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1  structure 191  species 2  interactions 420  sequences 18  architectures

Family: Rabaptin (PF03528)

Summary: Rabaptin

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Rabaptin Edit Wikipedia article

Rabaptin
1TU3.pdb.png
Crystallographic structure of the C-terminal Rabaptin5 domain homodimer (colored orange and magenta at the center of the figure) complexed with two independent molecules of the GTPase domain of RAB5A (rainbow colored, N-terminus = blue, C-terminus = red).[1]
Identifiers
Symbol Rabaptin
Pfam PF03528
InterPro IPR003914

Rabaptin is a key protein involved in regeneration of injured axons.

Regeneration of injured axons at neuromuscular junctions is regulated by extra-cellular protein factors that promote neurite outgrowth. A novel neurite outgrowth factor from chick denervated skeletal muscle has been cloned and characterised. The protein, termed neurocrescin (rabaptin), has been shown to be secreted in an activity-dependent fashion.[2]

Rabaptin is a 100kDa coiled-coil protein that interacts with the GTP form of the small GTPase Rab5 (see RAB5A, RAB5B, RAB5C) a potent regulator of endocytic transport.[3] It is mainly cytosolic, but a fraction co-localises with Rab5 to early endosomes. Rab5 recruits rabaptin-5 to purified early endosomes in a GTP-dependent manner, demonstrating functional similarities with other members of the Ras family. Immunodepletion of rabaptin-5 from cytosol strongly inhibits Rab5-dependent early endosome membrane fusion. Thus, rabaptin-5 is a Rab effector required for membrane docking and fusion.

Rab5 contributes to early endosome fusion that works through the coordination of other effector proteins, as mentioned above. Rabaptin components may serve to control the SNARE activity which are vital in membrane fusion.[4]

Structure

A crystal structure of the GTPase domain of RAB5A complexed with the C-terminal domain of Rabaptin5 has been determined.[1] The two proteins form a symmetric RAB5A-Rabaptin5 ternary complex with a parallel coiled-coil Rabaptin5 homodimer in the middle complexed with two molecules of Rabaptin5, one on each side (see figure to the right).

Human proteins

RABEP1; RABEP2;

References

  1. ^ a b PDB: 1tu3​; Zhu G, Zhai P, Liu J, Terzyan S, Li G, Zhang XC (October 2004). "Structural basis of Rab5-Rabaptin5 interaction in endocytosis". Nat. Struct. Mol. Biol. 11 (10): 975–83. doi:10.1038/nsmb832. PMID 15378032. 
  2. ^ Nishimune H, Uyeda A, Nogawa M, Fujimori K, Taguchi T (1997). "Neurocrescin: a novel neurite-outgrowth factor secreted by muscle after denervation". NeuroReport. 8 (16): 3649–3654. doi:10.1097/00001756-199711100-00045. PMID 9427343. 
  3. ^ Zerial M, Stenmark H, Vitale G, Ullrich O (1995). "Rabaptin-5 is a direct effector of the small GTPase Rab5 in endocytic membrane fusion". Cell. 83 (3): 423–432. doi:10.1016/0092-8674(95)90120-5. PMID 8521472. 
  4. ^ Deneka M, Neeft M, Popa I, van Oort M, Sprong H, Oorschot V, Klumperman J, Schu P, van der Sluijs P (June 2003). "Rabaptin-5alpha/rabaptin-4 serves as a linker between rab4 and gamma(1)-adaptin in membrane recycling from endosomes". EMBO J. 22 (11): 2645–57. doi:10.1093/emboj/cdg257. PMC 156754Freely accessible. PMID 12773381. 

This article incorporates text from the public domain Pfam and InterPro IPR003914


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Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018514

Regeneration of injured axons at neuromuscular junctions has been assumed to be regulated by extra-cellular factors that promote neurite outgrowth. A novel neurite outgrowth factor from chick denervated skeletal muscle has been cloned and characterised. The protein, termed neurocrescin (rabaptin), has been shown to be secreted in an activity-dependent fashion [PUBMED:9427343].

Rabaptin is a 100kDa coiled-coil protein that interacts with the GTP form of the small GTPase Rab5, a potent regulator of endocytic transport [PUBMED:8521472]. It is mainly cytosolic, but a fraction co-localises with Rab5 to early endosomes. Rab5 recruits rabaptin-5 to purified early endosomes in a GTP-dependent manner, demonstrating functional similarities with other members of the Ras superfamily. Immunodepletion of rabaptin-5 from cytosol strongly inhibits Rab5-dependent early endosome fusion. Thus, rabaptin-5 is a Rab effector required for membrane docking and fusion.

Gene Ontology

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Domain organisation

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Alignments

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  Seed
(3)
Full
(420)
Representative proteomes UniProt
(725)
NCBI
(1368)
Meta
(0)
RP15
(87)
RP35
(169)
RP55
(284)
RP75
(330)
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  Seed
(3)
Full
(420)
Representative proteomes UniProt
(725)
NCBI
(1368)
Meta
(0)
RP15
(87)
RP35
(169)
RP55
(284)
RP75
(330)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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Seed source: PRINTS
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Griffiths-Jones SR
Number in seed: 3
Number in full: 420
Average length of the domain: 260.10 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 45.53 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.7 26.7
Trusted cut-off 26.7 26.7
Noise cut-off 26.5 26.3
Model length: 486
Family (HMM) version: 15
Download: download the raw HMM for this family

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Interactions

There are 2 interactions for this family. More...

Rabaptin GAT

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Rabaptin domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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