BIOINFORMATICS APPLICATIONS NOTE
Vol. 20 no. 16 2004, pages 2874–2877
doi:10.1093/bioinformatics/bth314
Thermodynamics of enzyme-catalyzed
reactions—a database for quantitative
biochemistry
Robert N. Goldberg, Yadu B. Tewari and Talapady N. Bhat∗
Biotechnology Division, National Institute of Standards and Technology, Gaithersburg,
MD 20899, USA
Received on March 16, 2004; revised on accepted on May 4, 2004
Advance Access publication May 14, 2004
ABSTRACT
Summary: The Thermodynamics of Enzyme-catalyzed
Reactions Database (TECRDB) is a comprehensive collection of thermodynamic data on enzyme-catalyzed reactions.
The data, which consist of apparent equilibrium constants
and calorimetrically determined molar enthalpies of reaction,
are the primary experimental results obtained from thermodynamic studies of biochemical reactions. The results from
∼1000 published papers containing data on ∼400 different
enzyme-catalyzed reactions constitute the essential information in the database. The information is managed using Oracle
and is available on the Web.
Availability: http://xpdb.nist.gov/enzyme_thermodynamics/
Contact: For Web and database related issues: [email protected]
and for Scientific data, including additions and corrections:
[email protected]
Thermodynamic data on enzyme-catalyzed reactions play an
essential role in the prediction of the extent of reaction and
the position of equilibrium for any process in which these
reactions occur. The importance of understanding the thermodynamics of these biochemical reactions was emphasized
by Krebs and Kornberg 47 years ago in their monograph
A Survey of the Energy Transformations in Living Matter
(Krebs and Kornberg, 1957). Their monograph contains a
useful appendix on Gibbs free energy data of biological
interest and some data on the thermodynamics of enzymecatalyzed reactions. However, the amount of data available
at that time was extremely limited. While several reviews
on this subject have subsequently appeared, the absence of
a comprehensive collection of this information led two of us
(R.N.G. and Y.B.T.) to begin the systematic collection of this
∗ To
whom correspondence should be addressed.
Certain trade names and company products are identified in this paper to
specify adequately the computer products needed to develop this data system.
In no case does such identification imply endorsement by the National Institute of Standards and Technology (NIST), or does it imply that the products
are necessarily the best available for the purpose.
2874
data ∼15 years ago. Our evaluated data were published as
a series of reviews in the Journal of Physical and Chemical Reference Data (Goldberg et al., 1993; Goldberg and
Tewari, 1994a,b, 1995a,b; Goldberg, 1999). The results from
∼1000 published papers containing data on ∼400 different
enzyme-catalyzed reactions constitute the essential information in the database. The website database contains all
this information and is managed using Oracle. Having this
information available in a true database form on the Web
serves to complement several existing and related bioinformatics sources on the Web: UMBBD (Ellis et al., 2003,
http://umbbd.ahc.umn.edu/), ENZYME (Enzyme Nomenclature, 1992, http://www.chem.qmw.ac.uk/iubmb/enzyme/),
BRENDA (Schomburg et al., 2002, http://www.brenda.unikoeln.de/), KEGG (Kanehisa et al., 2002, http://www.genome.
ad.jp/kegg/kegg.html), and the SwissProt Enzyme Nomenclature Database (Bairoch, 2000, http://us.expasy.org/enzyme/).
The importance of this information lies in its applications
both in biochemistry and in industrial enzymology. The data
are also essential for metabolic control analysis (MCA) (see
Fell, 1997, http://bms-mudshark.brookes.ac.uk/), an important part of systems biology. Specifically, the full application of
MCA requires both thermodynamic and kinetic data as well
as a knowledge of metabolite concentrations. The result is
a quantitative description of metabolic processes, a detailed
understanding of which may yield an understanding of the
differences between the normal and the diseased states of
the living system as well as the ability to successfully engineer
organisms to accomplish specific aims. This approach requires
a very significant amount of data (and effort) and has thus
far seen limited application. However, the application of the
thermodynamic data to industrial processes involves straightforward calculations, which permit engineers to optimize
product yields and to calculate the energy requirements of
a reaction or process.
The TECRDB contains several pages of discussion of
the essential background on the thermodynamics of enzymecatalyzed reactions (see: Thermodynamic Background, the
Bioinformatics vol. 20 issue 16 © Oxford University Press 2004; all rights reserved.
Thermodynamics of enzyme-catalyzed reactions
Table 1. Layers used for the expression of data.
Layer 1
Layer 2
phosphoenolpyruvate3(aq), + H2O(l) = pyruvate(aq) + HPO42-(aq)
phosphoenolpyruvate<sup>3</sup>(aq) + H<sub>2</sub>O(l) =
pyruvate<sup></sup>(aq) + HPO<sub>4</sub>
<sup>2-</sup>(aq)
5alpha-pregnane5<img SRC = "./alpha.gif">-pregnane-3
3beta,17alpha,21-triol-20<img SRC = "./beta.gif">,
one(aq) + NAD(aq) = 5alpha17<img SRC = "./alpha.gif">,21-triolpregnane-17alpha,21-diol20-one(aq) + NAD(aq) = 5<img
3,20SRC = "./alpha.gif">-pregnane-17<img
dione(aq) + NADH(aq)
SRC = "./alpha.gif">,21-diol-3,20dione(aq) + NADH(aq)
first item on the website’s main page). This background
material contains definitions of the thermodynamic quantities that are of interest in this area. In this regard, two of the
most important quantities are the apparent equilibrium constant K and the calorimetrically determined molar enthalpy
of reaction r H (cal). The standard transformed molar Gibbs
free energy change r G◦ = −RT loge K , where R is the
gas constant and T is the thermodynamic temperature. Also
discussed is the fundamental distinction (Alberty et al., 1994;
Alberty, 1996, 2003) between biochemical reactants and species. Specifically, biochemical reactions are written in terms
of sums of species (e.g. ATP4− , HATP3− , MgATP2− , and so
on), which are referred to as reactants (e.g. ATP). This important distinction has been maintained throughout the database.
The background material also contains a bibliography of 37
references in which the reader can gain further information
on this subject.
Fundamental to both thermodynamics and to bioinformatics is the precise definition and specification of physical
quantities, consistency in usage, and standardization of names
and symbols. In this regard, the TECRDB has adhered to
IUPAC recommendations for biochemical thermodynamics
(Alberty et al., 1994) and, for the most part, to the biochemical names recommended by the Nomenclature Committee of
the IUBMB (Webb, 1992). Also, the ordering of the data in the
TECRDB is done in accordance with the Enzyme Commission
number assigned to the enzyme used to catalyze the reaction
studied. The database allows the user to perform searches
based on the reactant(s), enzyme name and number, buffer,
pH, cofactor(s) and method(s) used in the study.
The existing collection of thermodynamic data has seen use
in the calculation of standard molar Gibbs free energies of
formation for a substantial number of biochemical species
(Alberty, 2001,
http://library.wolfram.com/infocenter/
MathSource/797). The website (http://library.wolfram.com/
infocenter/MathSource/797/) from which these property data
are available also allows the user to download Mathematica
Layer 3
Layer 4
phosphoenolpyruvate3(aq) + H2O(l) = pyruvate(aq) + HPO42-(aq); H2O; phosphate;
orthophosphate
phosphoenolpyruvate3− (aq) +
H2 O(l) = pyruvate− (aq) +
HPO2−
4 (aq)
5alpha-pregnane-3beta,17alpha,21-triol20-one(aq) + NAD(aq) =
5alpha-pregnane-17alpha,21-diol-3,
20-dione(aq) + NADH(aq);
NAD;NADH
5α-pregnane-3β,17α,21-triol-20one(aq) + NAD(aq) = 5αpregnane-17α,21-diol-3,20dione(aq) + NADH(aq)
programs that permit one to calculate values of apparent
equilibrium constants K of biochemical reactions as a function of pH and ionic strength. Computer codes (Akers and
Goldberg, 2001, http://www.mathematica-journal.com) that
permit one to conveniently calculate values of apparent equilibrium constants K from values of (standard) equilibrium
constants K and also to perform the inverse calculation significantly enhance the usefulness of the information in the
database.
The website is constructed using PERL and an ORACLE
database. IUPAC recommendations for enzyme thermodynamic data are rich in the use of special characters (e.g. greek
letters), superscripts and subscripts. The use of these special
characters presents special difficulties for database software.
For this reason, many databases [e.g. the Protein Data
Bank (http://www.rcsb.org/pdb/) and the SwissProt Enzyme
Nomenclature Database (http://us.expasy.org/enzyme/)] use
a flat naming convention, which is devoid of greek letters,
superscripts and subscripts. We developed new techniques and
tools for the implementation of IUPAC recommendations in
a database environment. In our implementation, the data are
expressed in four layers (Table 1). Layer 1 has the data in the
flat form and Layer 2 has the data in the IUPAC form stored
as HTML code. Layer 3 has the data in the flat form together
with synonyms (if any). Layer 4 has the data in the IUPAC
form. This form is generated from Layer 2 as text during the
display of results. Each of these layers is generated for every
data item (e.g. reaction, enzyme, and so on).
The Web interface provides several different search
options for querying the database. The query results
are generated dynamically, sorted and displayed in tabular form. The options from the first Web page are:
Thermodynamic Background; How to Use This Database
(Help); Enzyme-Catalyzed Reactions: Search using predefined values; Enzyme-Catalyzed Reactions: Search with
user defined values; Enzyme-Catalyzed Reactions: Show distinct values; Enzyme-Catalyzed Reactions: Show all values;
2875
R.N.Goldberg et al.
Fig. 1. Representative thermodynamic data found in a search.
References: Search references; Abbreviations; and Prior
Version: Search prior version.
Search option No. 1 (Predefined Values) provides dropdown lists (scroll bars) that give values for each of the data
items, such as reaction, enzyme and EC number by using the
components of data in Layer 1. The user can make a selection
of multiple values using different data items. The user can
control the sorting and display of data by the use of check
boxes. Search option No. 2 (User Defined Values) allows the
user to enter his own selection and is designed to support
several constraints for different data items in a query. Search
option No. 3 (Distinct Values) allows the user to view all the
unique data values of a particular data item, such as enzyme
or reactant. Each of these search options allows the user to
view the thermodynamic data (Fig. 1) found in the search.
The user can also establish a direct link to the database by
using one or more of the following key words: Reactant, EC,
Method, Enzyme, Buffer, pH and Cofactor. For example, http:
//xpdb.nist.gov/enzyme_thermodynamics/enzyme_compose_
query.pl?EC=1.1.1.47 displays the data for EC number
1.1.1.47.
ACKNOWLEDGEMENTS
We thank Drs Gary L. Gilliland and Frederick P. Schwarz for
helpful discussions and Mr M.D. Prasanna for maintaining
2876
the server. Partial funding of this effort was provided by the
Systems Integration for Manufacturing Applications (SIMA).
REFERENCES
Alberty,R.A. (1996) IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN). Recommendations for nomenclature and tables in biochemical thermodynamics. Recommendations 1994. Eur. J. Biochem., 15, 1–14. [Erratum (1996) Eur.
J. Biochem., 242, 433.]
Alberty,R.A. (2001) BasicBiochemData 2—Data and Programs for
Biochemical Thermodynamics.
Alberty,R.A. (2003) Thermodynamics of Biochemical Reactions.
Wiley-Interscience, Hoboken, NJ.
Alberty,R.A., Cornish-Bowden,A., Gibson,Q.H., Goldberg,R.N.,
Hammes,G., Jencks,W., Tipton,K.F., Veech,R., Westerhoff,H.V.
and Webb,E.C. (1994) Recommendations for nomenclature and
tables in biochemical thermodynamics. Pure Appl. Chem., 66,
1641–1666.
Akers,D.L. and Goldberg,R.N. (2001) BioEqCalc: a package for
performing equilibrium calculations on biochemical reactions.
Mathematica J., 8, 86-113.
Bairoch,A. (2000) The ENZYME database in 2000. Nucleic Acids
Res., 28, 304–305.
Ellis,L.B.M., Hou,B.K., Kang,W. and Wackett,L.P. (2003) The
University of Minnesota Biocatalysis/Biodegradation Database:
post-genomic data mining. Nucleic Acids Res., 31, 262–265.
Thermodynamics of enzyme-catalyzed reactions
Enzyme Nomenclature 1992. Academic Press, San Diego, CA; also
see Supplements 1–5 [Eur. J. Biochem., 223, 1–5 (1994); Eur.
J. Biochem., 232, 1–6 (1995); Eur. J. Biochem., 237, 1–5 (1996);
Eur. J. Biochem., 250; 1–6 (1997), and Eur. J. Biochem., 264,
610-650 (1999)].
Fell,D.A. (1997) Understanding the Control of Metabolism. Portland
Press, London.
Goldberg,R.N. (1999) Thermodynamics of enzyme-catalyzed reactions: part 6—1999 update. J. Phys. Chem. Ref. Data, 28,
931–965.
Goldberg,R.N. and Tewari,Y.B. (1994a) Thermodynamics of
enzyme-catalyzed reactions: part 2. Transferases. J. Phys. Chem.
Ref. Data, 23, 547–617.
Goldberg,R.N. and Tewari,Y.B. (1994b) Thermodynamics of
enzyme-catalyzed reactions: part 3. Hydrolases. J. Phys. Chem.
Ref. Data, 23, 1035–1103.
Goldberg,R.N. and Tewari,Y.B. (1995a) Thermodynamics of
enzyme-catalyzed reactions: part 4. Lyases. J. Phys. Chem. Ref.
Data, 24, 1669–1698.
Goldberg,R.N.
and
Tewari,Y.B.
(1995b)
Thermodynamics
of
enzyme-catalyzed
reactions:
part
5.
Isomerases and ligases. J. Phys. Chem. Ref. Data, 24,
1765–1801.
Goldberg,R.N., Tewari,Y.B., Bell,D., Fazio,K. and Anderson,E.
(1993) Thermodynamics of enzyme-catalyzed reactions:
part 1. Oxidoreductases. J. Phys. Chem. Ref. Data, 22,
515–582.
Kanehisa,M., Goto,S., Kawashima,S. and Nakaya,A. (2002) The
KEGG databases at GenomeNet. Nucleic Acids Res., 30,
42–46.
Krebs,H.A. and Kornberg,H.L. (Appendix by Burton,K.) (1957) A
Survey of the Energy Transformations in Living Matter. SpringerVerlag, Berlin.
Schomburg,I., Chang,A. and Schomburg,D. (2002) BRENDA,
enzyme data and metabolic information. Nucleic Acids Res., 30,
47–49.
Webb,E.C. (1992) Enzyme Nomenclature. Academic Press, San
Diego.
2877