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UniProt release 8.6

Published September 5, 2006

Headlines

3D-structure information for over 10,000 proteins

3D-structure information is now available for over 10,000 proteins in UniProtKB/Swiss-Prot (containing more than 36,000 individual cross-references to PDB.).

Protein structures not only delight the eye, they shed light on protein architecture and provide proof for the existence of a given protein fold. They are indispensable to determine the interactions of a protein with its ligands (substrates, ions, cofactors or regulatory molecules) and provide solid proof for post-translational modifications. Likewise, 3D-structures pinpoint the exact position of residues that cause a genetic disease when mutated (e.g. Q8NBK3). They help to design experiments and make it possible to attribute a function to so-far hypothetical proteins (e.g. Q46856).

UniProtKB aims to be fully synchronized with PDB and provide access to information about protein 3D-structures via cross-references to PDB, and by giving high priority to the annotation of proteins with known 3D-structures. A semi-automated mapping procedure was established in collaboration with the Macromolecular Structure Database (MSD), so that the whole PDB archive could be mapped to UniProtKB.


UniProtKB News

Cross-references to ArrayExpress

ArrayExpress is a public repository database for microarray gene expression data. We introduced a new cross-reference to the ArrayExpress, which stores gene-indexed expression profiles from a curated subset of experiments in the repository.

The format of the explicit links in the flat file is:

Resource abbreviation ArrayExpress
Resource identifier UniProtKB primary AC.
Example
O00139:
DR   ArrayExpress; O00139; -.

Cross-references to PeroxiBase

PeroxiBase is a database that centralizes most of the peroxidase superfamilies encoding sequences (classes I, II, III peroxidase superfamily, glutathione peroxidases, NADPH oxidases, and animal peroxidases), to follow the evolution of peroxidase among living organism and to compile the information concerning putative functions and transcription regulation.

The format of the explicit links in the flat file is:

Resource abbreviation PeroxiBase
Resource identifier PeroxiBase accession number.
Optional information 1 PeroxiBase entry name
Example
O23044:
DR   PeroxiBase; 79; AtPrx03.

Changes concerning keywords

PTMs

Terms introduced in the controlled vocabulary for PTMs:

Terms for the feature key 'CROSSLNK':

  • 3-(S-cysteinyl)-tyrosine (Cys-Tyr)
  • 3'-(S-cysteinyl)-tyrosine (Tyr-Cys)
  • 4-amino-3-isothiazolidinone serine (Cys-Ser)
  • Peptide (Met-Gly) (interchain with G-...)
  • Tryptophyl-tyrosyl-methioninium (Trp-Tyr)
  • Tryptophyl-tyrosyl-methioninium (Tyr-Met)

Terms for the feature key 'LIPID':

  • 3'-geranyl-2',N2-cyclotryptophan
  • GPI-like-anchor amidated alanine
  • GPI-like-anchor amidated asparagine
  • N6-myristoyl lysine
  • N6-palmitoyl lysine
  • S-stearoyl cysteine

Terms for the feature key 'MOD_RES':

  • 1-thioglycine
  • 2-oxobutanoic acid
  • Citrulline
  • Cysteine sulfenic acid (-SOH)
  • Cysteine sulfinic acid (-SO2H)
  • Cysteinyl-selenocysteine (Sec-Cys)
  • Methionine sulfone
  • N2-succinyltryptophan
  • Nitrated tyrosine
  • O-acetylserine
  • O-acetylthreonine
  • S-selanylcysteine