Reviewed, UniProtKB/Swiss-Prot Q9QX73 (ARHG9_RAT)

Names and origin

Protein names

Recommended name:
    Rho guanine nucleotide exchange factor 9
Alternative name(s):
    Rac/Cdc42 guanine nucleotide exchange factor 9
    Collybistin

Gene names

Name:

Arhgef9

Organism

Rattus norvegicus (Rat)

Taxonomic identifier

10116 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length	493 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Acts as guanine nucleotide exchange factor (GEF) for CDC42. Promotes formation of GPHN clusters. Ref.1 Ref.2 Ref.3
Subunit structure	Interacts with GPHN. Ref.1 Ref.2 Ref.3
Subcellular location	Cytoplasm. Ref.1 Ref.2 Ref.3
Tissue specificity	Detected in brain, throughout the gray matter. Detected at low levels in heart and skeletal muscle. Ref.1
Sequence similarities	Contains 1 DH (DBL-homology) domain. Contains 1 PH domain. Contains 1 SH3 domain.

Ontologies

Keywords
Cellular component	Cytoplasm
Coding sequence diversity	Alternative splicing
Domain	SH3 domain
Molecular function	Guanine-nucleotide releasing factor
Technical term	3D-structure
Gene Ontology (GO)
Biological process	postsynaptic membrane organization Ref.1 Inferred from mutant phenotype. Source: RGD regulation of Rho protein signal transduction Inferred from electronic annotation. Source: InterPro small GTPase mediated signal transduction Ref.1 Inferred from physical interaction. Source: RGD
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	Rho guanyl-nucleotide exchange factor activity Inferred from electronic annotation. Source: InterPro protein binding Ref.1 Inferred from mutant phenotype. Source: RGD
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Note: Additional isoforms seem to exist.

Isoform 1 (identifier: Q9QX73-1)

Also known as: Collybistin I;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q9QX73-2)

Also known as: Collybistin II;

The sequence of this isoform differs from the canonical sequence as follows:
     12-71: Missing.
     464-493: GRVGEEENQSLELKRACEVLQRLWSPGKKS → VTQRKWHY

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 493

493

Rho guanine nucleotide exchange factor 9

PRO_0000253898

Regions

Domain

15 – 74

60

SH3

Domain

110 – 294

185

DH

Domain

325 – 432

108

PH

Region

107 – 117

11

Interaction with GPHN

Natural variations

Alternative sequence

12 – 71

60

Missing in isoform 2.

VSP_021147

Alternative sequence

464 – 493

30

GRVGE…PGKKS → VTQRKWHY in isoform 2.

VSP_021148

Experimental info

Mutagenesis

107

1

R → A: No effect on formation of GPHN clusters; when associated with A-108 and A-117. Ref.2 Ref.4

Mutagenesis

108

1

D → A: No effect on GPHN clusters; when associated with A-107 and A-117. Ref.2 Ref.4

Mutagenesis

111

1

R → A: Loss of formation of GPHN clusters. Ref.2 Ref.4

Mutagenesis

117

1

E → A: No effect on GPHN clusters; when associated with A-107 and A-108. Ref.2 Ref.4

Secondary structure

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493

Helix Strand Turn

Details...

Helix

107 – 135

29

Helix

137 – 142

6

Turn

144 – 146

3

Helix

149 – 156

8

Helix

159 – 176

18

Helix

182 – 184

3

Helix

188 – 193

6

Turn

194 – 196

3

Helix

197 – 199

3

Helix

200 – 218

19

Helix

222 – 234

13

Helix

242 – 246

5

Helix

248 – 265

18

Helix

274 – 299

26

Helix

301 – 310

10

Helix

319 – 321

3

Beta strand

326 – 337

12

Beta strand

343 – 350

8

Beta strand

353 – 359

7

Beta strand

367 – 374

8

Helix

375 – 377

3

Beta strand

378 – 382

5

Beta strand

385 – 387

3

Beta strand

389 – 391

3

Beta strand

394 – 407

14

Beta strand

409 – 413

5

Helix

417 – 440

24

Helix

446 – 458

13

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 (Collybistin I) [UniParc]. Last modified May 1, 2000. Version 1. Checksum: 41040671B9398BFA	FASTA	493	58,157
	10 20 30 40 50 60 MQWIRGGSGM LITGDSIVSA EAVWDHVTMA NRGVAFKAGD VIKVLDASNK DWWWGQIDDE 70 80 90 100 110 120 EGWFPASFVR LWVNQEDGVE EGPSDVQNGH LDPNSDCLCL GRPLQNRDQM RANVINEIMS 130 140 150 160 170 180 TERHYIKHLK DICEGYLKQC RKRRDMFSDE QLKVIFGNIE DIYRFQMGFV RDLEKQYNND 190 200 210 220 230 240 DPHLSEIGPC FLEHQDGFWI YSEYCNNHLD ACMELSKLMK DSRYQHFFEA CRLLQQMIDI 250 260 270 280 290 300 AIDGFLLTPV QKICKYPLQL AELLKYTAQD HSDYRYVAAA LAVMRNVTQQ INERKRRLEN 310 320 330 340 350 360 IDKIAQWQAS VLDWEGDDIL DRSSELIYTG EMAWIYQPYG RNQQRVFFLF DHQMVLCKKD 370 380 390 400 410 420 LIRRDILYYK GRIDMDKYEV IDIEDGRDDD FNVSMKNAFK LHNKETEEVH LFFAKKLEEK 430 440 450 460 470 480 IRWLRAFREE RKMVQEDEKI GFEISENQKR QAAMTVRKAS KQKGRVGEEE NQSLELKRAC 490 EVLQRLWSPG KKS
	Isoform 2 (Collybistin II). Checksum: 4AFFE36CFEE5A820	FASTA	411	49,156
	10 20 30 40 50 60 MQWIRGGSGM LWVNQEDGVE EGPSDVQNGH LDPNSDCLCL GRPLQNRDQM RANVINEIMS 70 80 90 100 110 120 TERHYIKHLK DICEGYLKQC RKRRDMFSDE QLKVIFGNIE DIYRFQMGFV RDLEKQYNND 130 140 150 160 170 180 DPHLSEIGPC FLEHQDGFWI YSEYCNNHLD ACMELSKLMK DSRYQHFFEA CRLLQQMIDI 190 200 210 220 230 240 AIDGFLLTPV QKICKYPLQL AELLKYTAQD HSDYRYVAAA LAVMRNVTQQ INERKRRLEN 250 260 270 280 290 300 IDKIAQWQAS VLDWEGDDIL DRSSELIYTG EMAWIYQPYG RNQQRVFFLF DHQMVLCKKD 310 320 330 340 350 360 LIRRDILYYK GRIDMDKYEV IDIEDGRDDD FNVSMKNAFK LHNKETEEVH LFFAKKLEEK 370 380 390 400 410 IRWLRAFREE RKMVQEDEKI GFEISENQKR QAAMTVRKAS KQKVTQRKWH Y

References

[1]	"Collybistin, a newly identified brain-specific GEF, induces submembrane clustering of gephyrin." Kins S., Betz H., Kirsch J. Nat. Neurosci. 3:22-29(2000) [PubMed: 10607391] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), FUNCTION, INTERACTION WITH GPHN, SUBCELLULAR LOCATION, TISSUE SPECIFICITY. Tissue: Brain.
[2]	"Identification of a gephyrin-binding motif in the GDP/GTP exchange factor collybistin." Grosskreutz Y., Hermann A., Kins S., Fuhrmann J.C., Betz H., Kneussel M. Biol. Chem. 382:1455-1462(2001) [PubMed: 11727829] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH GPHN, MUTAGENESIS OF ARG-107; ASP-108; ARG-111 AND GLU-117.
[3]	"The GDP-GTP exchange factor collybistin: an essential determinant of neuronal gephyrin clustering." Harvey K., Duguid I.C., Alldred M.J., Beatty S.E., Ward H., Keep N.H., Lingenfelter S.E., Pearce B.R., Lundgren J., Owen M.J., Smart T.G., Luescher B., Rees M.I., Harvey R.J. J. Neurosci. 24:5816-5826(2004) [PubMed: 15215304] [Abstract] Cited for: ALTERNATIVE SPLICING, FUNCTION, INTERACTION WITH GPHN, SUBCELLULAR LOCATION.
[4]	"The crystal structure of Cdc42 in complex with collybistin II, a gephyrin-interacting guanine nucleotide exchange factor." Xiang S., Kim E.Y., Connelly J.J., Nassar N., Kirsch J., Winking J., Schwarz G., Schindelin H. J. Mol. Biol. 359:35-46(2006) [PubMed: 16616186] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 10-411 IN COMPLEX WITH CDC42, MUTAGENESIS OF ARG-107; ASP-108; ARG-111 AND GLU-117.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AJ250425 mRNA. Translation: CAB65966.1.
AJ302676 mRNA. Translation: CAC16410.1.

IPI

IPI00212702.
IPI00562212.

RefSeq

NP_076447.1.

UniGene

Rn.163449

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2DFK	X-ray	2.15	A/C	71-463	[»]

ModBase

Search...

Genome annotation databases

Ensembl

ENSRNOG00000007733. Rattus norvegicus. [Contig view]

GeneID

66013.

KEGG

rno:66013.

Organism-specific databases

RGD

620719. Arhgef9.

Phylogenomic databases

HOVERGEN

Q9QX73.

Gene expression databases

ArrayExpress

Q9QX73.

GermOnline

ENSRNOG00000007733. Rattus norvegicus.

Family and domain databases

InterPro

IPR000219. DH-domain.
IPR001331. GDS_CDC24_CS.
IPR001849. Pleckstrin_homology.
IPR011511. SH3_2.
IPR001452. SH3_domain.
[Graphical view]

Gene3D

G3DSA:1.20.900.10. RhoGEF. 1 hit.

Pfam

PF00169. PH. 1 hit.
PF00621. RhoGEF. 1 hit.
PF07653. SH3_2. 1 hit.
[Graphical view]

ProDom

PD000066. SH3. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00233. PH. 1 hit.
SM00325. RhoGEF. 1 hit.
SM00326. SH3. 1 hit.
[Graphical view]

PROSITE

PS00741. DH_1. False negative.
PS50010. DH_2. 1 hit.
PS50003. PH_DOMAIN. 1 hit.
PS50002. SH3. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

614272.

Entry information

Entry name

ARHG9_RAT

Accession

Primary (citable) accession number: Q9QX73
Secondary accession number(s): Q9ER22

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 17, 2006
Last sequence update:	May 1, 2000
Last modified:	June 16, 2009
This is version 54 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)