What is Protein Data Bank?
- A repository for 3-D biological macromolecular structure
- All data are available to the public
- It includes proteins, nucleic acids and viruses
- Obtained by X-Ray crystallography (80%) or NMR spectroscopy (16%)
- Submitted by biologists and biochemists from around the world
History of Protein Data Bank
- Founded in 1971 by Brookhaven National Laboratory, New York
- First set of data were entered on punched cards. Then with magnetic tapes
- Transferred to the Research Collaborators for Structural Bioinformatics (RCSB) in 1998
- Currently it holds 29,000 released structures
FtsH peptidase
The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes PUBMED:17622352, PUBMED:16469117. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor PUBMED:17507650. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane.
This entry represents the N-terminal helical bundle domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species.
These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.
| Experiment Details |
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Method: ELECTRON MICROSCOPY
Resolution [Å]: 13.5
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE
Specimen Type: VITREOUS ICE |
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| Gene Ontology |
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| Type | Synonym |
| narrow: | protein folding chaperone |
| related: | protein tagging activity |
| related: | protein degradation tagging activity |
| exact: | protein amino acid binding |
| related: | alpha-2 macroglobulin receptor-associated protein activity |
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| Thermolysin |
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Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site PUBMED:7674922. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases PUBMED:7674922.
In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:
- Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
- Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.
In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding.
This group of metallopeptidases constitutes the MEROPS peptidase family M4 (thermolysin family, clan MA(E)). The protein fold of the peptidase domain of thermolysin, is the type example for members of the clan MA. The thermolysin family is composed only of secreted eubacterial endopeptidases. The zinc-binding residues are H-142, H-146 and E-166, with E-143 acting as the catalytic residue. Thermolysin also contains 4 calcium-binding sites, which contribute to its unusual thermostability. The family also includes enzymes from a number of pathogens, including Legionella and Listeria, and the protein pseudolysin, all with a substrate specificity for an aromatic residue in the P1' position. Three-dimensional structure analysis has shown that the enzymes undergo a hinge-bend motion during catalysis. Pseudolysin has a broader specificity, acting on large molecules such as elastin and collagen, possibly due to its wider active site cleft PUBMED:7674922.
Authors: Juers, D.H., Weik, M.
Experiment Details
Method: X-RAY DIFFRACTION
Exp. Data:
Structure Factors
EDS
| Unit Cell: |
| | Length [Å] | Angles [°] |
| a = 93.26 | α = 90.00 |
| b = 93.26 | β = 90.00 |
| c = 128.69 | γ = 120.00 | |
Gene Ontology
| Type | Synonym |
| exact : | metalloendoproteinase activity |
| exact : | metalloendoprotease activity |
Primary Citation
Radiation damage study of thermolysin - 100K structure B (2.5 MGy)
Juers, D.H., Weik, M.
Journal: To be Published
Not in PubMed
Molecular Description
| Classification: | Hydrolase |
| Structure Weight: | 34588.30 |
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| Molecule: | Thermolysin |
| Polymer: | 1 | Type: | polypeptide(L) | Length: | 316 |
| Chains: | E |
| EC#: | 3.4.24.27 |
| Fragment: | UNP residues 233-548 |
Source
Polymer: 1
Scientific Name Bacillus thermoproteolyticus
Aminopeptidases are exopeptidases involved in the processing and regular turnover of intracellular proteins, although their precise role in cellular metabolism is unclear PUBMED:1555602, PUBMED:2395881. Leucine aminopeptidases cleave leucine residues from the N-terminal of polypeptide chains, but substantial rates are evident for all amino acids PUBMED:2395881.
The enzymes exist as homo-hexamers, comprising 2 trimers stacked on top of one another PUBMED:2395881. Each monomer binds 2 zinc ions and folds into 2 alpha/beta-type quasi-spherical globular domains, producing a comma-like shape PUBMED:2395881. The N-terminal 150 residues form a 5-stranded beta-sheet with 4 parallel and 1 anti-parallel strand sandwiched between 4 alpha-helices PUBMED:2395881. An alpha-helix extends into the C-terminal domain, which comprises a central 8-stranded saddle-shaped beta-sheet sandwiched between groups of helices, forming the monomer hydrophobic core PUBMED:2395881. A 3-stranded beta-sheet resides on the surface of the monomer, where it interacts with other members of the hexamer PUBMED:2395881. The two zinc ions and the active site are entirely located in the C-terminal catalytic domain PUBMED:2395881.
Authors : Natarajan, S., Huynh, K.-H., Kang, L.W.
Experimental Details
Method: X-RAY DIFFRACTION
Exp. Data:
Structure Factors
EDS
| Unit Cell: |
| | Length [Å] | Angles [°] |
| a = 152.13 | α = 90.00 |
| b = 152.13 | β = 90.00 |
| c = 152.13 | γ = 90.00 |
Gene Ontology
Type Synonym
related : nucleocytoplasm
exact : internal to cell
related : protoplast
exact : protoplasm
Primary Citation
Crystal structure of Leucyl Aminopeptidase (pepA) from Xoo0834,Xanthomonas oryzae pv. oryzae KACC10331
Natarajan, S., Huynh, K.-H., Kang, L.W.
Journal: to be published
Not in PubMed
Molecular Description
| Classification: | Hydrolase |
| Structure Weight: | 102628.49 |
Molecule:Probable cytosol aminopeptidase
Polymer:1 Type:polypeptide(L)
Length:490
Source
Polymer: 1
Scientific Name: Xanthomonas oryzae pv. oryzae
Expression System: Escherichia coli
For More Further Information, visit:
http://www.rcsb.org/pdb/home/home.do |
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