboxypeptidase 3.4.21.14e Arthrobacter serine proteinase
3.6.1.7 Acylphosphatase 3.4.22.7 Asclepain
3.6.1.20 5'-Acylphosphoadenosine 3.4.17.5 Aspartale carboxypeptidase
hydro Iase 3.4.13.1 0 Beta-aspartyldipeptidase
3.6.1.3 Adenosinetriphosphatase 3.4.13.16 Aspartylphenylalanine
3.6.1.14 Adenosine-tetraphosphatase dipeptidase
3.3.1.1 Adenosylhomocysteinase 3.4.21.14c Aspergillus alkaline proteinase
3.3.1.2 Adenosylmethionine hydrolase 3.4.23.6c Aspergillusniger var. macro-
3.6.2.1 Adenylylsulfatase sporus aspartic proteinase
3.6.1.13 ADPribose pyrophosphatase 3.4.23.6a Aspergillus oryzae aspartic
3.6.1.21 ADPsugar pyrophosphatase proteinase
3.4.11.10 Aeromonas proteolytica 3.4.24.41 Aspergillus oryzae neutral
aminopeptidase proteinase
3.4.24.4a Aeromonas proteolytica neutral 3.4.23.6b Aspergillus saitoi aspartic
proteinase proteinase
3.4.99.2 Agavain 3.6.1.8 ATP pyrophosphatase
3.4.21.28 Agkistrodon serine proteinase 3.6.1.34 H + -transporting ATP synthase
3.4.17.6 Alanine carboxypeptidase 3.6.1.35 H + -transporting ATPase
3.4.13.15 N2-Beta-alanylarginine 3.6.1.36 H+ /K+ -transporting ATPase
dipeptidase 3.6.1.37 Na+ /K+ -transporting ATPase
3.4.16.4 D-Aianyi-D-alanine 3.6.1.38 Ca2+ -transporting ATPase
carboxypeptidase 3.4.24.41 Bacillus subtilis neutral
3.3.2.2 Alkenylglycerophosphocholine proteinase
hydro Iase
3.4.24.4e Bacillus thermoproteolyticus
3.3.2.5 Alkenylglycerophospho- neutral proteinase
ethanolamine hydrolase
3.6.1.29 Bis(5'-adenosyl)-
3.4.21.16 Alternaria serine proteinase
triphosphatase
3.4.21.47 Alternative-complement-
3.6.1.17 Bis(5'-nucleosyl)-
pathway C3/C5 convertase
tetraphosphatase
3.4.13.3 Aminoacylhistidine dipeptidase
(asymmetrical)
3.4.13.4 Aminoacyl-lysine dipeptidase
3.4.21.29 Bothrops atrox serine
3.4.13.5 Aminoacyl-methylhistidine
proteinase
dipeptidase
3.4.11.11 Aminopeptidase 3.4.22.4 Bromelain
3.4.11.7 Aminopeptidase A 3.4.22.17 Calpain
3.4.11.9 Aminopeptidase P 3.4.23.6h Candida albicans aspartic
3.4.11.16 Aminopeptidase X-Trp proteinase
XIII