AiPD: Autoinhibited Protein Database

Q04982

Gene name	BRAF (RMIL)
Protein name	Serine/threonine-protein kinase B-raf
Names	EC 2.7.11.1 , Proto-oncogene B-Raf , Proto-oncogene c-Rmil , Serine/threonine-protein kinase Rmil
Species	Gallus gallus (Chicken)
KEGG Pathway	gga:396239
EC number	2.7.11.1: Protein-serine/threonine kinases
Protein Class

Descriptions

Raf proteins are Ras-regulated serine/threonine protein kinases that control the activation of the ERK/MARK cascade, and consists of three isoforms, A-Raf, B-Raf, and Raf-1 (C-Raf), which exhibit a high degree of homology within three conserved regions (CR) known as CR1, CR2, and CR3. In Raf’s autoinhibited conformation, the N-terminal tail, Ras binding domain (RBD), cysteine-rich domain (CRD), and linker together with its Ser/Thr-rich segment prevent kinase domain dimerization. The RBD-CRD region is CR1 and the Ser/Thr-rich region is CR2. In active membrane-anchored Raf, RBD interacts with Ras, and CRD binds to the membrane. Two events are expected to regulate the release of B-Raf autoinhibition: dephosphorylation of pSer365 and release of RBD-CRD from the kinase domain. Full Raf activation requires KD dimerization. Ras recruits Raf to the membrane, gathering Raf proteins through dimers or nanoclusters. The high affinity of Ras-Raf-RBD interaction, coupled with pSer365 dephosphorylation, disrupts the autoinhibited B-Raf states, thereby promoting full activation of Raf.

Autoinhibitory domains (AIDs)

157-377 (N-terminal region, CR1 and CR2) SS

Target domain	457-717 (Protein kinase domain)
Relief mechanism	Partner binding, PTM
Assay

AID

157-377 (N-terminal region, CR1 and CR2)

Target domain

457-717 (Protein kinase domain)

Relief mechanism

Partner binding (Ras binding to Raf-RBD), PTM (Dephosphorylation at Ser-365)

Assay

Accessory elements

593-618 (Activation loop from InterPro)

Target domain	458-712 (Serine-threonine/tyrosine-protein kinase, catalytic domain)
Relief mechanism
Assay

References

Tran NH et al. (2005) "B-Raf and Raf-1 are regulated by distinct autoregulatory mechanisms", The Journal of biological chemistry, 280, 16244-53

Zhang M et al. (2021) "B-Raf autoinhibition in the presence and absence of 14-3-3", Structure (London, England : 1993), 29, 768-777.e2

Nussinov R et al. (2018) "Autoinhibition in Ras effectors Raf, PI3Kα, and RASSF5: a comprehensive review underscoring the challenges in pharmacological intervention", Biophysical reviews, 10, 1263-1282

Hmitou I et al. (2007) "Differential regulation of B-raf isoforms by phosphorylation and autoinhibitory mechanisms", Molecular and cellular biology, 27, 31-43

Hubbard SR (2004) "Oncogenic mutations in B-Raf: some losses yield gains", Cell, 116, 764-6

Park E et al. (2019) "Architecture of autoinhibited and active BRAF-MEK1-14-3-3 complexes", Nature, 575, 545-550

Cutler RE Jr et al. (1998) "Autoregulation of the Raf-1 serine/threonine kinase", Proceedings of the National Academy of Sciences of the United States of America, 95, 9214-9

Tran NH et al. (2003) "Phosphorylation of Raf-1 by p21-activated kinase 1 and Src regulates Raf-1 autoinhibition", The Journal of biological chemistry, 278, 11221-6

Niault T et al. (2009) "From autoinhibition to inhibition in trans: the Raf-1 regulatory domain inhibits Rok-alpha kinase activity", The Journal of cell biology, 187, 335-42

Cookis T et al. (2021) "Crystal Structure Reveals the Full Ras-Raf Interface and Advances Mechanistic Understanding of Raf Activation", Biomolecules, 11,

Autoinhibited structure

Activated structure

1 structures for Q04982

Entry ID	Method	Resolution	Chain	Position	Source
AF-Q04982-F1	Predicted				AlphaFoldDB

No variants for Q04982

Variant ID(s)	Position	Change	Description	Diseaes Association	Provenance
No variants for Q04982

No associated diseases with Q04982

9 regional properties for Q04982

Type	Name	Position	InterPro Accession
domain	Protein kinase domain	457 - 717	IPR000719
domain	Serine-threonine/tyrosine-protein kinase, catalytic domain	457 - 712	IPR001245
domain	Protein kinase C-like, phorbol ester/diacylglycerol-binding domain	234 - 281	IPR002219
domain	Raf-like Ras-binding	155 - 227	IPR003116
active_site	Serine/threonine-protein kinase, active site	572 - 584	IPR008271
binding_site	Protein kinase, ATP binding site	463 - 483	IPR017441
domain	Diacylglycerol/phorbol-ester binding	232 - 246	IPR020454-1
domain	Diacylglycerol/phorbol-ester binding	248 - 268	IPR020454-2
domain	Diacylglycerol/phorbol-ester binding	269 - 281	IPR020454-3

Functions

		Description
EC Number	2.7.11.1	Protein-serine/threonine kinases
Subcellular Localization	Nucleus Cytoplasm Cell membrane
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category	No pathway information available

4 GO annotations of cellular component

Name	Definition
cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

4 GO annotations of molecular function

Name	Definition
ATP binding	Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
MAP kinase kinase kinase activity	Catalysis of the phosphorylation and activation of a MAP kinase kinase; each MAP kinase kinase can be phosphorylated by any of several MAP kinase kinase kinases.
metal ion binding	Binding to a metal ion.
protein serine kinase activity	Catalysis of the reactions

3 GO annotations of biological process

Name	Definition
MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain an additional tiers
phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
Ras protein signal transduction	The series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.

15 homologous proteins in AiPD

UniProt AC	Gene Name	Protein Name	Species	Evidence Code
A7E3S4	RAF1	RAF proto-oncogene serine/threonine-protein kinase	Bos taurus (Bovine)	SS
P05625	RAF1	RAF proto-oncogene serine/threonine-protein kinase	Gallus gallus (Chicken)	PR
P11346	Raf	Raf homolog serine/threonine-protein kinase Raf	Drosophila melanogaster (Fruit fly)	PR
P04049	RAF1	RAF proto-oncogene serine/threonine-protein kinase	Homo sapiens (Human)	EV
P10398	ARAF	Serine/threonine-protein kinase A-Raf	Homo sapiens (Human)	PR
P15056	BRAF	Serine/threonine-protein kinase B-raf	Homo sapiens (Human)	EV
Q99N57	Raf1	RAF proto-oncogene serine/threonine-protein kinase	Mus musculus (Mouse)	SS
P04627	Araf	Serine/threonine-protein kinase A-Raf	Mus musculus (Mouse)	PR
P28028	Braf	Serine/threonine-protein kinase B-raf	Mus musculus (Mouse)	SS
O19004	ARAF	Serine/threonine-protein kinase A-Raf	Sus scrofa (Pig)	PR
P11345	Raf1	RAF proto-oncogene serine/threonine-protein kinase	Rattus norvegicus (Rat)	SS
P14056	Araf	Serine/threonine-protein kinase A-Raf	Rattus norvegicus (Rat)	PR
Q07292	lin-45	Raf homolog serine/threonine-protein kinase	Caenorhabditis elegans	PR
Q05609	CTR1	Serine/threonine-protein kinase CTR1	Arabidopsis thaliana (Mouse-ear cress)	PR
Q9FPR3	EDR1	Serine/threonine-protein kinase EDR1	Arabidopsis thaliana (Mouse-ear cress)	PR

10	20	30	40	50	60
MAALSSGSSA	EGASLFNGDM	EPEPPPPVLG	ACYAGSGGGD	PAIPEEVWNI	KQMIKLTQEH
70	80	90	100	110	120
IEALLDKFGG	EHNPPSIYLE	AYEEYTSKLD	ALQQREQQLL	ESMGNGTDFS	VSSSASTDTV
130	140	150	160	170	180
ASSSSSSLSV	APSSLSVYQN	PTDMSRNNPK	SPQKPIVRVF	LPNKQRTVVP	ARCGVTVRDS
190	200	210	220	230	240
LKKALMMRGL	IPECCAVYRI	QDGEKKPIGW	DTDISWLTGE	ELHVEVLENV	PLTTHNFVRK
250	260	270	280	290	300
TFFTLAFCDF	CRKLLFQGFR	CQTCGYKFHQ	RCSTEVPLMC	VNYDQLDLLF	VSKFFEHHPI
310	320	330	340	350	360
SQEETTLGET	TPASGSYPSV	PPSDSVGPPI	LPSPSPSKSI	PIPQPFRPAD	EDHRNQFGQR
370	380	390	400	410	420
DRSSSAPNVH	INTIEPVNID	DLIRDQGVRG	EGGSTAGLSA	TPPASLPGSL	TNVKALQKSP
430	440	450	460	470	480
GPQRERKSSS	SSEDRNRMKT	LGRRDSSDDW	EIPDGQITVG	QRIGSGSFGT	VYKGKWHGDV
490	500	510	520	530	540
AVKMLNVTAP	TPQQLQAFKN	EVGVLRKTRH	VNILLFMGYS	TKPQLAIVTQ	WCEGSSLYHH
550	560	570	580	590	600
LHIIETKFEM	IKLIDIARQT	AQGMDYLHAK	SIIHRDLKSN	NIFLHEDLTV	KIGDFGLATV
610	620	630	640	650	660
KSRWSGSHQF	EQLSGSILWM	APEVIRMQDK	NPYSFQSDVY	AFGIVLYELM	TGQLPYSNIN
670	680	690	700	710	720
NRDQIIFMVG	RGYLSPDLSK	VRSNCPKAMK	RLMAECLKKK	RDERPLFPQI	LASIELLARS
730	740	750	760
LPKIHRSASE	PSLNRAGFQT	EDFSLYACAS	PKTPIQAGGY	GGFPVH