Protein Data Bank

Assalamualaikum w.b.t

Hello again, my fellow vicegerents on Earth! Alhamdulillah, all praises to Allah that we got the chance to post this time entry as usual every Wednesday.

So, this time we are going to tell you about what we learned today in KOS1110 lecture. It is about Protein Data Bank (PDB).

First and foremost,  let us introduce to you what PDB is like. All of us have at least one bank account to keep our money. The same goes with protein. In Biology world, we keep informations of many biological molecules in banks.Protein Data Bank is a repository for the 3D structural data of large biological molecules, such as proteins and nucleic acids. The data typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations. Unfortunately, X-Ray crystallography is currently not available in IIUM Kuantan. But you can find it in Universiti Kebangsaan Malaysia.

X-Ray Crystallography

The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. 

The PDB is a key resource in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, such as the NIH in the USA, now require scientists to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently. 

PDB is an important resource for research in biological studies such as Biotechnology, Medicine and Pharmaceutical. Using the information provided by PDB helps scientists a lot to determine if certain molecules can cause cancer, or if certain combination of molecules can cure common colds, or if radiation can affect the RNA and DNA.

The PDB is updated on a weekly basis. This is the records dated on 8th September 2013: 

Experimental Method	Proteins	Nucleic Acids	Protein/Nucleic Acid complexes	Other	Total
X-ray diffraction	77139	1481	4059	3	82682
NMR	8829	1044	193	7	10073
Electron microscopy	466	45	128	0	639
Hybrid	51	3	2	1	57
Other	150	4	6	13	173
Total:	86635	2577	4388	24	93624

So, now we will show you some examples of protein that can be found in the PDB.


1)Prolyl oligopeptidase  

Classification:	Hydrolase
Structure Weight:	80842.69

Molecule:	prolyl oligopeptidase
Polymer:	1	Type:	protein	Length:	741
Chains:	A
EC#:	3.4.21.26
Organism	Novosphingobium capsulatum

Prolyl oligopeptidase

Prolyl oligopeptidase contains a peptidase domain and its catalytic triad is covered by the central tunnel of a seven-bladed beta-propeller. This domain makes the enzyme an oligopeptidase by excluding large structured peptides from the active site. The apparently rigid crystal structure does not explain how the substrate can approach the catalytic groups. Two possibilities of substrate access were investigated: either blades 1 and 7 of the propeller domain move apart, or the peptidase and/or propeller domains move to create an entry site at the domain interface. Engineering disulfide bridges to the expected oscillating structures prevented such movements, which destroyed the catalytic activity and precluded substrate binding. This indicated that concerted movements of the propeller and the peptidase domains are essential for the enzyme action.

2)Thermolysin

Classification:	Hydrolase (metalloproteinase)
Structure Weight:	34734.49

Molecule:	THERMOLYSIN
Polymer:	1	Type:	protein	Length:	316
Chains:	A
EC#:	3.4.24.27
Organism	Bacillus thermoproteolyticus

Thermolysin

The mode of binding of the irreversible thermolysin inhibitor ClCH2CO-DL-(N-OH)Leu-OCH3 [Rasnick, D., & Powers, J.C. (1978) Biochemistry 17, 4363-4369] has been determined by X-ray crystallography at a resolution of 2.3 A and the structure of the covalent complex refined to give a crystallographic residual of 17.0%. This is the first such structural study of an active-site-directed covalent complex of a zinc protease. As anticipated by Rasnick and Powers, the inhibitor alkylates Glu-143 in the thermolysin active site, and the hydroxamic acid moiety coordinates the zinc ion. The formation of the covalent complex is associated with a significant shift in a segment of the polypeptide backbone in the vicinity of the active site. This conformational adjustment appears to be necessary to relieve steric hindrance which would otherwise prevent alkylation of Glu-143. It is suggested that this steric hindrance, which occurs for thermolysin but would not be expected for carboxypeptidase A, accounts for the previously inexplicable difference in reactivity of these two metalloproteases toward N-haloacetyl amino acids. The relevance of this steric hindrance to the mechanism of catalysis is discussed. In agreement with previous results [Kester, W. R., & Matthews, B. W. (1977) Biochemistry 16, 2506-2516], it appears that steric hindrance prevents the direct attack of Glu-143 on the carbonyl carbon of an extended substrate, therefore ruling out the anhydride pathway in thermolysin-catalyzed hydrolysis of polypeptide substrates and their ester analogues. 

3) Oligopeptidase 

Classification:	Hydrolase
Structure Weight:	133341.53

Molecule:	Oligopeptidase
Polymer:	1	Type:	protein	Length:	564
Chains:	A, B
Fragment:	PEPTIDASE
Organism	Geobacillus sp. MO-1

Classification:

Hydrolase

Structure Weight:

133341.53

Molecule:

Oligopeptidase

Polymer:

1

Type:

protein

Length:

564

Chains:

A, B

Fragment:

PEPTIDASE

Organism

Geobacillus sp. MO-1

Oligopeptidase

Pz-peptidase A, from the thermophilic bacterium Geobacillus collagenovorans MO-1, hydrolyzes a synthetic peptidesubstrate, 4-phenylazobenzyloxycarbonyl-Pro-Leu-Gly-Pro-D-Arg (Pz-PLGPR), which contains a collagen-specific tripeptidesequence, -Gly-Pro-X-, but does not act on collagen proteins themselves. The mammalian enzyme, thimet oligopeptidase(TOP), which has comparable functions with bacterial Pz-peptidases but limited identity at the primary sequence level, hasrecently been subjected to x-ray crystallographic analysis; however, no crystal structure has yet been reported forcomplexes of TOP with substrate analogues. Here, we report crystallization of recombinant Pz-peptidase A in complex withtwo phosphinic peptide inhibitors (PPIs) that also function as inhibitors of TOP and determination of the crystal structure of these complexes at 1.80-2.00 Å resolution. The most striking difference between Pz-peptidase A and TOP is that there is no channel running the length of bacterial protein. Whereas the structure of TOP resembles an open bivalve, that of Pz-peptidase A is closed and globular. This suggests that collagenous peptide substrates enter the tunnel at the top gatewayof the closed Pz-peptidase A molecule, and reactant peptides are released from the bottom gateway after cleavage at theactive site located in the center of the tunnel. One of the two PPIs, PPI-2, which contains the collagen-specific sequence,helped to clarify the exquisite structure and reaction mechanism of Pz-peptidase A toward collagenous peptides. This studydescribes the mode of substrate binding and its implication for the mammalian enzymes. 

4) Signal peptidase

Classification:	Hydrolase
Structure Weight:	112635.13

Molecule:	SIGNAL PEPTIDASE I
Polymer:	1	Type:	protein	Length:	248
Chains:	A, B, C, D
EC#:	3.4.21.89
Fragment:	CATALYTIC DOMAIN
Organism	Escherichia coli BL21(DE3)

Signal peptidase

The signal peptidase (SPase) from Escherichia coli is a membrane-bound endopeptidase with two amino-terminal transmembrane segments and a carboxy-terminal catalytic region which resides in the periplasmic space. SPase functions to release proteins that have been translocated into the inner membrane from the cell interior, by cleaving off their signal peptides. We report here the X-ray crystal structure of a catalytically active soluble fragment of E. coli SPase (SPase delta2-75). We have determined this structure at 1.9 A resolution in a complex with an inhibitor, a beta-lactam (5S,6S penem), which is covalently bound as an acyl-enzyme intermediate to the gamma-oxygen of a serine residue at position 90, demonstrating that this residue acts as the nucleophile in the hydrolytic mechanism of signal-peptide cleavage. The structure is consistent with the use by SPase of Lys 145 as a general base in the activation of the nucleophilic Ser90, explains the specificity requirement at the signal-peptide cleavage site, and reveals a large exposed hydrophobic surface which could be a site for an intimate association with the membrane. As enzymes that are essential for cell viability, bacterial SPases present a feasible antibacterial target: our determination of the SPase structure therefore provides a template for the rational design of antibiotic compounds. 

5)Collagenase 

Classification:	Cell Adhesion
Structure Weight:	18426.06

Molecule:

Collagenase

Polymer:

1

Type:

protein

Length:

87

Chains:

A, B

EC#:

3.4.24.3

Fragment:

PKD domain

Organism

Clostridium histolyticum Collagenase

The crystal structure of a collagen-binding domain (CBD) with an N-terminal domain linker from Clostridium histolyticum class I collagenase was determined at 1.00 A resolution in the absence of calcium (1NQJ) and at 1.65 A resolution in the presence of calcium (1NQD). The mature enzyme is composed of four domains: a metalloprotease domain, a spacing domain and two CBDs. A 12-residue-long linker is found at the N-terminus of each CBD. In the absence of calcium, the CBD reveals a beta-sheet sandwich fold with the linker adopting an alpha-helix. The addition of calcium unwinds the linker and anchors it to the distal side of the sandwich as a new beta-strand. The conformational change of the linker upon calcium binding is confirmed by changes in the Stokes and hydrodynamic radii as measured by size exclusion chromatography and by dynamic light scattering with and without calcium. Furthermore, extensive mutagenesis of conserved surface residues and collagen-binding studies allow us to identify the collagen-binding surface of the protein and propose likely collagen-protein binding models. 

So, these are the 5 examples of protein that can be found in PDB.
That's all for now. See you again. Bye
Assalamualaikum w.b.t