Indeed a single amino acid (a polar acidic amino acid in this case) determines the interaction of a antiviral protein APOBEC3G with to HIV-Vif and not with SIV-Vif (species specific), it was also shown that the single mutation can alter the specif specificity of the same protein! (Mangeat B, et al., JBC 2004 and Mariani R, et al., Cell, 2003). It is so funny that we could have HIV disease and not one more by SIV due to such selection!

So I imagine these charged polar amino acids are crucially playing the roles on protein protein interaction/ other functions, and you may expect such things with yours too!

Hi Manan!

I think yes, though your question is a bit generic. I don’t understand what you do mean by opposite effects. If you have X-ray 3D structure you may be able to tell more. In principle if you have more polar amino acids close to the catalytic site and if the catalytic site performs for example an acid-base catalytic cycle, the pKa of the responsible amino acid would be altered depending on the number of polar amino acids that are close nearby. That means your Kcat will change and also the nature of the substrate on which to perform the reaction. The other factor you will have to take into account is the substrate and how it will be accommodated within the catalytic center. In this case the binding may be altered. In summary, you can have altered binding or/and altered catalytic activity. So, that may provide a molecular basis for specificity toward related substrates

Thanks for the explanation .. Probably this could be the case...

You may draw your attention to the serine proteases family (e.g. trypsin, cymotrypsin, elastase,...). All of them share some structural/functional features: the catalytic triad instrumental for the hydrolytic activity. However, they show significant differences in other key residues important for the specificity. For example, in trypsin the S1 pocket contains an acidic residue which makes possible to cleave peptide bonds following a positively charged residue. In chymotrypsin the S1 pocket contains a hydrophobic residue which makes possible to cleave peptide bonds following a large hydrophobic residue. In elastase the S1 pocket is smaller than in chymotrypsn and, therefore, the specificity is directed to smaller hydrophobic residues.

Therefore, the geometry and chemical nature (not only polarity, but also nonpolarity) of the residues surrounding the catalytic residues are important for defining the specificity of the enzyme and promoting the efficient binding of the substrate in order to lower the energy of its transition state towards the product. The substrate must show geometric/structural/functional complementarity regarding the enzyme's active site.

Of course, if the polar residues have ionizable (de-/protonable) side chains they will define the pH dependency of the hydrolytic activity (Km, kcat, kcat/Km). This way, a certain enzyme may show higher activity at low/high pH.

The same catalytic site means similar binding, Difference in adjacent site is the site that actually is modulating protein functions among two.

Hi

I think that the nature of the amino acid residues, belonging to the outside environment of active site, could influence different factors, as the different approach of the substrate molecule, so by selecting alternative molecules having properties more similar to the polar residues. The long-range interactions play an important role on the "molecular recognition". The different polarity leads to a different charge distribution important for delineating the accessible area to the substrate.

This is my simple opinion.

Tiziana Marino, University of Calabria

Thank you for the answers..

This is a mighty big question and Abdelhalim has provided a very good answer. Polar residues at the active site of an enzyme can function in a number of ways including,(i) A direct role in the catalytic event event by acting as acid/base or nucleophilic reagents (ii) Contribute to the binding of the substrate by charge-charge interactions or H bonding (iii) Stabilisation of the transition state if this involves devopment of a charge during bond breaking etc. These actions are not mutally exclusive i.e. a polar residue may be important for a combination of possible actions. I can strongly recommend the text by Alan Fersht entitled Structure and Mechanism in Protein Science. You won't find a better account of enzymology than Fersht.

Peter

I would second the recommendation for the Fersht text, and also recommend looking at the following reference (and others relating to the MACiE database) for a statistical evaluation of the types of roles played by specific polar residues in well-characterized enzyme reactions:

Holliday GL, Mitchell JB, Thornton JM. Understanding the functional roles of amino acid residues in enzyme catalysis. J Mol Biol. 2009 Jul 17;390(3):560-77. doi: 10.1016/j.jmb.2009.05.015. Epub 2009 May 15. PubMed PMID: 19447117.

Hello there,

I will most definitely direct you to the following articles as there are not definite answer but precise examples:

Stereochemistry of the active site of -chymotrypsin. The influence of polar groups in locked substrates.

Pattabiraman TN, Lawson WB.

J Biol Chem. 1972 May 25;247(10):3029-38.

The role of active-site aromatic and polar residues in catalysis and substrate discrimination by xylose isomerase.

Meng M, Bagdasarian M, Zeikus JG.

Proc Natl Acad Sci U S A. 1993 Sep 15;90(18):8459-63.

Electrostatic stabilization in a pre-organized polar active site: the catalytic role of Lys-80 in Candida tenuis xylose reductase (AKR2B5) probed by site-directed mutagenesis and functional complementation studies.

Kratzer R, Nidetzky B.

Biochem J. 2005 Jul 15;389(Pt 2):507-15.

Role of polar and nonpolar residues at the active site for PPIase activity of FKBP22 from Shewanella sp. SIB1.

Budiman C, Tadokoro T, Angkawidjaja C, Koga Y, Kanaya S.

FEBS J. 2012 Mar;279(6):976-86.

Have a good read,

Dominique