Contact atlas: Protein 1JKY
[альфа-версия]
General information about the protein:
| Physico-chemical properties: |
| PDB ID |
1JKY |
| Uniprot ID |
P15917 |
| Gross formula |
C3602N977O1147S8 |
| Molar mass |
84040 |
The chosen protein with PDB ID 1JKY is the Crystal Structure of the Anthrax Lethal Factor (LF): Wild-type LF Complexed with the N-terminal Sequence of MAPKK2. The protein is synthesized by the bacteria Bacillus anthracis based on the sequence of human DNA.
Lethal factor (LF) is a protein (relative molecular mass 90,000) that is critical in the pathogenesis of anthrax. It is a highly specific protease that cleaves members of the mitogen-activated protein kinase kinase (MAPKK) family near to their amino termini, leading to the inhibition of one or more signalling pathways. Here we describe the crystal structure of LF and its complex with the N terminus of MAPKK-2.
LF comprises four domains: domain I binds the membrane-translocating component of anthrax toxin, the protective antigen (PA); domains II, III and IV together create a long deep groove that holds the 16-residue N-terminal tail of MAPKK-2 before cleavage. Domain II resembles the ADP-ribosylating toxin from Bacillus cereus, but the active site has been mutated and recruited to augment substrate recognition. Domain III is inserted into domain II, and seems to have arisen from a repeated duplication of a structural element of domain II. Domain IV is distantly related to the zinc metalloprotease family, and contains the catalytic centre; it also resembles domain I. The structure thus reveals a protein that has evolved through a process of gene duplication, mutation and fusion, into an enzyme with high and unusual specificity.[1]
Here is an applet showing our protein
Interprotein contacts information.
Covalent bonds:
Peptide bonds: These are covalent bonds that form through the interaction of -NH2 and -COOH aminoacid groups. As a result, a polipeptide chain is formed, which later composes the protein.[2]
Disulfide bonds: Bonds, comprised of cystein radical -SH groups. Our protein does not contain cystein, therefore there are no disulfide bonds.[3]
Hydrogen bonds:
These bonds are formed between a hydrogen atom, which is covalently bonded with an electronegative atom(A1-H), and another electronegative atom(A2)[4]Alpha-helixes and beta-sheets: they are the elements of the secondary protein structure[5]There is an applet demonstrating the secondary structure of our protein below.
Used commands
Salt bridges:
They are formed as a result of an interaction between negatively (aspartic, glutamic acids) and positively charged (lysine, arginine, histidine) aminoacid side chains. The applet demonstrating these bonds in our protein is on the up.
Used commands
Hydrophobic nucleus.
The dissolution of hydrophobic substances in water leads to a significant entropy decrease. The reason for this is the fact that water molecules situated close to the nonpolar molecule become fixed in a certain position and form a highly structured shell around the dissolved substance. This position is thermodynamically unfavourable to the system, therefore hydrophobic molecules interact in water: forces attractions betweeen nonpolar side chains hold together the nonpolar groups of molecules of the dissolved substance.[6].
Normally, the hydrophobic nucleus in proteins is comprised exclusively of hydrophobic side chains. It is compacted, often submerged into the globula. Hydrophobic nucleus has an outer shell that has contact with water. The shell is often mosaic: hydrophilic and hydrophobic areas alternate, which is functionally significant: hydrophobic areas might form zones of substrate binding and be involved in intraprotein interactions. Hydrophobic nuclei play an important part in stabilizing the third-order structure of the protein. Hydrophobic interactions take part in forming the fourth-order structure of the protein: in addition to hydrogen bonds between subunits they make the fourth-order structure strong and stable, yet flexible enough, which is important for the functionality of many proteins[7].
The applet below demonstrates the hydrophobic shell around Trp 501 radical.
Used commands
Having studied the hydrophobic nucleus of Trp501 radical, the following results were achieved:
| Minimal distance to a radical whose surface is completely covered by the atoms of the nucleus: |
6А |
| Average distance between covalently non bonded atoms: |
3А |
| Can a water molecule fit between neighbouring atoms (length 2.8A): |
No |
Authors:
Bezuglov Vitaly (general information about the protein), Belov Leonid (interprotein contacts), Danilina Arina (translations to English and Spanish)
Sources:
[1] RCSB
[2] Wikipedia
[3] Академик
[4] Ru-wiki
[5] www.biochemistry.ru
[6] Д. Нельсон, М. Кокс. "Основы биохимии Ленинджера"
[7] В. М. Степанов "Молекулярная биология. Структура и функции белков"
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