CDK5RAP1 (Q96SZ6) curation notes

Reviewed together with its paralog CDKAL1 (Q5VV42) as the two human radical SAM
methylthiotransferases (MTTases), within the RADICAL_SAM project.

Sources consulted

The Asta deep-research file (CDK5RAP1-deep-research-asta.md) is a raw retrieval and none of the
20 papers concerns CDK5RAP1. It was not used for any claim. Falcon failed (auth 403) and was not
re-run.
Full text in cache: PMID:22422838 (Reiter 2012), PMID:28981754 (Fakruddin 2017), PMID:34800366
(MitoCoP). Abstract only: PMID:25738458 (Wei 2015 Cell Metab), PMID:10721722, PMID:10915792,
PMID:11882646, PMID:17491008.

PMID:22422838 (MTS-less variant
expressed in a miaB-deficient E. coli strain.)
Substrate specificity: PMID:22422838. CDKAL1 is the t6A
enzyme, so the two paralogs have non-overlapping substrates.
Knockdown: PMID:22422838
In vivo targets: PMID:25738458
UniProt: EC 2.8.4.3, RHEA:37067; two [4Fe-4S] clusters; MiaB subfamily.

Mitochondrial targeting sequence (TRANSIT 1-33) on the main isoform; PMID:22422838
The variant without the MTS (v2) was found in cytoplasm and nucleus when overexpressed, and
antibody ICC suggested a nuclear preference: PMID:22422838
Reiter et al. proposed ms2i6A in nuclear RNA (polyA RNA, miRNA). This was refuted by
PMID:28981754 (rho0 cells have no ms2i6A; the
ms2i6A antibody signal co-localizes with mitochondria). Also PMID:28981754, so the extra-mitochondrial variant is probably
inactive.
UniProt CAUTION records this conflict.
Mitochondrial proteome (MitoCoP, PMID:34800366) and HPA immunofluorescence corroborate
mitochondrion.

PMID:25738458 Myopathy and cardiac
dysfunction under stress; ms2 levels lower in patients with mitochondrial disease.

Named C42 in a yeast two-hybrid screen for p35 (CDK5R1) binders (PMID:10721722). GST pull-down
co-precipitated p35 complexed with Cdk5.
PMID:11882646: C42 "specifically inhibits the activation of Cdk5 by Nck5a"; co-IP with p35 in
cultured cells; the inhibitory region is conserved with yeast Pho81. Abstract-only. The
experiment is in vitro or uses overexpression. The mature enzyme is in the mitochondrial matrix
and p35 is cytosolic or membrane-associated, so physiological relevance is doubtful. These rows
are not removed (experimental; full text not read) and are kept as non-core.
CDKAL1, the paralog, neither binds p35 nor inhibits CDK5 [PMID:21841312, see CDKAL1 notes].
NAS rows for brain development (PMID:10915792) and regulation of neuron differentiation
(PMID:10721722) extrapolate CDK5 biology to a binding partner; neither abstract tests CDK5RAP1 in
any neuronal process. They are removed.
TAS negative regulation of cell cycle (PMID:17491008): the abstract is about p35 binding
microtubules and does not mention CDK5RAP1/C42. The full text is not in the cache, so this is
UNDECIDED.

Generic radical SAM rows: GO:0003824 and GO:0051536 MODIFY; GO:0051539 ACCEPT (RADICAL_SAM
treatment table). GO:0016740 and GO:0035596 MODIFY to GO:0035597; GO:0006400 and GO:0009451 MODIFY
to GO:0035600 + GO:0070900.
Cytosol (IBA, IDA) and nucleoplasm (IDA): MARK_AS_OVER_ANNOTATED. The observations come from an
MTS-less variant whose activity outside mitochondria was refuted. The cytosol IBA comes from the
bacterial MiaB node and does not fit the mitochondrially targeted vertebrate clade.
GO:0051246 regulation of protein metabolic process (ARBA): MARK_AS_OVER_ANNOTATED. CDK5RAP1
contributes to mitochondrial translation through tRNA modification and does not regulate
protein metabolism as such.
Not added: mitochondrial translation (GO:0032543). CDK5RAP1 modifies the tRNA rather than
performing translation (participation test), and the mitochondrial tRNA modification term already
covers it. SAM binding (GO:1904047) added as a NEW ISS row from MiaB in vitro reconstitution (PMID:15339930) plus the UniProt PRU00780 exchangeable-SAM note, for consistency with LIAS and ELP3.