Wife is a Non-Resident Alien, How to enter in on Tax return for Married Filing Separately?

If you are a US citizen and your spouse does not have a Social Security number or an ITIN and you are not applying for an ITIN with the tax return then you can only file your tax return as Married Filing Separately.  Where asked to enter the spouse's Social Security number enter 999-88-9999.  You can only print and mail your tax return; it cannot be e-filed.  When you print the tax return erase the Social Security number for your spouse and manually enter NRA for non-resident alien.

See this TurboTax support FAQ for the procedure to print and mail a tax return using the online editions - https://ttlc.intuit.com/questions/1944348-how-do-i-print-and-mail-my-return-in-turbotax-online

If you are filing your tax return as Married Filing Jointly you must apply for an ITIN with the tax return and you would need to be providing a statement with your tax return that you want your Nonresident Alien Spouse Treated as a Resident.  See IRS Publication 54 Tax Guide for U.S. Citizens and Resident Aliens Abroad pages 6 and 7 - https://www.irs.gov/pub/irs-pdf/p54.pdf

Go to this IRS website for ITIN information - https://www.irs.gov/individuals/international-taxpayers/general-itin-information