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PR00185

Identifier
EUKARYTPORIN  [View Relations]  [View Alignment]  
Accession
PR00185
No. of Motifs
4
Creation Date
19-MAR-1993  (UPDATE 26-JUN-1999)
Title
Eukaryotic porin signature
Database References

PROSITE; PS00558 EUKARYOTIC_PORIN; PS00576 GRAM_NEG_PORIN
INTERPRO; IPR001925
PDB; 2POR
SCOP; 2POR
Literature References
1. JAP, B.K. AND WALIAN, P.J.
Biophysics of the structure and function of porins.
Q.REV.BIOPHYS. 23 367-403 (1990).
 
2. NIKAIDO, H.
Porins and specific channels of bacterial outer membranes.
MOL.MICROBIOL. 6 435-442 (1992).
 
3. WEISS, M.S., KREUSCH, A., SCHILTZ, E., NESTEL, U., WELTE, W., 
WECKESSER, J. AND SCHULZ, G.E.
The structure of porin from Rhodobacter casulatus at 1.8A resolution.
FEBS LETT. 280 379-382 (1991).
 
4. PAUPTIT, R.A., SCHIRMER, T., JANSONIUS, J.N., ROSENBUSCH, J.P,
PARKER, M.W., TUCKER, A.D., TSERNOGLOU, D., WIESS, M.S. AND SCHULZ, G.E.
A common channel-forming motif in evolutionarily distant porins
J.STRUCT.BIOL. 107 136-145 (1991).
 
5. KREUSCH, A. AND SCHULZ, G.E. 
Refined structure of the porin from Rhodopseudomonas blastica. 
Comparison with the porin from Rhodobacter capsulatus.
J.MOL.BIOL. 243 891-905 (1994).
 
6. COWAN, S.W.
Bacterial porins: lessons from three high-resolution structures.
CURR.OPIN.STRUCT.BIOL. 3 501-507 (1993).

Documentation
Porins are found in the outer membranes of Gram-negative bacteria,
mitochondria and chloroplasts, where they form ion-selective channels for 
small hydrophilic molecules (up to ~600 Da) [1,2]. X-ray structure analyses
of several bacterial porins [3-5] have revealed a 16-stranded anti-parallel
beta-barrel structure enclosing the transmembrane pore, by contrast with
all other integral membrane proteins described to date, which are alpha-
helical. Three subunits form a trimer; the 3-fold axis is approximately
parallel to the barrel axes and is assumed to be perpendicular to the
membrane plane [6].  
 
From the range of porins now known, similarities have been observed between
porins from different species, and between porins of different specificity
within the same species. But most porins cannot be related to each other on
the basis of sequence alone, and this is reflected in the lengths of the 
known porin sequences, which range from 282-483 residues/monomer.
 
EUKARYTPORIN is a 4-element fingerprint that provides a signature for 
eukaryotic porins. The fingerprint was derived from an initial alignment 
of 3 sequences: motif 2 includes the well-conserved region encoded by
PROSITE pattern EUKARYOTIC_PORIN (PS00558). Two iterations on OWL19.1 were
required to reach convergence, at which point a true set comprising 4
sequences was identified. The fingerprint is selective for this family
alone, and there is no cross-reaction with E.coli/Salmonella-type porins,
or with porins from Neisseria.
 
An update on SPTR37_9f identified a true set of 13 sequences.
Summary Information
13 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
413131313
30000
20000
1234
True Positives
P81155        POR1_BOVIN    POR1_HUMAN    POR1_YEAST    
POR2_HUMAN POR2_XENLA PORI_NEUCR Q21752
Q60930 Q60931 Q60932 Q94920
Q94997
Sequence Titles
P81155      VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 2 (VDAC2) (OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN) (B36-VDAC) - RATTUS NORVEGICUS (RAT). 
POR1_BOVIN VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1 (VDAC1) (PLASMALEMMAL PORIN) (BRAIN-DERIVED VOLTAGE-DEPENDENT ANION CHANNEL 1) (BR1-VDAC) - BOS TAURUS (BOVINE).
POR1_HUMAN VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1 (VDAC1) (PLASMALEMMAL PORIN) (OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN) (PORIN 31HL) (PORIN 31HM) - HOMO SAPIENS (HUMAN).
POR1_YEAST OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN 1 (VOLTAGE-DEPENDENT ANION- SELECTIVE CHANNEL PROTEIN 1) (VDAC 1) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
POR2_HUMAN VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 2 (VDAC2) (OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN) - HOMO SAPIENS (HUMAN).
POR2_XENLA VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 2 (OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
PORI_NEUCR OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN - NEUROSPORA CRASSA.
Q21752 PROBABLE VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL - CAENORHABDITIS ELEGANS.
Q60930 VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 2 (VDAC2) (VDAC6) - MUS MUSCULUS (MOUSE).
Q60931 VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 3 (VDAC3) - MUS MUSCULUS (MOUSE).
Q60932 VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1 (VDAC1) (VDAC5) - MUS MUSCULUS (MOUSE).
Q94920 VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q94997 VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL - DROSOPHILA MELANOGASTER (FRUIT FLY).
Scan History
OWL19_1    2  100  NSINGLE    
OWL25_3 2 100 NSINGLE
SPTR37_9f 2 16 NSINGLE
Initial Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
PAFSDIAKSANDLLNK PORI_NEUCR 4 4 -
PTYADLGKSARDVFTK PORI_HUMAN 4 4 -
PVYSDISRNINDLLNK PORI_YEAST 4 4 -

Motif 2 width=16
Element Seqn Id St Int Rpt
GLTVTQTWNTANALET PORI_NEUCR 67 47 -
GLTFTEKWNTDNTLGT PORI_HUMAN 67 47 -
GLGLTQGWSNTNNLQT PORI_YEAST 68 48 -

Motif 3 width=12
Element Seqn Id St Int Rpt
EGIVGGAEFGYD PORI_YEAST 145 61 -
EGFLAGASAGYD PORI_NEUCR 145 62 -
EGWLAGYQMNFE PORI_HUMAN 146 63 -

Motif 4 width=18
Element Seqn Id St Int Rpt
YNVLLREGVTLGVGASFD PORI_NEUCR 247 90 -
YKQLLRPGVTLGVGSSFD PORI_YEAST 247 90 -
YTQTLKPGIKLTLSALLD PORI_HUMAN 246 88 -
Final Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
PSYADLGKSARDIFNK POR2_XENLA 4 4 -
PSYADLGKAARDIFNK POR2_HUMAN 31 31 -
PPYADLGKAARDIFNK P81155 17 17 -
PPYADLGKAARDIFNK Q60930 17 17 -
PTYADLGKSARDVFTK POR1_HUMAN 4 4 -
PTYADLGKSARDVFTK Q60932 5 5 -
PTYCDLGKAAKDVFNK Q60931 5 5 -
RPYADLGKSARDVFTK POR1_BOVIN 4 4 -
PSYSDLGKQARDIFSK Q94920 4 4 -
PSYSDLGKQARDIFSK Q94997 4 4 -
PTFADLGKSAKDLFNK Q21752 4 4 -
PAFSDIAKSANDLLNK PORI_NEUCR 4 4 -
PVYSDISRNINDLLNK POR1_YEAST 4 4 -

Motif 2 width=16
Element Seqn Id St Int Rpt
GLTFTEKWNTDNTLGT POR2_XENLA 67 47 -
GLTFTEKWNTDNTLGT POR2_HUMAN 94 47 -
GLTFTEKWNTDNTLGT P81155 80 47 -
GLTFTEKWNTDNTLGT Q60930 80 47 -
GLTFTEKWNTDNTLGT POR1_HUMAN 67 47 -
GLTFTEKWNTDNTLGT Q60932 68 47 -
GLTFTQKWNTDNTLGT Q60931 68 47 -
GLTFTEKWNTDNTLGT POR1_BOVIN 67 47 -
GLTLTEKWNTDNTLFT Q94920 67 47 -
GLTLTEKWNTDNTLFT Q94997 67 47 -
GITLTEKWNTENQLGT Q21752 69 49 -
GLTVTQTWNTANALET PORI_NEUCR 67 47 -
GLGLTQGWSNTNNLQT POR1_YEAST 68 48 -

Motif 3 width=12
Element Seqn Id St Int Rpt
EGWLAGYQMTFD POR2_XENLA 146 63 -
EGWLAGYQMTFD POR2_HUMAN 173 63 -
EGWLAGYQMTFD P81155 159 63 -
EGWLAGYQMTFD Q60930 159 63 -
EGWLAGYQMNFE POR1_HUMAN 146 63 -
EGWLAGYQMNFE Q60932 147 63 -
EGWLAGYQMSFD Q60931 147 63 -
EGWLAGYQMNFE POR1_BOVIN 146 63 -
QGWLAGYQTAFD Q94920 146 63 -
QGWLAGYQTAFD Q94997 146 63 -
DGWLIGAAATFD Q21752 174 89 -
EGFLAGASAGYD PORI_NEUCR 145 62 -
EGIVGGAEFGYD POR1_YEAST 145 61 -

Motif 4 width=18
Element Seqn Id St Int Rpt
YTQTLRPGVKLTLSALVD POR2_XENLA 246 88 -
YTQTLRPGVKLTLSALVD POR2_HUMAN 273 88 -
YTQTLRPGVKLTLSALVD P81155 259 88 -
YTQTLRPGVKLTLSALVD Q60930 259 88 -
YTQTLKPGIKLTLSALLD POR1_HUMAN 246 88 -
YTQTLKPGIKLTLSALLD Q60932 247 88 -
YTQTLRPGVKLTLSALID Q60931 247 88 -
YTQTLKPGIKLTLSALLD POR1_BOVIN 246 88 -
YQQKLRDGVTLTLSTLVD Q94920 246 88 -
YQQKLRTGVTLTLSTLVD Q94997 246 88 -
ATHSLSPALKLTLSTQFN Q21752 274 88 -
YNVLLREGVTLGVGASFD PORI_NEUCR 247 90 -
YKQLLRPGVTLGVGSSFD POR1_YEAST 247 90 -