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Q03555

- GEPH_RAT

UniProt

Q03555 - GEPH_RAT

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Protein

Gephyrin

Gene
Gphn, Gph
Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Microtubule-associated protein involved in membrane protein-cytoskeleton interactions. It is thought to anchor the inhibitory glycine receptor (GLYR) to subsynaptic microtubules By similarity. Catalyzes two steps in the biosynthesis of the molybdenum cofactor. In the first step, molybdopterin is adenylated. Subsequently, molybdate is inserted into adenylated molybdopterin and AMP is released.2 Publications

Catalytic activityi

ATP + molybdopterin = diphosphate + adenylyl-molybdopterin.
Adenylyl-molybdopterin + molybdate = molybdenum cofactor + AMP.

Cofactori

Magnesium.

Enzyme regulationi

Inhibited by copper and tungsten By similarity.

Pathwayi

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. metal ion binding Source: UniProtKB-KW
  3. molybdopterin adenylyltransferase activity Source: MGI
  4. molybdopterin molybdotransferase activity Source: MGI
  5. protein binding Source: UniProtKB
  6. protein binding, bridging Source: RGD
  7. protein complex scaffold Source: RGD
  8. protein homodimerization activity Source: RGD
  9. receptor binding Source: RGD
  10. tubulin binding Source: RGD

GO - Biological processi

  1. establishment of protein localization Source: BHF-UCL
  2. Mo-molybdopterin cofactor biosynthetic process Source: MGI
  3. protein homooligomerization Source: RGD
  4. protein targeting Source: RGD
  5. synapse assembly Source: RGD
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Molybdenum cofactor biosynthesis

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Molybdenum, Nucleotide-binding

Enzyme and pathway databases

UniPathwayiUPA00344.

Names & Taxonomyi

Protein namesi
Recommended name:
Gephyrin
Alternative name(s):
Putative glycine receptor-tubulin linker protein
Including the following 2 domains:
Molybdopterin adenylyltransferase (EC:2.7.7.75)
Short name:
MPT adenylyltransferase
Alternative name(s):
Domain G
Molybdopterin molybdenumtransferase (EC:2.10.1.1)
Short name:
MPT Mo-transferase
Alternative name(s):
Domain E
Gene namesi
Name:Gphn
Synonyms:Gph
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494: Unplaced

Organism-specific databases

RGDi69194. Gphn.

Subcellular locationi

Cell junctionsynapse. Cell junctionsynapsepostsynaptic cell membrane; Peripheral membrane protein; Cytoplasmic side. Cytoplasmcytoskeleton
Note: Cytoplasmic face of glycinergic postsynaptic membranes.1 Publication

GO - Cellular componenti

  1. cell junction Source: UniProtKB-KW
  2. cytoplasm Source: RGD
  3. cytoskeleton Source: UniProtKB-SubCell
  4. inhibitory synapse Source: BHF-UCL
  5. postsynaptic membrane Source: UniProtKB-SubCell
  6. synapse Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cell membrane, Cytoplasm, Cytoskeleton, Membrane, Postsynaptic cell membrane, Synapse

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi362 – 3621F → A: Reduced GLRB binding. 1 Publication
Mutagenesisi745 – 7462PP → AA: Reduced GLRB binding. 1 Publication
Mutagenesisi745 – 7451P → A: Loss of GLRB binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 768768GephyrinPRO_0000170965Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei201 – 2011Phosphoserine By similarity
Modified residuei207 – 2071Phosphoserine By similarity
Modified residuei279 – 2791Phosphothreonine By similarity
Modified residuei337 – 3371Phosphoserine By similarity

Post-translational modificationi

Phosphorylated.

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ03555.
PRIDEiQ03555.

PTM databases

PhosphoSiteiQ03555.

Expressioni

Tissue specificityi

Expressed in tissues including spinal cord, brain, liver, kidney and lung.

Gene expression databases

GenevestigatoriQ03555.

Interactioni

Subunit structurei

Homotrimer, homodimer and homooligomer. Interacts with SRGAP2 (via SH3 domain) By similarity. Interacts with GLRB and GABARAP.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Gabra3P202365EBI-5273276,EBI-5273284
GlrbP481684EBI-349317,EBI-7069198From a different organism.

Protein-protein interaction databases

BioGridi249211. 8 interactions.
DIPiDIP-33263N.
IntActiQ03555. 5 interactions.
MINTiMINT-241818.

Structurei

Secondary structure

1
768
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi16 – 227
Helixi24 – 274
Helixi34 – 4411
Turni46 – 494
Beta strandi52 – 598
Helixi63 – 7513
Beta strandi80 – 867
Beta strandi89 – 913
Helixi112 – 1165
Beta strandi118 – 1203
Helixi122 – 13514
Helixi137 – 1415
Beta strandi146 – 1494
Beta strandi152 – 1576
Helixi161 – 17111
Helixi172 – 1743
Helixi175 – 1828
Helixi188 – 1936
Beta strandi355 – 3573
Helixi358 – 36811
Beta strandi374 – 3785
Helixi379 – 3813
Beta strandi386 – 3894
Beta strandi397 – 4004
Beta strandi402 – 4109
Helixi412 – 4143
Beta strandi418 – 4247
Beta strandi439 – 4435
Beta strandi455 – 4584
Helixi459 – 4613
Beta strandi462 – 4687
Beta strandi469 – 4724
Beta strandi474 – 4796
Turni485 – 4884
Beta strandi494 – 4963
Beta strandi501 – 5033
Helixi511 – 52010
Beta strandi524 – 5285
Beta strandi533 – 5386
Helixi558 – 56710
Turni568 – 5703
Beta strandi573 – 5797
Helixi583 – 59614
Beta strandi598 – 6047
Beta strandi607 – 6093
Helixi612 – 6198
Turni620 – 6223
Beta strandi625 – 6328
Beta strandi640 – 6467
Beta strandi649 – 6568
Helixi660 – 67819
Beta strandi688 – 6958
Beta strandi704 – 7118
Beta strandi716 – 7183
Beta strandi720 – 7234
Beta strandi728 – 7303
Beta strandi740 – 7445
Beta strandi752 – 7543
Beta strandi759 – 7646

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IHCX-ray1.90A1-201[»]
1T3EX-ray3.25A/B348-768[»]
2FTSX-ray2.41A350-768[»]
2FU3X-ray2.70A/B350-768[»]
ProteinModelPortaliQ03555.
SMRiQ03555. Positions 13-194, 350-768.

Miscellaneous databases

EvolutionaryTraceiQ03555.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 166153MPT Mo-transferaseAdd
BLAST
Regioni153 – 348196Interaction with GABARAPAdd
BLAST
Regioni326 – 768443MPT adenylyltransferaseAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi213 – 2186Glu-rich (acidic)

Sequence similaritiesi

In the N-terminal section; belongs to the MoaB/Mog family.
In the C-terminal section; belongs to the MoeA family.

Phylogenomic databases

eggNOGiCOG0303.
HOGENOMiHOG000280651.
HOVERGENiHBG005828.
InParanoidiQ03555.
KOiK15376.
PhylomeDBiQ03555.

Family and domain databases

Gene3Di2.40.340.10. 1 hit.
3.40.980.10. 2 hits.
InterProiIPR020817. Mo_cofactor_synthesis.
IPR008284. MoCF_biosynth_CS.
IPR005111. MoeA_C_domain_IV.
IPR005110. MoeA_linker/N.
IPR001453. Mopterin-bd_dom.
[Graphical view]
PfamiPF00994. MoCF_biosynth. 2 hits.
PF03454. MoeA_C. 1 hit.
PF03453. MoeA_N. 1 hit.
[Graphical view]
SMARTiSM00852. MoCF_biosynth. 2 hits.
[Graphical view]
SUPFAMiSSF53218. SSF53218. 2 hits.
SSF63867. SSF63867. 1 hit.
SSF63882. SSF63882. 1 hit.
TIGRFAMsiTIGR00177. molyb_syn. 2 hits.
PROSITEiPS01078. MOCF_BIOSYNTHESIS_1. 1 hit.
PS01079. MOCF_BIOSYNTHESIS_2. 1 hit.
[Graphical view]

Sequences (6)i

Sequence statusi: Complete.

This entry describes 6 isoformsi produced by alternative splicing. Align

Note: Additional isoforms seem to exist.

Isoform 6 (identifier: Q03555-1) [UniParc]FASTAAdd to Basket

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.

« Hide

MATEGMILTN HDHQIRVGVL TVSDSCFRNL AEDRSGINLK DLVQDPSLLG    50
GTISAYKIVP DEIEEIKETL IDWCDEKELN LILTTGGTGF APRDVTPEKF 100
PTFPFCGLQK GATKEVIERE APGMALAMLM GSLNVTPLGM LSRPVCGIRG 150
KTLIINLPGS KKGSQECFQF ILPALPHAID LLRDAIVKVK EVHDELEDLP 200
SPPPPLSPPP TTSPHKQTED KGVQCEEEEE EKKDSGVAST EDSSSSHITA 250
AALAAKIPDS IISRGVQVLP RDTASLSTTP SESPRAQATS RLSTASCPTP 300
KQIRRPDESK GVASRVGSLK VQSRCSSKEN ILRASHSAVD ITKVARRHRM 350
SPFPLTSMDK AFITVLEMTP VLGTEIINYR DGMGRVLAQD VYAKDNLPPF 400
PASVKDGYAV RAADGPGDRF IIGESQAGEQ PTQTVMPGQV MRVTTGAPIP 450
CGADAVVQVE DTELIRESDD GTEELEVRIL VQARPGQDIR PIGHDIKRGE 500
CVLAKGTHMG PSEIGLLATV GVTEVEVNKF PVVAVMSTGN ELLNPEDDLL 550
PGKIRDSNRS TLLATIQEHG YPTINLGIVG DNPDDLLNAL NEGISRADVI 600
ITSGGVSMGE KDYLKQVLDI DLHAQIHFGR VFMKPGLPTT FATLDIDGVR 650
KIIFALPGNP VSAVVTCNLF VVPALRKMQG ILDPRPTIIK ARLSCDVKLD 700
PRPEYHRCIL TWHHQEPLPW AQSTGNQMSS RLMSMRSANG LLMLPPKTEQ 750
YVELHKGEVV DVMVIGRL 768
Length:768
Mass (Da):83,266
Last modified:May 16, 2006 - v3
Checksum:iFAD1B6DD76ED79EA
GO
Isoform 1 (identifier: Q03555-2) [UniParc]FASTAAdd to Basket

Also known as: GE124'56

The sequence of this isoform differs from the canonical sequence as follows:
     1-22: MATEGMILTNHDHQIRVGVLTV → MSFPLSPAFTLLHILV

Show »
Length:762
Mass (Da):82,616
Checksum:iCF467AB5D3BE99BE
GO
Isoform 2 (identifier: Q03555-3) [UniParc]FASTAAdd to Basket

Also known as: GE236

The sequence of this isoform differs from the canonical sequence as follows:
     99-111: Missing.
     256-256: K → KNHPFYTSPAVFMANHGQPIPGLISYSHHATGSADKR
     302-320: Missing.

Show »
Length:772
Mass (Da):83,638
Checksum:iD25D2294184BE3D4
GO
Isoform 3 (identifier: Q03555-4) [UniParc]FASTAAdd to Basket

Also known as: GE24'6

The sequence of this isoform differs from the canonical sequence as follows:
     99-111: Missing.

Show »
Length:755
Mass (Da):81,814
Checksum:i219EC28CC2910AC1
GO
Isoform 4 (identifier: Q03555-5) [UniParc]FASTAAdd to Basket

Also known as: GE245

The sequence of this isoform differs from the canonical sequence as follows:
     302-315: QIRRPDESKGVASR → ARLPSCSSTYSVSE
     316-320: Missing.

Show »
Length:763
Mass (Da):82,669
Checksum:i5E6039E40BDA68ED
GO
Isoform 5 (identifier: Q03555-6) [UniParc]FASTAAdd to Basket

Also known as: GE26

The sequence of this isoform differs from the canonical sequence as follows:
     99-111: Missing.
     302-320: Missing.

Show »
Length:736
Mass (Da):79,748
Checksum:iB3817E1BE1D4D41B
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 2222MATEG…GVLTV → MSFPLSPAFTLLHILV in isoform 1. VSP_003238Add
BLAST
Alternative sequencei99 – 11113Missing in isoform 5, isoform 2 and isoform 3. VSP_003239Add
BLAST
Alternative sequencei256 – 2561K → KNHPFYTSPAVFMANHGQPI PGLISYSHHATGSADKR in isoform 2. VSP_003240
Alternative sequencei302 – 32019Missing in isoform 5 and isoform 2. VSP_003243Add
BLAST
Alternative sequencei302 – 31514QIRRP…GVASR → ARLPSCSSTYSVSE in isoform 4. VSP_003241Add
BLAST
Alternative sequencei316 – 3205Missing in isoform 4. VSP_003242

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti255 – 2551A → R1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X66366 mRNA. Translation: CAA47009.2.
PIRiJH0681.
RefSeqiNP_074056.2. NM_022865.3. [Q03555-6]
UniGeneiRn.11032.

Genome annotation databases

GeneIDi64845.
KEGGirno:64845.
UCSCiRGD:69194. rat. [Q03555-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X66366 mRNA. Translation: CAA47009.2 .
PIRi JH0681.
RefSeqi NP_074056.2. NM_022865.3. [Q03555-6 ]
UniGenei Rn.11032.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1IHC X-ray 1.90 A 1-201 [» ]
1T3E X-ray 3.25 A/B 348-768 [» ]
2FTS X-ray 2.41 A 350-768 [» ]
2FU3 X-ray 2.70 A/B 350-768 [» ]
ProteinModelPortali Q03555.
SMRi Q03555. Positions 13-194, 350-768.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 249211. 8 interactions.
DIPi DIP-33263N.
IntActi Q03555. 5 interactions.
MINTi MINT-241818.

PTM databases

PhosphoSitei Q03555.

Proteomic databases

PaxDbi Q03555.
PRIDEi Q03555.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 64845.
KEGGi rno:64845.
UCSCi RGD:69194. rat. [Q03555-1 ]

Organism-specific databases

CTDi 10243.
RGDi 69194. Gphn.

Phylogenomic databases

eggNOGi COG0303.
HOGENOMi HOG000280651.
HOVERGENi HBG005828.
InParanoidi Q03555.
KOi K15376.
PhylomeDBi Q03555.

Enzyme and pathway databases

UniPathwayi UPA00344 .

Miscellaneous databases

EvolutionaryTracei Q03555.
NextBioi 613764.
PROi Q03555.

Gene expression databases

Genevestigatori Q03555.

Family and domain databases

Gene3Di 2.40.340.10. 1 hit.
3.40.980.10. 2 hits.
InterProi IPR020817. Mo_cofactor_synthesis.
IPR008284. MoCF_biosynth_CS.
IPR005111. MoeA_C_domain_IV.
IPR005110. MoeA_linker/N.
IPR001453. Mopterin-bd_dom.
[Graphical view ]
Pfami PF00994. MoCF_biosynth. 2 hits.
PF03454. MoeA_C. 1 hit.
PF03453. MoeA_N. 1 hit.
[Graphical view ]
SMARTi SM00852. MoCF_biosynth. 2 hits.
[Graphical view ]
SUPFAMi SSF53218. SSF53218. 2 hits.
SSF63867. SSF63867. 1 hit.
SSF63882. SSF63882. 1 hit.
TIGRFAMsi TIGR00177. molyb_syn. 2 hits.
PROSITEi PS01078. MOCF_BIOSYNTHESIS_1. 1 hit.
PS01079. MOCF_BIOSYNTHESIS_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Primary structure and alternative splice variants of gephyrin, a putative glycine receptor-tubulin linker protein."
    Prior P., Schmitt B., Grenningloh G., Pribilla I., Multhaup G., Beyreuther K., Maulet Y., Werner P., Langosch D., Kirsch J., Betz H.
    Neuron 8:1161-1170(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 5), PARTIAL PROTEIN SEQUENCE.
    Strain: Wistar.
    Tissue: Brain.
  2. Schmitt B.
    Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION TO 255.
  3. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2; 3; 4 AND 5).
  4. Cited for: PARTIAL PROTEIN SEQUENCE, IDENTIFICATION BY MASS SPECTROMETRY, X-RAY CRYSTALLOGRAPHY (3.25 ANGSTROMS) OF 348-768 IN COMPLEX WITH GLRB, SUBUNIT.
  5. "Gephyrin antisense oligonucleotides prevent glycine receptor clustering in spinal neurons."
    Kirsch J., Wolters I., Triller A., Betz H.
    Nature 366:745-748(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "The gamma-aminobutyric acid type A receptor (GABAAR)-associated protein GABARAP interacts with gephyrin but is not involved in receptor anchoring at the synapse."
    Kneussel M., Haverkamp S., Fuhrmann J.C., Wang H., Waessle H., Olsen R.W., Betz H.
    Proc. Natl. Acad. Sci. U.S.A. 97:8594-8599(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH GABARAP.
  7. "The neurotransmitter receptor-anchoring protein gephyrin reconstitutes molybdenum cofactor biosynthesis in bacteria, plants, and mammalian cells."
    Stallmeyer B., Schwarz G., Schulze J., Nerlich A., Reiss J., Kirsch J., Mendel R.R.
    Proc. Natl. Acad. Sci. U.S.A. 96:1333-1338(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "X-ray crystal structure of the trimeric N-terminal domain of gephyrin."
    Sola M., Kneussel M., Heck I.S., Betz H., Weissenhorn W.
    J. Biol. Chem. 276:25294-25301(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-201, SUBUNIT.
  9. "Deciphering the structural framework of glycine receptor anchoring by gephyrin."
    Kim E.Y., Schrader N., Smolinsky B., Bedet C., Vannier C., Schwarz G., Schindelin H.
    EMBO J. 25:1385-1395(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 350-768 IN COMPLEX WITH GLRB, SUBCELLULAR LOCATION, MUTAGENESIS OF PHE-362; PRO-745 AND 745-PRO-PRO-746.

Entry informationi

Entry nameiGEPH_RAT
AccessioniPrimary (citable) accession number: Q03555
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: May 16, 2006
Last modified: June 11, 2014
This is version 147 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Multifunctional enzyme, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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