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UniProt release 3.4

Published December 21, 2004

Headlines

Annotation of TRPA1 and TRPM8 transient receptors involved in sensing cold

Mammals detect temperature with specialized neurons in the peripheral nervous system. Two transient receptor-class channels, TRPA1 and TRPM8, have been implicated in sensing cold.

The first of these channels, TRPA1, is activated by temperatures below 17 degrees Celsius, which corresponds to the noxious cold threshold. The second channel, TRPM8, plays a role in sensing less extreme cool temperatures, being activated below 25 degrees Celsius.

Interestingly, the TRPM8 channel is also activated by products such as eucalyptol or menthol, which may provide a ready explanation for the sensation of coolness triggered by these flavors.

See:

UniProtKB News

Changes in the RP (Reference Position) line

We changed the following items of the RP line:

  • 'SEQUENCE FROM N.A.' became 'NUCLEOTIDE SEQUENCE'
  • ' This topic can be tagged with an optional qualifier indicating the origin of the sequence: 'NUCLEOTIDE SEQUENCE [ORIGIN OF SEQUENCE DATA]', where valid names are:
    • GENOMIC DNA: the individual gene has been sequenced
    • GENOMIC RNA: the individual gene has been sequenced
    • MRNA: the individual cDNA has been sequenced
    If the data originates from a genome project or cDNA large-scale project, the qualifier is preceded by the term "LARGE SCALE"; this generally indicates that the relevant publication describes the project rather than giving further details on the protein of interest.
    • LARGE SCALE GENOMIC DNA: the gene has been sequenced as part of a genome project
    • LARGE SCALE MRNA: the gene has been sequenced as part of a large-scale cDNA project
  • 'SEQUENCE' became 'PROTEIN SEQUENCE'
  • 'REVISION(S)' became 'SEQUENCE REVISION'

Example:

RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), PROTEIN SEQUENCE
RP   OF 108-131; 220-231 AND 349-393, CHARACTERIZATION, AND MUTAGENESIS OF
RP   ARG-336.

If 2 qualifiers apply, both are indicated, separated by a '/'.

Example:

RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].

New comment line (CC) topic: BIOPHYSICOCHEMICAL PROPERTIES

A new comment line (CC) topic has been introduced: BIOPHYSICOCHEMICAL PROPERTIES. This topic is used to convey information relevant to biophysical and physicochemical data and information on pH dependence, temperature dependence, kinetic parameters, redox potentials, and maximal absorption.

The format of this comment block is:

CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Absorption:
CC         Abs(max)=xx nm;
CC         Note=free_text;
CC       Kinetic parameters:
CC         KM=xx unit for substrate [(free_text)];
CC         Vmax=xx unit enzyme [free_text];
CC         Note=free_text;
CC       pH dependence:
CC         free_text;
CC       Redox potential:
CC         free_text;
CC       Temperature dependence:
CC         free_text;

A BIOPHYSICOCHEMICAL PROPERTIES block must contain at least one of the properties Absorption, Kinetic parameters, pH dependence, Redox potential, Temperature dependence and may have any combination of these properties (ordered as indicated above). The meaning of these subtopics is as follows:

Property Description
Absorption indicates the wavelength at which photoreactive proteins such as opsins and DNA photolyases show maximal absorption
Kinetic parameters mentions the Michaelis-Menten constant (KM) and maximal velocity (Vmax) of enzymes
pH dependence describes the optimum pH for enzyme activity and/or the variation of enzyme activity with pH variation
Redox potential reports the value of the standard (midpoint) oxido-reduction potential(s) for electron transport proteins
Temperature dependence indicates the optimum temperature for enzyme activity and/or the variation of enzyme activity with temperature variation; the thermostability/thermolability of the enzyme is also mentioned when it is known

Examples:

CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Absorption:
CC         Abs(max)=395 nm;
CC         Note=Exhibits a smaller absorbance peak at 470 nm. The
CC         fluorescence emission spectrum peaks at 509 nm with a shoulder
CC         at 540 nm;

CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=62 mM for glucose;
CC         KM=90 mM for maltose;
CC         Vmax=0.20 mmol/min/mg enzyme with glucose as substrate;
CC         Vmax=0.11 mmol/min/mg enzyme with maltose as substrate;
CC         Note=Acetylates glucose, maltose, mannose, galactose, and
CC         fructose with a decreasing relative rate of 1, 0.55, 0.20, 0.07,
CC         0.04;

CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=1.76 uM for chlorophyll;
CC       pH dependence:
CC         Optimum pH is 7.5. Active from pH 5.0 to 9.0;
CC       Temperature dependence:
CC         Optimum temperature is 45 degrees Celsius. Active from 30 to 60
CC         degrees Celsius;

Changes concerning keywords

New keywords:

Modified keyword:

Deleted keywords:

  • DNA priming
  • Noncapsid protein
  • Nonstructural protein
  • Nucleocapsid

Changes concerning the controlled vocabulary for PTMs

New terms for the feature key 'CROSSLNK':

  • 2-iminomethyl-5-imidazolinone (Glu-Gly)
  • 2-iminomethyl-5-imidazolinone (Met-Gly)
  • 5-imidazolinone (Asn-Gly)
  • 5-imidazolinone (Lys-Gly)
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