Butter a 9-by-13-inch baking pan and dust it with flour, knocking out the excess. Heat the oven to 350°.
For the topping, process the pecans, brown sugar, flour, and cinnamon in a food processor for about 10 seconds. Add the butter and process for about 10 seconds or until finely chopped. Transfer to a bowl and set aside.
For the cake, sift the flour, baking powder, baking soda, and salt into a bowl and set it aside. In the bowl of an electric mixer, beat the butter on medium until soft and creamy. Gradually add the sugar, beating on medium-high until well blended. Add the eggs, one at a time, mixing well after each. Mix in the vanilla and lemon zest.
Whisk the sour cream and milk in a measuring cup. Add about one third of the dry ingredients to the butter mixture from step 3 and beat well on medium-to-low speed until combined. Mix in half the sour cream mixture, another third of the dry, the rest of the sour cream, and the remaining dry, scraping down the sides of the bowl as necessary after each addition. Using a rubber spatula, fold 1 1/2 cups of the diced apple into the batter (reserve the remaining 1 1/2 cups), then transfer the batter to the prepared pan and spread it evenly.
Sprinkle the surface with half the topping mixture, then cover with the reserved apple. Spread the rest of the topping over the apples. Tamp lightly with your palm to embed the topping.
Bake on the center rack until a toothpick inserted in the center comes out clean, about 60 minutes. Cool on a wire rack before serving.
Variation: ANY BERRY COFFEE CAKE--Replace the apple with 2 1/2 cups fresh raspberries, blueberries, or blackberries. Do not fold in the berries in step 4. Instead, use them all in the topping in step 5.
Variation: PEAR-CARDAMOM COFFEE CAKE--Add 1/4 teaspoon ground cardamom (or more to taste) to the dry ingredients. Replace the apple with 3 cups (about 7 large pears) peeled and diced fresh pears, folding half into the batter and using half in the topping, as in the apple recipe.