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List of -TEMs -PEMs -NEMs

TEMs TEM1 TEM2 TEM3 TEM4 TEM5 TEM6 TEM7 TEM8 TEM9 TEM10 TEM11 TEM12 TEM13 TEM14 TEM15 TEM16 TEM17 TEM18 TEM19 TEM20 TEM21_1 TEM21_2 TEM22 TEM23 TEM24 TEM25 TEM26 TEM27 TEM28 TEM29 TEM30 TEM31_1 TEM31_2 TEM32 TEM33 TEM34 TEM35 TEM36 TEM37 TEM38 TEM39 TEM40 TEM41 TEM42 TEM43 TEM44 TEM45 TEM46

Summary -Overview of TEMs -extracellular TEMs -intrac. & membrane TEMs -TEM tissue distribution

Supplementary -SAGE -Seq.analysis Methods

FAQ

Tumor Endothelial Marker Report: TEM28 (RhoGAP protein)

	TEM domain structure

	TEM Sequence Analysis

name	from	to	source/E	description
unknown	1	250	predator	The region is a highly helical region, with aa 170-200 forming a coiled-coil structure with very high probability.
RhoGAP	269	419	Pfam E=5.4e-55	The finger-arginine residue, is positioned at residue 291, and is proposed to be involved in GAP catalysis by stabilizing the transition state and the critical glutamine. The arginine residue is preceded by an aromatic amino acid residue (F) which is proposed to stabilize the adjacent hydrophobic core and balance the orientation of the arginine finger.
proline-rich	526	756	SEG25	Highly proline-rich regions usually serve as binding sites for Src homology (SH3) domains and other protein modules. These interactions often mediate the generation of dynamic macromolecular signalling complexes. Five proline-rich sequences contain the potential SH3 binding motif pXPpXP (p proline-preferred, X non-conserved residue): PXPXXP: 559-564, 630-635, 739-744, XXPPXP: 543-548, 738-743.
	658	724	SAPS	The region is uncharged, particularly the region from 704 to 724.
818

	Remarks

• CLASSIFICATION: Nedrin related Rho-GAP.

• HOMOLOGUES: TEM28 shows 44% allover (64% in the first 419aa) identity to nedrin in rat (dbj|BAB12426) and human (dbj|BAB14506). The protein organization is further conserved in 3BP-1 human (emb|CAB42896) and mouse (sp|P55194) SH3-domain binding protein 1. The conservation is highest in the Rho-GAP domain as seen in the alignment.

• DOMAIN ARCHITECTURE: TEM28 is a protein showing a proline-content above average and is composed of three regions:
  • A N-terminal coiled-coil region.
    An N-terminal region found N-terminally in several SH3-containing adaptor proteins (blast against nr of 1-260 aa). Amino acids 170 to 200 are very likely to form a coiled-coil structure. The SH3-binding protein 3BP-1 contains a region with 40% identity in its N-terminus. The several endophilins (coiled-coil-linker-SH3) are 22% identical in this region that is predicted to form a coiled-coil structure.
  • A central GAP region.
    A psi-blast search with the amino acids central region 250 to 430 shows the relation to the GAPs of Rho-family GTPases nadrin, 3BP-1, bcr. The 70% identical nedrin GAP domain and 60% 3BP-1s GAP domain have been shown to stimulate the intrinsic GTPase activity of RhoA, Cdc42, Rac1 and Rac1, Cdc42 respectively.
    

    ASSESSMENT OF A POTENTIAL TEM28GAP CATALYTIC ACTIVITY: The TEM28 RhoGAP domain shows conservation of several residues with a prospective role GAP activity. The RhoGAP domain has been shown to be fully alpha-helical containing 8 helices of which two adjacent helices (helices B and F) and an adjoining loop (the catalytic A-A1 loop) generate the G-protein binding site. In TEM28, the finger-arginine residue, which is proposed to be involved in GAP catalysis by stabilizing the transition state and the critical glutamine of GTP-binding proteins is positioned at residue 291 in the A-A1 loop. This residue is preceeded by an aromatic amino acid residue (F290) which is proposed to stabilize the adjacent hydrophobic core and balance the orientation of the arginine finger in RhoGAPs. During the transition state of the phosphoryl transfer reaction rearrangment of the G-protein-RhoGAP complex occur:1 ) R291 is relocated such that it can assists in catalysis. 2) Switch I and II of the small G-protein are better ordered which is proposed to assist catalysis. This increased order is created through the interaction of a Tyr in switch I with an conserved Asn of Helix F (N401 in TEM28) and the R291 guanidinium group. Consequently, a catalytic GAP activity is proposed for TEM28.

    ASSESSMENT OF A POTENTIAL TEM28GAP BINDING ACTIVITY: The G-protein binding B and F helix can be located to the TEM28 regions 321-334 and 398-411 by superposition of the GAP domain with the respective p50RhoGAP domain. The proposed B and F helices are contained in parts of the GAP domain that show highest conservation (identity 92-94%) to nedrin GAP domain and 3BP-1s GAP domain (both identical in the restricted regions) which have been shown to stimulate the intrinsic GTPase activity of RhoA, Cdc42, Rac1 and Rac1, Cdc42 respectively. The specificity of the small GTPase binding activity of TEM28 cannot be predicted.

  • A C-terminal proline-rich region.
    Nine of thirteen mammalian RhoGAP proteins contain proline-rich regions considered to be likely SH3 binding domains. For p50rhoGAP and 3-BP1 such an interaction has been proven with the SH3 domains of c-Src or p85 and Abl-tyrosine kinase, respectively. The core SH3 ligand is a seven-residue peptide of the consensus sequence pXPpXP (p proline-preferred, X tend to be aliphatic). The two prolines are crucial for high-affinity binding. Several candidate SH3 binding-motifs can be found in TEM28: 559-564 (PLPEQP), 630-635 (PSPSQP), 543-548 (QPPAPP) and 738-743 (PPPQPP), whereby the latter has a homologous side predicted to be a SH3 binding-motif in nadrins.
  Two possible PEST-sequences are detectable 602-642 (PESTfind score:+6.83) and 735-776 (+7.54) which makes the protein a likely target of rapid turnover.

• FUNCTION: It is presumed that the primary cellular functions of many rhoGAPs are accomplished through the inactivation of rho GTPases. It has been suggested that GAP proteins may have additional signal transduction functions due to their multiple domain composition.
  Thus, TEM28 could provide multiple activities related to organisation of the actin network. TEM28 shows conservation of residues that are central in GAP activity and is, thus, a potentially active GAP. Additionally, the protein is proposed to contain a N-terminal coiled-coil and a C-terminal SH3-domain binding proline-rich region. This makes it likely that TEM28 is involved in the generation of dynamic macromolecular signalling complexes.

	Sequence Information

TEM	TEM28
Reliability of Gen2Tag mapping	Cid->tag (Hs.6336) frequency: tem28: CATG-TACAAATCGT=4/4 (cDNA) tem28: CATG-TACAAATCGT=10/11 (EST oriented)
Analysis	BlastP against nr BlastP against nr without LCR-filter Output Created by a Suite of Single Sequence Analysis Techniques
Protein Description	SEQ.SOURCE: gi|3327158|dbj|BAA31647.1| KIAA0672 protein
Protein Sequence	MKKQFNRMRQLANQTVGRAEKTEVLSEDLLQVEKRLELVKQVSHSTHKKLTACLQGQQGAEADKRSKKLP LTTLAQCLMEGSAILGDDTLLGKMLKLCGETEDKLAQELIHFELQVERDVIEPLFLLAEVEIPNIQKQRK HLAKLVLDMDSSRTRWQQTSKSSGLSSSLQPAGAKADALREEMEEAANRVEICRDQLSADMYSFVAKEID YANYFQTLIEVQAEYHRKSLTLLQAVLPQIKAQQEAWVEKPSFGKPLEEHLTISGREIAFPIEACVTMLL ECGMQEEGLFRVAPSASKLKKLKAALDCCVVDVQEYSADPHAIAGALKSYLRELPEPLMTFELYDEWIQA SNVQEQDKKLQALWNACEKLPKANHNNIRYLIKFLSKLSEYQDVNKMTPSNMAIVLGPNLLWPQAEGNIT EMMTTVSLQIVGIIEPIIQHADWFFPGEIEFNITGNYGSPVHVNHNANYSSMPSPDMDPADRRQPEQARR PLSVATDNMMLEFYKKDGLRKIQSMGVRVMDTNWVARRGSSAGRKVSCAPPSMQPPAPPAELAAPLPSPL PEQPLDSPAAPALSPSGLGLQPGPERTSTTKSKELSPGSAQKGSPGSSQGTACAGTQPGAQPGAQPGASP SPSQPPADQSPHTLRKVSKKLAPIPPKVPFGQPGAMADQSAGQLSPVSLSPTPPSTPSPYGLSYPQGYSL ASGQLSPAAAPPLASPSVFTSTLSKSRPTPKPRQRPTLPPPQPPTVNLSASSPQSTEAPMLDGMSPGESM STDLVHFDIPSIHIELGSTLRLSPLEHMRRHSVTDKRDSEEESESTAL
SAGE-Tag	CATG-TACAAATCGTT
EST/cluster Description	UNIGEN CLUSTER: Hs.6336 : KIAA0672 gene product SEQ.SOURCE: gi|3327157|dbj|AB014572.1|AB014572 Homo sapiens mRNA for KIAA0672 protein MARKINGS: Tem28 Tag in red first Poly-A-signal following the Tag in bold REMARKS: gene 301..2757 CDS 301..2757
EST/cluster Sequence	GACTGGGAGCAGGCAGCCCGGGCGGAGCGGGCCGGTGCCGAGGACGGCCCCAGGCATTGCTCTGCCCCGG GCATTGCGCGGCGCGCGTGAGGGGGATGCGGCAGGAGGCGGCGCGGCGGGAGGAGTAGGCGGCGGCGCCC TCGGGAGGGAGCTGCGCGCGGGCCAGACGGCGCCCGGAGGCTCCGCAGTGCCGCCGCCGTCGCCCGGGAG GCTCCGCGCGGGAGCCATGTAACCCTGCGGCGGGCTCCGGGCTGCTCCGTCCTTCCCCAGCTCCCGGGCT AGCGCGGCAGCGGGGCCACGATGAAGAAGCAGTTCAATCGCATGCGCCAGCTGGCCAACCAGACGGTGGG CAGGGCTGAAAAGACAGAAGTTTTGAGTGAAGACCTTCTTCAGGTGGAGAAGCGTCTGGAGCTGGTGAAA CAGGTGTCCCACAGCACGCACAAGAAGCTCACCGCATGTCTGCAGGGCCAGCAAGGGGCAGAGGCTGACA AGCGCTCCAAAAAGTTGCCTTTGACAACACTGGCTCAGTGTCTGATGGAGGGGTCAGCTATCCTGGGAGA TGACACACTTCTTGGGAAGATGCTGAAACTCTGTGGAGAGACGGAGGACAAGCTGGCTCAGGAGCTGATA CATTTTGAGTTGCAAGTAGAGAGAGACGTGATTGAGCCCCTGTTTTTGCTGGCGGAGGTGGAAATCCCAA ATATTCAAAAGCAGAGGAAACACTTAGCCAAGTTGGTGCTGGACATGGATTCCTCACGAACCAGGTGGCA GCAGACTTCCAAGTCTTCAGGTTTGTCCAGCAGCTTACAGCCTGCGGGTGCCAAGGCTGATGCCCTCAGG GAAGAAATGGAAGAGGCTGCCAACAGAGTGGAGATTTGCAGGGACCAGCTCTCAGCTGATATGTACAGTT TTGTGGCCAAAGAAATTGACTATGCAAACTACTTTCAAACGCTAATAGAAGTGCAAGCTGAATACCACAG GAAGTCCCTGACACTATTGCAGGCTGTATTGCCTCAGATCAAAGCACAACAGGAGGCCTGGGTAGAGAAG CCTTCCTTCGGGAAGCCGCTGGAGGAGCACCTCACCATCAGCGGCCGGGAGATCGCCTTCCCCATCGAGG CGTGTGTGACCATGCTGCTTGAGTGTGGGATGCAGGAGGAGGGACTCTTCCGAGTAGCCCCCTCTGCCTC CAAACTGAAGAAGCTGAAAGCGGCCCTGGACTGCTGCGTGGTGGATGTGCAGGAGTACTCGGCAGACCCC CACGCAATTGCAGGAGCTTTGAAATCTTACCTCCGAGAGTTGCCAGAACCTCTTATGACCTTTGAACTCT ATGATGAGTGGATCCAGGCTTCCAATGTCCAGGAGCAAGACAAGAAGCTTCAGGCTCTATGGAATGCTTG TGAAAAGTTGCCCAAGGCCAATCACAACAACATCCGATACTTGATAAAATTTTTATCCAAGCTGTCAGAA TATCAAGATGTAAACAAGATGACTCCCAGTAATATGGCAATTGTTTTAGGACCCAACCTCCTATGGCCAC AAGCAGAAGGGAACATTACAGAGATGATGACCACAGTGTCGCTGCAAATTGTTGGGATCATTGAACCTAT CATCCAGCATGCAGACTGGTTCTTCCCTGGGGAGATAGAGTTCAACATTACTGGCAATTATGGGAGTCCA GTACACGTGAACCATAATGCCAACTACAGCTCAATGCCCTCCCCAGACATGGACCCTGCTGACCGGCGCC AGCCCGAGCAGGCCCGCCGGCCCCTCAGCGTCGCCACGGATAATATGATGCTGGAGTTTTACAAAAAGGA TGGCCTTAGGAAAATCCAAAGCATGGGTGTGAGGGTCATGGACACAAACTGGGTGGCTCGAAGAGGCTCC TCGGCCGGTCGGAAAGTGTCCTGCGCCCCGCCCTCCATGCAGCCTCCCGCCCCGCCCGCCGAGCTGGCTG CGCCCCTGCCTTCGCCGCTGCCGGAGCAGCCCCTGGACAGCCCCGCGGCCCCCGCGCTCTCTCCATCCGG CCTGGGCCTCCAGCCTGGGCCCGAGCGCACCAGCACAACAAAAAGCAAGGAACTTTCTCCAGGCTCTGCA CAGAAAGGAAGTCCAGGCTCCAGCCAGGGCACAGCCTGTGCAGGGACTCAACCAGGGGCTCAACCTGGAG CTCAGCCGGGCGCCAGCCCCAGCCCCAGCCAGCCGCCTGCAGACCAGAGTCCTCACACCCTCCGGAAAGT TTCAAAGAAGCTGGCACCGATTCCACCCAAGGTCCCCTTTGGCCAGCCGGGGGCTATGGCAGACCAGTCC GCTGGCCAGCTGTCCCCAGTCAGCCTGTCCCCCACCCCGCCCAGCACCCCGTCACCCTATGGACTGAGCT ACCCTCAGGGGTACTCCTTGGCCTCGGGCCAGCTCTCCCCAGCTGCAGCTCCTCCCCTGGCCTCTCCTTC TGTCTTTACAAGCACTTTGAGCAAATCGCGGCCCACTCCTAAGCCGCGACAGAGACCTACTCTGCCGCCT CCTCAGCCTCCCACAGTAAACCTCTCGGCCTCTAGTCCACAGTCCACGGAGGCCCCCATGCTAGATGGCA TGTCCCCTGGGGAAAGCATGTCTACAGATCTTGTCCACTTTGATATTCCCTCGATCCACATAGAGCTCGG GTCGACGCTCCGCCTGAGTCCCCTGGAGCACATGCGGCGACACTCAGTAACTGACAAGAGGGACTCGGAG GAGGAGTCTGAGAGCACCGCCCTCTGACATGACACCGCCCATCCTGCCTCGCGTGTACATACATCACGGG CCCTAGGAACGCCGCCAGGAGCAGCGTCCATGAGCTTGCCAAGTGTTCTCTGCTGGCTCTTTCCTGCCAC TGCCAACACGAGGTTGGAATTTGGCAGAAAATTGTGATCTCCAGTCCGTGTGGTGATGCTGGTGGTGCAG GTTTTGTTTGTTCCTTTCGGGTGGTGACTTCGGCCTTTTGTTTGACCTTTGCCTTTTGACTTTGTGCCTC TTTTGATCCACTTTCAGCCTCCATGCCAGAAAACACCCACCTCTCCATCCAAGGCTGGTCAGGAACGTCC TTTGCAGGGTCGGGGTGGTGCGGGAGAGGCTCACTTTGCCTGGTTAGACCCAAGGGCTGCTACCTTTTCC TTGGACGGCTCATGTCAGGTCTTGCAGGATCAGTTTAATGGCCACAGAAAGGAAGCAGGACAGCAGGGCC CCTCTCACCCACAACTGGACCAGGTCCAGGATTCTAGCAGTCCTGGGGCACTGACCTTTGCCAGCTACCT GGGGGAGGGCTTGCCACTGGAAAACCTTTCAGGCCGCCCCCATCAGTGGGCTCCAAAGTAAATGGCTGAA AACAAAAATGTTTCACTTCCTAACAGTTTTCCTTTTTCCACTGTGTGACTGAAAGCTCCTATATCATTTT ATATTTCTGAATCTATAAAACAAAACAAACAAGCCTGAAAGTGTCTGGAGGAGCCAAAGGTGGCCTCCCT GTCCCCAAATATATTGGCTATATGAGAGTAATTTTACCCCTCTACGTACCTAAAGGCACCCAGTTCACTA GTCTGTGGGGTCCTGGAGCCTGTCTCTTCTTTCTGGAGGTTCAAACTGAATAGCAATAATTACGTTACCC AAAGCATGTGGAGGAAAAGTGAAACCAGCCACGGAGACGCTGGCCCACGGCTCGGCCTGCGGTGTGGCCT GCTTTGCTCACCAGCGTCAGCCGCTCATTTCCTTCTCATGAAGTCCCATCTGGTCATGGGGACGAGGGCC GGGAGGGCACCGGGTAGCCTTTTCACACTTGGGGATTAGGGGAGTGAGAAAAGATTTGGGCCATGCATGC AAAGTCAAAGTTTAAAATTTTATCCTTTTCAAATAGATGATATAATATACCTATACATGATATAATATTT GTATATATGAAATCTCTCTATATTTGTTTAATTTGAGCCATTCAATCTAAACCAATGTACAGGTGTACAA TGAAAAATTTAAATGCTTAGTTATTTTTCCCAACACAGTGTAAAGTCACCCTCCTCTGAGAGTGGGATGT GCAGAGTTTTGATGTTGCAGCTTTGCTCACTTCCTGGCAAGGGCAGGTCATGCCTCAATTTGTAATGGGA GTCTGGGGTAAGGGTGGGGGTTGAAAGTTGTTATCTTTAAATACATGTACAAATCGTTGTCAAAAGTAAC GTTATTAAAATAGATTTATTATCCCTG
Genomic Sequence Description	SEQ.SOURCE: gi|9247291|ref|NT_000765.3|Hs17_1388| Homo sapiens chr.17 REMARKS: The predicted first two exons have to splice over 100 kb as can be seen in the blastn
Genomic Sequence

	Literature

PubMed: 10967100	Nadrin, a novel neuron-specific GTPase-activating protein involved in regulated exocytosis. Harada A, Furuta B, Takeuchi Ki, Itakura M, Takahashi M, Umeda M. J Biol Chem. 2000 Nov 24;275(47):36885-91.
PubMed: 10899318	Functional specificity conferred by the unique plasticity of fully alpha-helical Ras and Rho GAPs. Souchet M, Poupon A, Callebaut I, Leger I, Mornon J, Bril A, Calmels TP. FEBS Lett. 2000 Jul 14;477(1-2):99-105.
PubMed: 7526465	Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions. Feng S, Chen JK, Yu H, Simon JA, Schreiber SL. Science. 1994 Nov 18;266(5188):1241-7.
PubMed: 7510218	Structural basis for the binding of proline-rich peptides to SH3 domains. Yu H, Chen JK, Feng S, Dalgarno DC, Brauer AW, Schreiber SL Cell 1994 Mar 11;76(5):933-45
PubMed: 8438166	Identification of a ten-amino acid proline-rich SH3 binding site. Ren R, Mayer BJ, Cicchetti P, Baltimore D Science 1993 Feb 19;259(5098):1157-61