diff --git a/common/lib/xmodule/xmodule/conditional_module.py b/common/lib/xmodule/xmodule/conditional_module.py
index 7ea3483aef..6e73ed3509 100644
--- a/common/lib/xmodule/xmodule/conditional_module.py
+++ b/common/lib/xmodule/xmodule/conditional_module.py
@@ -8,6 +8,8 @@ import logging
 from lazy import lazy
 from lxml import etree
 from pkg_resources import resource_string
+
+from opaque_keys.edx.locator import BlockUsageLocator
 from xblock.fields import ReferenceList, Scope, String
 from xblock.fragment import Fragment
 
@@ -265,7 +267,11 @@ class ConditionalDescriptor(ConditionalFields, SequenceDescriptor, StudioEditabl
         if not self.sources_list:
             if 'sources' in self.xml_attributes and isinstance(self.xml_attributes['sources'], basestring):
                 self.sources_list = [
-                    self.location.course_key.make_usage_key_from_deprecated_string(item)
+                    # TODO: it is not clear why we are replacing the run here (which actually is a no-op
+                    # for old-style course locators. However, this is the implementation of
+                    # CourseLocator.make_usage_key_from_deprecated_string, which was previously
+                    # being called in this location.
+                    BlockUsageLocator.from_string(item).replace(run=self.location.course_key.run)
                     for item in ConditionalDescriptor.parse_sources(self.xml_attributes)
                 ]
 
diff --git a/common/lib/xmodule/xmodule/modulestore/mongo/base.py b/common/lib/xmodule/xmodule/modulestore/mongo/base.py
index e1dc91afb4..aa9edf474a 100644
--- a/common/lib/xmodule/xmodule/modulestore/mongo/base.py
+++ b/common/lib/xmodule/xmodule/modulestore/mongo/base.py
@@ -837,7 +837,7 @@ class MongoModuleStore(ModuleStoreDraftAndPublished, ModuleStoreWriteBase, Mongo
         # first get non-draft in a round-trip
         query = {
             '_id': {'$in': [
-                course_key.make_usage_key_from_deprecated_string(item).to_deprecated_son() for item in items
+                UsageKey.from_string(item).map_into_course(course_key).to_deprecated_son() for item in items
             ]}
         }
         return list(self.collection.find(query))
@@ -1741,7 +1741,7 @@ class MongoModuleStore(ModuleStoreDraftAndPublished, ModuleStoreWriteBase, Mongo
                 )
             all_reachable = all_reachable.union(item.get('definition', {}).get('children', []))
         item_locs -= all_reachable
-        return [course_key.make_usage_key_from_deprecated_string(item_loc) for item_loc in item_locs]
+        return [UsageKey.from_string(item_loc).map_into_course(course_key) for item_loc in item_locs]
 
     def get_courses_for_wiki(self, wiki_slug, **kwargs):
         """
diff --git a/common/lib/xmodule/xmodule/modulestore/mongo/draft.py b/common/lib/xmodule/xmodule/modulestore/mongo/draft.py
index c7585a6ecc..9429f9d76b 100644
--- a/common/lib/xmodule/xmodule/modulestore/mongo/draft.py
+++ b/common/lib/xmodule/xmodule/modulestore/mongo/draft.py
@@ -9,6 +9,7 @@ and otherwise returns i4x://org/course/cat/name).
 import pymongo
 import logging
 
+from opaque_keys.edx.keys import UsageKey
 from opaque_keys.edx.locations import Location
 from openedx.core.lib.cache_utils import memoize_in_request_cache
 from xmodule.exceptions import InvalidVersionError
@@ -424,7 +425,7 @@ class DraftModuleStore(MongoModuleStore):
             # collect the children's ids for future processing
             next_tier = []
             for child in item.get('definition', {}).get('children', []):
-                child_loc = Location.from_deprecated_string(child)
+                child_loc = Location.from_string(child)
                 next_tier.append(child_loc.to_deprecated_son())
 
             # insert a new DRAFT version of the item
@@ -582,7 +583,7 @@ class DraftModuleStore(MongoModuleStore):
             to_be_deleted.append(self._id_dict_to_son(current_entry['_id']))
             next_tier = []
             for child_loc in current_entry.get('definition', {}).get('children', []):
-                child_loc = course_key.make_usage_key_from_deprecated_string(child_loc)
+                child_loc = UsageKey.from_string(child_loc).map_into_course(course_key)
 
                 # single parent can have 2 versions: draft and published
                 # get draft parents only while deleting draft module
@@ -813,7 +814,7 @@ class DraftModuleStore(MongoModuleStore):
                 item = versions_found[0]
                 assert item.get('_id').get('revision') != MongoRevisionKey.draft
                 for child in item.get('definition', {}).get('children', []):
-                    child_loc = Location.from_deprecated_string(child)
+                    child_loc = Location.from_string(child)
                     delete_draft_only(child_loc)
 
         delete_draft_only(location)
@@ -829,7 +830,7 @@ class DraftModuleStore(MongoModuleStore):
             user_id (int)   : User id
         """
         for child_location in published_version.get('definition', {}).get('children', []):
-            item_location = original_parent_location.course_key.make_usage_key_from_deprecated_string(child_location)
+            item_location = UsageKey.from_string(child_location).map_into_course(original_parent_location.course_key)
             try:
                 source_item = self.get_item(item_location)
             except ItemNotFoundError:
@@ -838,7 +839,7 @@ class DraftModuleStore(MongoModuleStore):
 
             if source_item.parent and source_item.parent.block_id != original_parent_location.block_id:
                 if self.update_item_parent(item_location, original_parent_location, source_item.parent, user_id):
-                    delete_draft_only(Location.from_deprecated_string(child_location))
+                    delete_draft_only(Location.from_string(child_location))
 
     def _query_children_for_cache_children(self, course_key, items):
         # first get non-draft in a round-trip
@@ -852,7 +853,7 @@ class DraftModuleStore(MongoModuleStore):
             # now query all draft content in another round-trip
             query = []
             for item in items:
-                item_usage_key = course_key.make_usage_key_from_deprecated_string(item)
+                item_usage_key = UsageKey.from_string(item).map_into_course(course_key)
                 if item_usage_key.category not in DIRECT_ONLY_CATEGORIES:
                     query.append(as_draft(item_usage_key).to_deprecated_son())
             if query:
diff --git a/common/lib/xmodule/xmodule/modulestore/mongoengine_fields.py b/common/lib/xmodule/xmodule/modulestore/mongoengine_fields.py
index 03a033f857..6c3f422e6c 100644
--- a/common/lib/xmodule/xmodule/modulestore/mongoengine_fields.py
+++ b/common/lib/xmodule/xmodule/modulestore/mongoengine_fields.py
@@ -73,7 +73,7 @@ class UsageKeyField(mongoengine.StringField):
             return None
         if isinstance(location, basestring):
             location = super(UsageKeyField, self).to_python(location)
-            return Location.from_deprecated_string(location)
+            return Location.from_string(location)
         else:
             return location
 
diff --git a/common/lib/xmodule/xmodule/modulestore/xml_importer.py b/common/lib/xmodule/xmodule/modulestore/xml_importer.py
index 382e0cbde2..b7ed7c00a4 100644
--- a/common/lib/xmodule/xmodule/modulestore/xml_importer.py
+++ b/common/lib/xmodule/xmodule/modulestore/xml_importer.py
@@ -829,7 +829,7 @@ def _import_course_draft(
         # filtered out from the non-draft store export.
         if parent_url is not None and index is not None:
             course_key = descriptor.location.course_key
-            parent_location = course_key.make_usage_key_from_deprecated_string(parent_url)
+            parent_location = UsageKey.from_string(parent_url).map_into_course(course_key)
 
             # IMPORTANT: Be sure to update the parent in the NEW namespace
             parent_location = parent_location.map_into_course(target_id)
diff --git a/common/lib/xmodule/xmodule/tests/test_conditional.py b/common/lib/xmodule/xmodule/tests/test_conditional.py
index 73d9ddd041..5704e439bf 100644
--- a/common/lib/xmodule/xmodule/tests/test_conditional.py
+++ b/common/lib/xmodule/xmodule/tests/test_conditional.py
@@ -10,6 +10,7 @@ from xblock.fields import ScopeIds
 from xmodule.error_module import NonStaffErrorDescriptor
 from opaque_keys.edx.keys import CourseKey
 from opaque_keys.edx.locations import Location
+from opaque_keys.edx.locator import BlockUsageLocator
 from xmodule.modulestore.xml import ImportSystem, XMLModuleStore, CourseLocationManager
 from xmodule.conditional_module import ConditionalDescriptor
 from xmodule.tests import DATA_DIR, get_test_system, get_test_descriptor_system
@@ -318,9 +319,11 @@ class ConditionalModuleXmlTest(unittest.TestCase):
             dummy_field_data,
             dummy_scope_ids,
         )
+        new_run = conditional.location.course_key.run
         self.assertEqual(
             conditional.sources_list[0],
-            conditional.location.course_key.make_usage_key_from_deprecated_string(conditional.xml_attributes['sources'])
+            # Matching what is in ConditionalDescriptor.__init__.
+            BlockUsageLocator.from_string(conditional.xml_attributes['sources']).replace(run=new_run)
         )
 
     def test_conditional_module_parse_sources(self):
diff --git a/common/lib/xmodule/xmodule/x_module.py b/common/lib/xmodule/xmodule/x_module.py
index 7e707f4884..b4a6e41264 100644
--- a/common/lib/xmodule/xmodule/x_module.py
+++ b/common/lib/xmodule/xmodule/x_module.py
@@ -1632,7 +1632,8 @@ class XMLParsingSystem(DescriptorSystem):
         """
         if isinstance(value, UsageKey):
             return value
-        return course_key.make_usage_key_from_deprecated_string(value)
+        usage_key = UsageKey.from_string(value)
+        return usage_key.map_into_course(course_key)
 
     def _convert_reference_fields_to_keys(self, xblock):
         """
diff --git a/lms/djangoapps/class_dashboard/dashboard_data.py b/lms/djangoapps/class_dashboard/dashboard_data.py
index f078258664..77944a2206 100644
--- a/lms/djangoapps/class_dashboard/dashboard_data.py
+++ b/lms/djangoapps/class_dashboard/dashboard_data.py
@@ -5,6 +5,8 @@ import json
 
 from django.db.models import Count
 from django.utils.translation import ugettext as _
+
+from opaque_keys.edx.keys import UsageKey
 from opaque_keys.edx.locations import Location
 
 from courseware import models
@@ -43,7 +45,7 @@ def get_problem_grade_distribution(course_id):
 
     # Loop through resultset building data for each problem
     for row in db_query:
-        curr_problem = course_id.make_usage_key_from_deprecated_string(row['module_state_key'])
+        curr_problem = UsageKey.from_string(row['module_state_key']).map_into_course(course_id)
 
         # Build set of grade distributions for each problem that has student responses
         if curr_problem in prob_grade_distrib:
@@ -83,7 +85,7 @@ def get_sequential_open_distrib(course_id):
     # Build set of "opened" data for each subsection that has "opened" data
     sequential_open_distrib = {}
     for row in db_query:
-        row_loc = course_id.make_usage_key_from_deprecated_string(row['module_state_key'])
+        row_loc = UsageKey.from_string(row['module_state_key']).map_into_course(course_id)
         sequential_open_distrib[row_loc] = row['count_sequential']
 
     return sequential_open_distrib
@@ -120,7 +122,7 @@ def get_problem_set_grade_distrib(course_id, problem_set):
 
     # Loop through resultset building data for each problem
     for row in db_query:
-        row_loc = course_id.make_usage_key_from_deprecated_string(row['module_state_key'])
+        row_loc = UsageKey.from_string(row['module_state_key']).map_into_course(course_id)
         if row_loc not in prob_grade_distrib:
             prob_grade_distrib[row_loc] = {
                 'max_grade': 0,
@@ -433,7 +435,7 @@ def get_students_opened_subsection(request, csv=False):
     If 'csv' is True, returns a header array, and an array of arrays in the format:
     student names, usernames for CSV download.
     """
-    module_state_key = Location.from_deprecated_string(request.GET.get('module_id'))
+    module_state_key = Location.from_string(request.GET.get('module_id'))
     csv = request.GET.get('csv')
 
     # Query for "opened a subsection" students
@@ -485,7 +487,7 @@ def get_students_problem_grades(request, csv=False):
     If 'csv' is True, returns a header array, and an array of arrays in the format:
     student names, usernames, grades, percents for CSV download.
     """
-    module_state_key = Location.from_deprecated_string(request.GET.get('module_id'))
+    module_state_key = Location.from_string(request.GET.get('module_id'))
     csv = request.GET.get('csv')
 
     # Query for "problem grades" students
diff --git a/lms/djangoapps/courseware/entrance_exams.py b/lms/djangoapps/courseware/entrance_exams.py
index 00c5d70ee5..cbdd0f19bf 100644
--- a/lms/djangoapps/courseware/entrance_exams.py
+++ b/lms/djangoapps/courseware/entrance_exams.py
@@ -3,6 +3,7 @@ This file contains all entrance exam related utils/logic.
 """
 
 from courseware.access import has_access
+from opaque_keys.edx.keys import UsageKey
 from student.models import EntranceExamConfiguration
 from util.milestones_helpers import get_required_content, is_entrance_exams_enabled
 from xmodule.modulestore.django import modulestore
@@ -59,7 +60,7 @@ def get_entrance_exam_content(user, course):
 
     exam_module = None
     for content in required_content:
-        usage_key = course.id.make_usage_key_from_deprecated_string(content)
+        usage_key = UsageKey.from_string(content).map_into_course(course.id)
         module_item = modulestore().get_item(usage_key)
         if not module_item.hide_from_toc and module_item.is_entrance_exam:
             exam_module = module_item
diff --git a/lms/djangoapps/courseware/module_render.py b/lms/djangoapps/courseware/module_render.py
index 02e8e4b0af..46872723d4 100644
--- a/lms/djangoapps/courseware/module_render.py
+++ b/lms/djangoapps/courseware/module_render.py
@@ -886,7 +886,7 @@ def get_module_by_usage_id(request, course_id, usage_id, disable_staff_debug_inf
 
     try:
         course_id = CourseKey.from_string(course_id)
-        usage_key = course_id.make_usage_key_from_deprecated_string(unquote_slashes(usage_id))
+        usage_key = UsageKey.from_string(unquote_slashes(usage_id)).map_into_course(course_id)
     except InvalidKeyError:
         raise Http404("Invalid location")
 
diff --git a/lms/djangoapps/courseware/views/views.py b/lms/djangoapps/courseware/views/views.py
index 691792de19..8cfe2fd71a 100644
--- a/lms/djangoapps/courseware/views/views.py
+++ b/lms/djangoapps/courseware/views/views.py
@@ -1086,7 +1086,7 @@ def submission_history(request, course_id, student_username, location):
     course_key = CourseKey.from_string(course_id)
 
     try:
-        usage_key = course_key.make_usage_key_from_deprecated_string(location)
+        usage_key = UsageKey.from_string(location).map_into_course(course_key)
     except (InvalidKeyError, AssertionError):
         return HttpResponse(escape(_(u'Invalid location.')))
 
diff --git a/lms/djangoapps/instructor/views/api.py b/lms/djangoapps/instructor/views/api.py
index ae87e1d753..f3f4d8ea55 100644
--- a/lms/djangoapps/instructor/views/api.py
+++ b/lms/djangoapps/instructor/views/api.py
@@ -987,7 +987,7 @@ def get_problem_responses(request, course_id):
         # Are we dealing with an "old-style" problem location?
         run = problem_key.run
         if not run:
-            problem_key = course_key.make_usage_key_from_deprecated_string(problem_location)
+            problem_key = UsageKey.from_string(problem_location).map_into_course(course_key)
         if problem_key.course_key != course_key:
             raise InvalidKeyError(type(problem_key), problem_key)
     except InvalidKeyError:
@@ -1937,7 +1937,7 @@ def reset_student_attempts(request, course_id):
             return HttpResponseForbidden("Requires instructor access.")
 
     try:
-        module_state_key = course_id.make_usage_key_from_deprecated_string(problem_to_reset)
+        module_state_key = UsageKey.from_string(problem_to_reset).map_into_course(course_id)
     except InvalidKeyError:
         return HttpResponseBadRequest()
 
@@ -2025,7 +2025,7 @@ def reset_student_attempts_for_entrance_exam(request, course_id):  # pylint: dis
             return HttpResponseForbidden(_("Requires instructor access."))
 
     try:
-        entrance_exam_key = course_id.make_usage_key_from_deprecated_string(course.entrance_exam_id)
+        entrance_exam_key = UsageKey.from_string(course.entrance_exam_id).map_into_course(course_id)
         if delete_module:
             lms.djangoapps.instructor_task.api.submit_delete_entrance_exam_state_for_student(
                 request,
@@ -2083,7 +2083,7 @@ def rescore_problem(request, course_id):
         )
 
     try:
-        module_state_key = course_id.make_usage_key_from_deprecated_string(problem_to_reset)
+        module_state_key = UsageKey.from_string(problem_to_reset).map_into_course(course_id)
     except InvalidKeyError:
         return HttpResponseBadRequest("Unable to parse problem id")
 
@@ -2215,7 +2215,7 @@ def rescore_entrance_exam(request, course_id):
         )
 
     try:
-        entrance_exam_key = course_id.make_usage_key_from_deprecated_string(course.entrance_exam_id)
+        entrance_exam_key = UsageKey.from_string(course.entrance_exam_id).map_into_course(course_id)
     except InvalidKeyError:
         return HttpResponseBadRequest(_("Course has no valid entrance exam section."))
 
@@ -2300,7 +2300,7 @@ def list_instructor_tasks(request, course_id):
 
     if problem_location_str:
         try:
-            module_state_key = course_id.make_usage_key_from_deprecated_string(problem_location_str)
+            module_state_key = UsageKey.from_string(problem_location_str).map_into_course(course_id)
         except InvalidKeyError:
             return HttpResponseBadRequest()
         if student:
@@ -2338,7 +2338,7 @@ def list_entrance_exam_instructor_tasks(request, course_id):  # pylint: disable=
         student = get_student_from_identifier(student)
 
     try:
-        entrance_exam_key = course_id.make_usage_key_from_deprecated_string(course.entrance_exam_id)
+        entrance_exam_key = UsageKey.from_string(course.entrance_exam_id).map_into_course(course_id)
     except InvalidKeyError:
         return HttpResponseBadRequest(_("Course has no valid entrance exam section."))
     if student:
diff --git a/lms/djangoapps/instructor_analytics/basic.py b/lms/djangoapps/instructor_analytics/basic.py
index 3393e19530..4622b55589 100644
--- a/lms/djangoapps/instructor_analytics/basic.py
+++ b/lms/djangoapps/instructor_analytics/basic.py
@@ -414,7 +414,7 @@ def list_problem_responses(course_key, problem_location):
     # Are we dealing with an "old-style" problem location?
     run = problem_key.run
     if not run:
-        problem_key = course_key.make_usage_key_from_deprecated_string(problem_location)
+        problem_key = UsageKey.from_string(problem_location).map_into_course(course_key)
     if problem_key.course_key != course_key:
         return []
 
diff --git a/lms/djangoapps/instructor_task/tasks_helper/module_state.py b/lms/djangoapps/instructor_task/tasks_helper/module_state.py
index e27b67f777..175943c5ea 100644
--- a/lms/djangoapps/instructor_task/tasks_helper/module_state.py
+++ b/lms/djangoapps/instructor_task/tasks_helper/module_state.py
@@ -81,7 +81,7 @@ def perform_module_state_update(update_fcn, filter_fcn, _entry_id, course_id, ta
 
     # if problem_url is present make a usage key from it
     if problem_url:
-        usage_key = course_id.make_usage_key_from_deprecated_string(problem_url)
+        usage_key = UsageKey.from_string(problem_url).map_into_course(course_id)
         usage_keys.append(usage_key)
 
         # find the problem descriptor:
diff --git a/lms/djangoapps/instructor_task/tests/test_base.py b/lms/djangoapps/instructor_task/tests/test_base.py
index 3bc4a6baad..9bfce46389 100644
--- a/lms/djangoapps/instructor_task/tests/test_base.py
+++ b/lms/djangoapps/instructor_task/tests/test_base.py
@@ -207,7 +207,7 @@ class InstructorTaskModuleTestCase(InstructorTaskCourseTestCase):
         Create an internal location for a test problem.
         """
         if "i4x:" in problem_url_name:
-            return Location.from_deprecated_string(problem_url_name)
+            return Location.from_string(problem_url_name)
         elif course_key:
             return course_key.make_usage_key('problem', problem_url_name)
         else:
diff --git a/lms/lib/courseware_search/lms_result_processor.py b/lms/lib/courseware_search/lms_result_processor.py
index c1045c9de3..633528c03e 100644
--- a/lms/lib/courseware_search/lms_result_processor.py
+++ b/lms/lib/courseware_search/lms_result_processor.py
@@ -4,7 +4,7 @@ This file contains implementation override of SearchResultProcessor which will a
     * Confirms user access to object
 """
 from django.core.urlresolvers import reverse
-from opaque_keys.edx.keys import CourseKey
+from opaque_keys.edx.keys import CourseKey, UsageKey
 from search.result_processor import SearchResultProcessor
 
 from lms.djangoapps.course_blocks.api import get_course_blocks
@@ -28,7 +28,8 @@ class LmsSearchResultProcessor(SearchResultProcessor):
     def get_usage_key(self):
         """ fetch usage key for component from string representation - retain result for subsequent uses """
         if self._usage_key is None:
-            self._usage_key = self.get_course_key().make_usage_key_from_deprecated_string(self._results_fields["id"])
+            usage_key = UsageKey.from_string(self._results_fields["id"])
+            self._usage_key = usage_key.map_into_course(self.get_course_key())
         return self._usage_key
 
     def get_module_store(self):