*******************************************************************************
****** ******
****** PROTEIN MUTANT DATA BASE ******
****** ******
****** National Institute of Genetics ******
****** (NIG) ******
****** 1111, Yata, Mishima, Shizuoka-ken 411, Japan ******
****** ******
****** In collaboration with: ******
****** Protein Engineering Research Institute (PERI) ******
****** 6-2-3, Furuedai, Suita, Osaka 565, Japan ******
****** and ******
****** Protein Research Foundation (PRF) ******
****** 4-1-2, Ina, Mino, Osaka 562,Japan ******
****** ******
****** Correspondence: Dr. Ken Nishikawa ******
****** National Institute of Genetics ******
****** 1111, Yata, Mishima, Shizuoka 411, Japan ******
****** ******
****** TEL: +81-559-81-6859 ******
****** FAX: +81-559-81-6889 ******
****** E-Mail: knishika@genes.nig.ac.jp ******
****** ******
****** This document has been updated on November 24, 2000. ******
*******************************************************************************
Mutant database of proteins would be valuable as a basis of protein
engineering. Our database is of a type based on literature (not on
proteins); that is, each entry of the database corresponds to one
article which describes protein mutations.
Each entry of the database is identified with a serial number, and
distinguished either "variant" or "artificial" depending on the type
of mutation. For each entry the following items are to be typed in:
AUTHORS/JOURNAL/TITLE/CROSS-REFERENCE/PROTEIN/SOURCE/N-TERMINAL/EXPRESSION-SYSTEM/
CHANGE/CHIMERA/EXTENSION/INSERTION/REPLACEMENT/DE NOVO/MULTIPLE/
/FUNCTION/STRUCTURE/STABILITY/EXPRESSION/TRANSPORT/DISEASE/COMMENT/SEQUENCE,
and ends with '///'.
'CROSS-REFERENCE' indicates code names of the protein given in other
databases such as PIR/SWISS-PROT or PDB. 'N-TERMINAL' shows the N-terminal
five amino acids which may help to show the unambiguous numbering of the
sequence. 'CHANGE', 'REPLACEMENT', 'EXTENSION', 'INSERTION', 'CHIMERA',
'DE NOVO' and 'MULTIPLE' indicate the position and kind of mutations (see
the attached listing for the notation).
Any mutant irrespective of the number of amino acids involved is described
under a single headline of CHANGE, so that the number of header 'CHANGE',
'REPLACEMENT', 'EXTENSION', 'INSERTION', 'CHIMERA', 'DE NOVO' and 'MULTIPLE'
imply the number of different mutants. Any functional, structural features
observed in the mutant are described right after them.
Relative differences in activity and/or stability in comparison with the
wild type is indicated with symbols [- -], [-], [=], [+], or [+ +].
Special comments or important remarks if mentioned in the article are given
in 'COMMENT' lines. 'SEQUENCE' shows a amino acid sequence of wild type.
*******************************************************************************
****** CONTENTS ******
*******************************************************************************
ENTRY *___++++ - ****** +++++++
| | | |
| | |_ Kind of mutations |_Article number
| | Artificial in PRF/LITDB
| | Variant
| | Chemical
| | Chimera
| | Enzymatic
| | Synthetic
| | Signal
| |
| |_ Number in "MUTANT DATABASE"
|
|_ A;article
R;review
B;preliminaly entry, type 'B',
which contains the "CHANGE" items, but does not contain
results of mutations('FUNCTION','STABILITY'.etc)
C;preliminaly entry, type 'C', which does not contain
the "CHANGE" items.
AUTHORS
JOURNAL
TITLE
CROSS-REFERENCE Code names of the proteins given in the databases such as
SWISS-PROT, PIR.
e.g. 1. MYG_HUMAN ( this is for SWISS_PROT)
2. MYHU ( this is for PIR)
2. /databases other than SWISS-PROT/PIR (if the protein is not found
in SWISS-PROT/PIR)
If the code names of proteins are not identified, they are
shown for the similar structural proteins using the
parenthesis.
e.g. (JKLCN)
PROTEIN Names of the protein including EC number and/or length
e.g. protein names in the article (abbrevation in the
article); entry names of PIR
SEQUENCE In the cases of "CHIMERA" and "FRAGMENT", the sequence is
shown as follows.
e.g. FRAGMENT- SEQUENCE MDLVVVLGLCSCALHHddd
SOURCE The source of the protein
N-TERMINAL The N-terminal five amino acids which may help to show the
unambiguous numbering of the sequence
EXPRESSION-SYSTEM Only for artificial mutants
CHANGE The position and the kind of mutations such as amino acid
substitution, replacement or deletion (see "Notation of
mutants")
Any mutant irrespective of the number of amino acids
involved is described under a single headline of "CHANGE"
so that each header CHANGE corresponds to a different
mutant.
REPLACEMENT The number of replaced amino acids are different from the
wild type.
EXTENSION
INSERTION
CHIMERA For chimeric proteins
FUNCTION Any features observed in the mutant; Relative defferences
STRUCTURE in comparison with the wild-type protein is,if possible,
STABILITY indicated with symbols [- -],[-],[=],[+],[+ +]. Complete
EXPRESSION loss of activity is indicated as [0].
TRANSPORT
MATURATION
DISEASE In cases where a given mutation is associated with some
disease, the name of disease is described.
COMMENT Special comments or important remarks if mentioned in the
article
/// End of entry
*******************************************************************************
****** NOTATION OF MUTANTS ******
*******************************************************************************
[CHANGE]
CHANGE-POINT His 44 Arg
; His-44 replaced by Arg
CHANGE-MODIFY Ala 63 (L-parafluorophenyl)Ala
; Ala-63 replaced by (L-parafluorophenyl)Ala
CHANGE-DELETE Lys 35
; Deletion of Lys-35
CHANGE-DELETE Glu--Gln 32-46
; Deletion from Glu-32 to Gln-46
CHANGE-DELETE Leu 8
-DELETE Glu--Gln 15-26
; Deletion of Leu-8 & deletion from Glu--Gln 15-26
CHANGE-STOP Pro 76 (termination)
; Pro 76 codon changed to the termination codon, resulting in
the truncated protein
CHANGE-INSERT Phe^Gly 441^442 GALKE
; Gly-Ala-Leu-Lys-Glu inserted between Phe-441 and Gly-442
CHANGE-EXTEND Ala^ 53^ YVACN
; Tyr-Val-Ala-Cys-Asn added to the C-terminus of Ala-53
CHANGE-REPLACE Ala--Arg 14-16 Gly-Thr-Phe-Val
; The region from Ala-14 to Arg-16 replaced by Gly-Thr-Phe-Val
CHANGE-REPLACE Val--Ile 64-70 GLIVPHALLSFRTHIIK
CHANGE-FRAGMENT Ala--Val 35-187 (fragmented)
; Fragmentated region from Ala--35 to Val-187
CHANGE-FRAME Ala 39 (frameshift)
; Translational frameshift after amino acid 38
CHANGE-POINT His 3 Ala
-POINT Asp 11 Asn
-REPLACE Ala--Arg 14-16 GTFVAP
; Combination of point mutation and replacement (the region
from Ala-14 to Arg-16 replaced by Gly-Thr-Phe-Val-Ala-Pro)
CHANGE-REPLACE Ala--Arg 14-16 GTFVM
-INSERT Phe^Gly 441^442 GALKE
; Combination of replacement (the region from Ala-14 to Arg-16
replaced by Gly-Thr-Phe-Val-Met) and insertion (Gly-Ala-Leu-
Lys-Glu inserted between Phe-441 and Gly-442) is done
simultaneity.
[CHIMERA]
CHANGE-CHIMERA (Ala--Ala 1-25 of GST1-1) - (Ala--Gly 25-114 of GST2-2)
; The region from Ala-1 to Ala-25 of GST1-1 protein fused to
the region from Ala-25 to Gly-114 of GST2-2 protein
CHANGE-CHIMERA Arg--Val 307-490 of cytochrome P450 2C2 is replaced by the
corresponding region of 2Cl.
; The region from Arg-307 to Val-490 of cytochrome P450 2CS is
replaced by the corresponding region of 2Cl
* See "EXAMPLES OF CHIMERIC PROTEIN" for practical examples.
*******************************************************************************
"EXAMPLES OF CHIMERIC PROTEIN"
*Example I
CROSS-REFERENCE O4RBP2
PROTEIN Cytochrome P450 2C2
SOURCE Rabbit
N-TERMINAL MDLVV
CROSS-REFERENCE O4RBP1
PROTEIN Cytochrome P450 2C1
SOURCE Rabbit
N-TERMINAL MDPVV
EXPRESSION-SYSTEM COS-1 cells
CHANGE-CHIMERA Arg--Val 307-490 of cytochrome P450 2C2 is replaced by the
corresponding region of cytochrome P450 2C1.
-SEQUENCE MDLVVVLGLCLSCLLLLSLWKQSHGGGKLPPGPTPFPILGNVLQLDFKDLSKSLTNLSKV
YGPVFTVYLGMKPTVVVHGYEAVKEALVDLGHELSGRSRFLVTAKLNKGFGVIFSNGKRW
TETRRFSLMTLRNFGMGKRSIEERVQEEAHCLVEELRKTNASPCDPTFILGAAPCNVICS
VIFQNRFDYTDQDFLSLMGKFNENFKILNSPWVQFCNCFPILFDYFPGSHRKAVKNIFYV
KNYITEQ/IKEHQK ddddd
FUNCTION Enzyme activity [-] (compared to cytochrome P450 2C2)
///
*Example II
CROSS-REFERENCE SYISC3
PROTEIN Chalcone synthase (CHS); naringenin-chalcone synthase
SOURCE Sinapis alba
N-TERMINAL MVMGT
CROSS-REFERENCE SYNPHS
PROTEIN Stilbene synthase (STS); trihydroxystilbene synthase
SOURCE Arachis hypogaea
N-TERMINAL MVSVS
EXPRESSION-SYSTEM Escherichia coli
CHANGE-CHIMERA (Met--Val 1-107 of CHS) - (Pro--Ile 103-389 of STS)
-POINT Pro 42 Ala (numbered as in CHS)
-SEQUENCE MVMGTPSSLDEIRKAQRADGPAGILAIGTANPANHVIQAEY(A)DYYFRITNSEHMTDLK
EKKRMCDKSTIRKRHMHLTEEFLKDNPNMCAYMAPSLDARQDIVVVEV/PRVGKEAATKA
IKEWGQPMSKITHLIFCTTSGVALPGVDYELIVLLGLDPSVKRYMMYHQGCFAGGTVLRL
AKDLAENNKDARVLIVCSENTAVTFRGPSETDMDSLVGQALFADGAAAIIIGSDPVPEVE
NPLFEIVSTDQKLVPNSHGAIGGLLREVGLTFYLNKSVPDIISQNINDALSKAFDPLGIS
DYNSIFWIAHPGGPAILDQVEQKVNLKPEKMNATRDVLSNYGNMSSACVFFIMDLMRKKS
LEEGLKTTGEGLDWGVLFGFGPGLTIETVVLRSVAI
FUNCTION CHS activity [0] (compared to CHS): STS activity [0] (compared
to STS)
///