KLK1

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Kallikrein 1
Image:PBB Protein KLK1 image.jpg
PDB rendering based on 1spj.
Available structures:
For the file format that describes the 3D structures of molecules found in the Protein Data Bank, see Protein Data Bank (file format).

The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. These data, typically obtained by X-ray crystallography or NMR spectroscopy, are submitted by biologists and biochemists from around the world, are released into the public domain, and can be accessed for free.

History

Founded in 1971 by Drs. Edgar Meyer and Walter Hamilton Brookhaven National Laboratory, management of the Protein Data Bank was transferred in 1998 to members of the Research Collaboratory for Structural Bioinformatics (RCSB).

The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.

The PDB is a key resource in structural biology and is critical to more recent work in structural genomics.

Countless derived databases and projects have been developed to integrate and classify the PDB in terms of protein structure, protein function and protein evolution.

Growth

When the PDB was originally founded it contained just 7 protein structures. Since then it has undergone an approximate exponential growth in the number of structures, which does not show any sign of falling off.

The growth rate of the PDB has been the subject of fairly extensive analysis.

Contents

As of 26 September, 2006, the database contained 39,051 released atomic coordinate entries (or "structures"), 35,767 of that proteins, the rest being nucleic acids, nucleic acid-protein complexes, and a few other molecules. About 5,000 new structures are released each year. Data are stored in the mmCIF format specifically developed for the purpose.

Note that the database stores information about the exact location of all atoms in a large biomolecule (although, usually without the hydrogen atoms, as their positions are more of a statistical estimate); if one is only interested in sequence data, i.e. the list of amino acids making up a particular protein or the list of nucleotides making up a particular nucleic acid, the much larger databases from Swiss-Prot and the International Nucleotide Sequence Database Collaboration should be used.

Statistics

As of 11 September, 2007, the "PDB Holdings List" at RCSB reported the following statistics:

Proteins Nucleic Acids Protein/NA complexes Other Total
X-ray diffraction 36223 983 1684 24 38914
NMR 5665 781 134 7 6587
Electron microscopy 105 10 38 0 153
Other 80 4 4 2 90
Total 42073 1778 1860 33 45744

Note that theoretical models are no longer accepted in the PDB.

22461 structures in the PDB have a structure factor file. 3138 structures in the PDB have an NMR restraint file.

The current breakdown of holdings is updated weekly.

File format

Through the years the PDB file format has undergone many, many changes and revisions. Its original format was dictated by the width of computer punch cards.

This legacy format has caused many problems with the format, and consequently there are 'clean-up' projects;

The MMDB uses ASN.1 (and an XML conversion of this format). The wwPDB members RCSB PDB, MSD-EBI, and PDBj are working together to make the data uniform across the archive. Some believe this to be desirable; others argue that, without a universal repository of information (i.e., a common dictionary), it is not possible to draw comparisons.

Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. This should not be used as an identifier for biomolecules, since often several structures for the same molecule (in different environments or conformations) are contained in PDB with different PDB IDs.

If a biologist submits structure data for a protein or nucleic acid, wwPDB staff reviews and annotates the entry. The data are then automatically checked for plausibility. The source code for this validation software has been released for free. The main data base accepts only experimentally derived structures, and not theoretically predicted ones (see protein structure prediction).

Various funding agencies and scientific journals now require scientists to submit their structure data to PDB.

Viewing the data

The structural data can be used to visualize the biomolecules with appropriate software, such as VMD, RasMol, PyMOL, Jmol, MDL Chime, QuteMol, web browser VRML plugin or any web-based software designed to visualize and analyse the protein structures such as STING. A recent desktop software addition is Sirius. The RCSB PDB website also contains resources for education, structural genomics, and related software.

References

Printed

  • H.M. Berman, K. Henrick, H. Nakamura (2003): Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980 PMID 14634627.
  • H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000). PMID 10592235
  • Bernstein FC, Koetzle TF, Williams GJ, Meyer Jr EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542. PMID 875032.
  • E.F. Meyer “The First Years of the Protein Data Bank“, Protein Science 6:1591-1597 (1997)
  • Sussman, JL, Lin, D, Jiang, J, Manning, NO, Prilusky, J, Ritter, O & Abola, EE. Protein data bank (PDB): a database of 3D structural information of biological macromolecules. Acta Cryst 1998; D54:1078-1084. PMID 10089483.

Online

Other external links

Links to enzyme database data

  • [1] The best mapping is provided by Kim Henrick's group at EBI as part of the MSD SIFTS initiative.
  • [2] PDB provide a mapping on their beta site, but it is at the whole PDB level not chain level.
  • [3] Search at BRENDA enzyme database portal.
  • [4] PDBSProtEC:

Molecular graphic visualisation tools

Identifiers
Symbol(s) KLK1; KLKR; Klk6; hK1
External IDs OMIM: 147910 MGI: 97322 Homologene: 88436
RNA expression pattern

Image:PBB GE KLK1 216699 s at tn.png

More reference expression data

Orthologs
Human Mouse
Entrez 3816 18050
Ensembl ENSG00000167748 ENSMUSG00000066515
Uniprot P06870 Q62284
Refseq NM_002257 (mRNA)
NP_002248 (protein) 		NM_008693 (mRNA)
NP_032719 (protein)
Location Chr 19: 56.01 - 56.02 Mb Chr 7: 44.07 - 44.07 Mb
Pubmed search [5] [6]

Kallikrein 1, also known as KLK1, is a human gene.


Kallikreins are a subgroup of serine proteases having diverse physiological functions. Growing evidence suggests that many kallikreins are implicated in carcinogenesis and some have potential as novel cancer and other disease biomarkers. This gene is one of the fifteen kallikrein subfamily members located in a cluster on chromosome 19. This protein is functionally conserved in its capacity to release the vasoactive peptide, Lys-bradykinin, from low molecular weight kininogen.[1]


References

Further reading

  • Clements J, Hooper J, Dong Y, Harvey T (2001). "The expanded human kallikrein (KLK) gene family: genomic organisation, tissue-specific expression and potential functions.". Biol. Chem. 382 (1): 5-14. PMID 11258672.
  • Lottspeich F, Geiger R, Henschen A, Kutzbach C (1980). "N-Terminal amino acid sequence of human urinary kallikrein homology with other serine proteases.". Hoppe-Seyler's Z. Physiol. Chem. 360 (12): 1947-50. PMID 393608.
  • Riegman PH, Vlietstra RJ, Suurmeijer L, et al. (1992). "Characterization of the human kallikrein locus.". Genomics 14 (1): 6-11. PMID 1385301.
  • Richards RI, Holman K, Shen Y, et al. (1992). "Human glandular Kallikrein genes: genetic and physical mapping of the KLK1 locus using a highly polymorphic microsatellite PCR marker.". Genomics 11 (1): 77-82. PMID 1684954.
  • Henttu P, Lukkarinen O, Vihko P (1990). "Expression of the gene coding for human prostate-specific antigen and related hGK-1 in benign and malignant tumors of the human prostate.". Int. J. Cancer 45 (4): 654-60. PMID 1691151.
  • Qin H, Kemp J, Yip MY, et al. (1992). "Localization of human glandular kallikrein-1 gene to chromosome 19q13.3-13.4 by in situ hybridization.". Hum. Hered. 41 (4): 222-6. PMID 1783409.
  • Lu HS, Lin FK, Chao L, Chao J (1989). "Human urinary kallikrein. Complete amino acid sequence and sites of glycosylation.". Int. J. Pept. Protein Res. 33 (4): 237-49. PMID 2666327.
  • Angermann A, Bergmann C, Appelhans H (1990). "Cloning and expression of human salivary-gland kallikrein in Escherichia coli.". Biochem. J. 262 (3): 787-93. PMID 2686621.
  • Evans BA, Yun ZX, Close JA, et al. (1988). "Structure and chromosomal localization of the human renal kallikrein gene.". Biochemistry 27 (9): 3124-9. PMID 2898948.
  • Fukushima D, Kitamura N, Nakanishi S (1986). "Nucleotide sequence of cloned cDNA for human pancreatic kallikrein.". Biochemistry 24 (27): 8037-43. PMID 3004571.
  • Kellermann J, Lottspeich F, Geiger R, Deutzmann R (1988). "Human urinary kallikrein--amino acid sequence and carbohydrate attachment sites.". Protein Seq. Data Anal. 1 (3): 177-82. PMID 3163150.
  • Takahashi S, Irie A, Katayama Y, et al. (1986). "N-terminal amino acid sequence of human urinary prokallikrein.". J. Biochem. 99 (3): 989-92. PMID 3635530.
  • Baker AR, Shine J (1986). "Human kidney kallikrein: cDNA cloning and sequence analysis.". DNA 4 (6): 445-50. PMID 3853975.
  • Del Nery E, Chagas JR, Juliano MA, et al. (1996). "Evaluation of the extent of the binding site in human tissue kallikrein by synthetic substrates with sequences of human kininogen fragments.". Biochem. J. 312 ( Pt 1): 233-8. PMID 7492318.
  • Chen LM, Richards GP, Chao L, Chao J (1995). "Molecular cloning, purification and in situ localization of human colon kallikrein.". Biochem. J. 307 ( Pt 2): 481-6. PMID 7733886.
  • Clements J, Mukhtar A, Ehrlich A, Yap B (1995). "Glandular kallikrein gene expression in the human uterus.". Braz. J. Med. Biol. Res. 27 (8): 1855-63. PMID 7749374.
  • Lin FK, Lin CH, Chou CC, et al. (1993). "Molecular cloning and sequence analysis of the monkey and human tissue kallikrein genes.". Biochim. Biophys. Acta 1173 (3): 325-8. PMID 7916636.
  • Gomes RA, Juliano L, Chagas JR, Hial V (1997). "Characterization of kininogenase activity of an acidic proteinase isolated from human kidney.". Can. J. Physiol. Pharmacol. 75 (6): 757-61. PMID 9276160.
  • Bourgeois L, Brillard-Bourdet M, Deperthes D, et al. (1997). "Serpin-derived peptide substrates for investigating the substrate specificity of human tissue kallikreins hK1 and hK2.". J. Biol. Chem. 272 (47): 29590-5. PMID 9368023.
  • Chen VC, Chao L, Chao J (2000). "Reactive-site specificity of human kallistatin toward tissue kallikrein probed by site-directed mutagenesis.". Biochim. Biophys. Acta 1479 (1-2): 237-46. PMID 10862973.
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