ENZYME data bank: announcement and description. (fwd)

Dan Davison davison at UHNIX2.UH.EDU
Thu Apr 12 22:35:22 EST 1990


A new database of interest to Matrixers (Matrixen?)

dan


Forwarded message:


> ENZYME DATA BANK PRE-ANNOUNCEMENT
> =================================
> 
> A new "secondary" data bank is being established. It is called the 'ENZYME'
> data bank and it contains the following data for each type of enzyme:
> 
>   1) EC number.
>   2) Recommended name.
>   3) Alternative names (if any).
>   4) Catalytic activity.
>   5) Cofactors (if any).
>   6) Pointers to SWISS-PROT entrie(s) corresponding to that enzyme (if any).
> 
> We think that the ENZYME data bank will be useful to anybody working with
> enzymes and will allow programs to  be  developped that can help with the
> creation of new metabolic pathways.
> 
> With the ENZYME data bank  the  current situation,  in term of data bases
> interconnections, will now be the following:
> 
> 
>           +------+      +------------+
>           |      |      |            |  <--> ENZYME
>  EPD  <-- | EMBL | <--> | SWISS-PROT |  ---> PDB
>           |      |      |            |  <--> PROSITE
>           +------+      +------------+
> 
> 
> IMPACT ON SWISS-PROT
> 
> This new data bank will have the following impact on SWISS-PROT:
> 
>   1) The existence of this data bank will make the ECINDEX.TXT document
>      obsolete and it will thus be discarded.
> 
>   2) Instead of having CC (comments) lines with the topics:
> 
>      CC   -!- CATALYTIC ACTIVITY: description_of_catalytic_activity.
>      CC   -!- COFACTOR: description_of_cofactor.
> 
>      The enzyme entries in SWISS-PROT will have two new types of lines:
> 
>      CA   Description_of_catalytic_activity.
>      CF   Description_of_cofactor.
> 
>      These lines will be carried over from the ENZYME data bank and
>      will be automatically generated at each release of SWISS-PROT
>      from the information stored in the ENZYME data bank.
> 
>      The introduction of the new line types is planned for release 16 of
>      SWISS-PROT (October 1990).
> 
> 
> CREATION AND MAINTENANCE
> 
> How will this data bank be created and maintained ?
> 
> The source of the majority of the data in the ENZYME data bank comes from
> the IUPAC/IUB 1984 enzyme nomenclature book [1] and the two supplements
> (1986 and 1989) [2,3].
> 
> Unfortunatly these documents  do  not  seem to be available on any computer
> media and we were  forced  to  type-in  the information relevant to all the
> different enzymes  which  are  represented  in  SWISS-PROT.  There are 3056
> different  EC numbers,  the  information concerning 30% of these enzymes is
> already entered.   We have decided to type-in the rest of the data (optical
> reading of the documents has been attempted, but is not reliable enough).
> 
> The full data bank will be available probably in late autumn.   Preliminary
> versions  will be distributed along with SWISS-PROT, starting with the next
> release (release 14 in mid-April).
> 
> This data bank will be very easy to maintain. Except for error corrections,
> or new information concerning cofactors,  updates  of  the enzyme list will
> only occur when  a  new supplement is published (every two or three years).
> The pointers to SWISS-PROT are also not a problem, the program that used to
> build the ECINDEX file now automatically creates the DR lines in the ENZYME
> data bank. This program will be run at every release of SWISS-PROT.
> 
> 
> PRELIMINARY FORMAT DESCRIPTION
> 
> Global format: EMBL/SWISS-PROT like.
> 
> Line-types:
> 
> ID  Identification line
>     Contains the EC number of the enzyme.
> DE  Description line(s).
>     Contains the recommended name of the enzyme.
> AN  Alternative name(s) line(s)
>     Contains the alternative name(s) of the enzyme.
> CA  Catalytic activity line(s)
>     Contains the description of the catalytic activity. The format used
>     is that of IUPAC/IUB.
> CF  Cofactor(s) line(s).
>     Description of known cofactors.
> CC  Comments line(s)
>     Free text comments.
> DR  Data bank cross-reference line(s).
>     Cross-reference to the SWISS-PROT entries corresponding to the enzyme
>     described.
> //  Entry termination line.
> 
> 
> SAMPLE ENTRY.
> 
> ID   1.14.17.3
> DE   PEPTIDYLGLYCINE MONOOXYGENASE.
> AN   PEPTIDYL ALPHA-AMIDATING ENZYME.
> CA   PEPTIDYLGLYCINE + ASCORBATE + O(2) = PEPTIDYL(2-HYDROXYGLYCINE) +
> CA   DEHYDROASCORBATE + H(2)O.
> CC   THE PRODUCT IS UNSTABLE AND DISMUTATES TO GLYOXYLATE AND THE
> CC   CORRESPONDING DESGLYCINE PEPTIDE AMIDE.
> CF   COPPER.
> DR   P10731, AMD$BOVIN ;  P14925, AMD$RAT   ;  P08478, AMD1$XENLA;
> DR   P12890, AMD2$XENLA;
> //
> 
> 
> [1] Enzyme Nomenclature, NC-IUB, Academic Press, New-York, (1984).
> [2] Supp. 1: Corrections and Additions, Eur. J. Biochem. 157:1-26(1986).
> [3] Supp. 2: Corrections and Additions, Eur. J. Biochem. 179:489-533(1989).
> 
> ----------------------------------
> 
> This is a pre-announcement, feedback is welcomed and encouraged.
> 
> *****************************************************************************
> * Amos Bairoch                * Email: bairoch at cgecmu51                     *
> * Dept. Medical Biochemistry  * Tel  : +(41 22) 61 84 92                    *
> * CMU                         ***********************************************
> 
> * 1, rue Michel Servet        * Greer's third law:                          *
> * 1211 Geneva 4               * To err is human, but to really foul things  *
> * Switzerland                 * up you need a computer.                     *
> *****************************************************************************
> 


-- 
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77054-5500/davison at uh.edu/DAVISON at UHOU

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.





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