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PR00909

Identifier
SPERMDNBNDNG  [View Relations]  [View Alignment]  
Accession
PR00909
No. of Motifs
10
Creation Date
03-APR-1998  (UPDATE 10-JUN-1999)
Title
Bacterial periplasmic spermidine/putrescine-binding protein signature
Database References

INTERPRO; IPR001188
PDB; 1POT; 1POY
SCOP; 1POT; 1POY
CATH; 1POT; 1POY
Literature References
1. FURUCHI, T., KASHIWAGI, K., KOBAYASHI, H. AND IGARASHI, K.
Characteristics of the gene for a spermidine and putrescine transport
system that maps at 15 min on the Escherichia coli chromosome. 
J.BIOL.CHEM. 266 20928-20933 (1991). 
 
2. PISTOCCHI, R., KASHIWAGI, K., MIYAMOTO, S., NUKUI, E., SADAKATA, Y.,
KOBAYASHI, H. AND IGARASHI, K.
Characteristics of the operon for a putrescine transport system that maps
at 19 minutes on the Escherichia coli chromosome. 
J.BIOL.CHEM. 268 146-152 (1993). 
 
3. SUGIYAMA, S., VASSYLYEV, D.G., MATSUSHIMA, M., KASHIWAGI, K., 
IGARASHI, K. AND MORIKAWA, K.
Crystal structure of PotD, the primary receptor of the polyamine transport
system in Escherichia coli.
J.BIOL.CHEM. 271 9519-9525 (1996). 

Documentation
The nucleotide sequences of the genes for the spermidine and putrescine
transport systems that map at 15 and 19 min on the E.coli chromosome have
been determined [1,2]. The former was shown to contain four open reading 
frames encoding protein products PotA to PotD [1]; the latter also contained
four ORFs, designated PotF to PotI [2]. The D protein has been inferred to
be a periplasmic polyamine binding protein that regulates polyamine content
in E.coli [1]; similarly, PotF was inferred to be a periplasmic putrescine-
specific binding protein [2]. the PotD and PotF proteins show a high degree
of sequence similarity.
 
The 3D structure of PotD complexed with spermidine has been solved to 2.5A
resolution [2]. The structure comprises two domains, with alternating beta-
alpha-beta topology. The polyamine binding site lies in a central cleft at
the domain interface. Within the cleft, four acidic residues recognise the
three positively charged nitrogen atoms of spermidine, and five aromatic
side chains anchor the methylene backbone by van der Waals interactions [2].
The overall fold of PotD is similar to that of other periplasmic binding
proteins, especially to the E.coli maltodextrin-binding protein, despite 
low sequence identity [2]. Structure comparisons suggest that spermidine
binding rearranges the relative orientation of the PotD domains, creating
a more compact structure [2].
 
SPERMDNBNDNG is a 10-element fingerprint that provides a signature for
bacterial periplasmic spermidine/putrescine-binding proteins. The 
fingerprint was derived from an initial alignment of 5 sequences: the 
motifs were drawn from short conserved regions spanning the full alignment
length. A single iteration on OWL30.1 was required to reach convergence,
no further sequences being identified beyond the starting set. Several
partial matches were found, all of which are fragments.
 
An update on SPTR37_9f identified a true set of 7 sequences, and 3
partial matches.
Summary Information
   7 codes involving 10 elements
0 codes involving 9 elements
0 codes involving 8 elements
0 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
2 codes involving 4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
107777777777
90000000000
80000000000
70000000000
60000000000
50000000000
41111201100
30000000000
20000100010
12345678910
True Positives
O69760        O85821        POT1_HAEIN    POT2_HAEIN    
POTD_ECOLI POTF_ECOLI Q51848
True Positive Partials
Codes involving 4 elements
O51584 O83661
Codes involving 2 elements
O86741
Sequence Titles
O69760      PUTATIVE PUTRESCINE/SPERMIDINE BINDING PROTEIN - PSEUDOMONAS FLUORESCENS. 
O85821 POTD - ACTINOBACILLUS ACTINOMYCETEMCOMITANS (HAEMOPHILUS ACTINOMYCETEMCOMITANS).
POT1_HAEIN SPERMIDINE/PUTRESCINE-BINDING PERIPLASMIC PROTEIN 1 PRECURSOR (SPBP) - HAEMOPHILUS INFLUENZAE.
POT2_HAEIN SPERMIDINE/PUTRESCINE-BINDING PERIPLASMIC PROTEIN 2 PRECURSOR (SPBP) - HAEMOPHILUS INFLUENZAE.
POTD_ECOLI SPERMIDINE/PUTRESCINE-BINDING PERIPLASMIC PROTEIN PRECURSOR (SPBP) - ESCHERICHIA COLI.
POTF_ECOLI PUTRESCINE-BINDING PERIPLASMIC PROTEIN PRECURSOR - ESCHERICHIA COLI.
Q51848 LPP38 - PASTEURELLA HAEMOLYTICA.

O51584 SPERMIDINE/PUTRESCINE ABC TRANSPORTER, SPERMIDINE/PUTRESCINE-BINDING PERIPLASMIC PROTEIN (POTD) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
O83661 SPERMIDINE/PUTRESCINE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN (POTD) - TREPONEMA PALLIDUM.

O86741 PUTATIVE POLYAMINE-BINDING LIPOPROTEIN - STREPTOMYCES COELICOLOR.
Scan History
OWL30_1    1  100  NSINGLE    
SPTR37_9f 2 17 NSINGLE
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
YNWTDYVPSDLVAQFSK POT2_HAEIN 36 36 -
YNWTEYVPPGLLEQFTK POTD_ECOLI 32 32 -
YTWTEYVPDGLLDEFTK POT1_HAEIN 43 43 -
YNWSDYIAPDTVANFEK POTF_ECOLI 35 35 -
YTWTEYVPEGLLDEFTK PHU25682 47 47 -

Motif 2 width=22
Element Seqn Id St Int Rpt
KETGIKVIYSTYESNETMYAKL POTD_ECOLI 48 -1 -
KETGIEVIYSTFESNEEMYAKL POT2_HAEIN 52 -1 -
KETGIKVEVSSLESNETMYAKL PHU25682 63 -1 -
KETGIKVVYDVFDSNEVLEGKL POTF_ECOLI 51 -1 -
KETGIKVIVSSLESNETMYAKL POT1_HAEIN 59 -1 -

Motif 3 width=15
Element Seqn Id St Int Rpt
AYDLVVPSTYYVDKM POTD_ECOLI 76 6 -
GYDLVFPSSYYVNKM POT2_HAEIN 82 8 -
GFDLVVPSASFLERQ POTF_ECOLI 78 5 -
GYDVIAPSNYFVSKM POT1_HAEIN 88 7 -
GYDVIAPSNYFVSKM PHU25682 92 7 -

Motif 4 width=14
Element Seqn Id St Int Rpt
TAGVFQPLDKSKLP POTF_ECOLI 94 1 -
KEGMLAELDHAQLP PHU25682 108 1 -
REGMLKELDHSKLP POT1_HAEIN 104 1 -
KEGMIQKIDKSKLT POTD_ECOLI 92 1 -
KEKMLQPIDQSKLT POT2_HAEIN 98 1 -

Motif 5 width=17
Element Seqn Id St Int Rpt
NKFAMPYMWATTGIGYN POTF_ECOLI 127 19 -
NKYSLPQLLGAPGIAFN PHU25682 139 17 -
NKYSLPQLLGAPGIAFN POT1_HAEIN 135 17 -
NDYSIPYIWGATAIGVN POTD_ECOLI 123 17 -
NKYSLPYVYGLTGIEVN POT2_HAEIN 129 17 -

Motif 6 width=15
Element Seqn Id St Int Rpt
TSWADLWKPEFANKV POT1_HAEIN 161 9 -
TSWGDLWKPEFAGKV PHU25682 165 9 -
DSWDLILKPENLEKL POTF_ECOLI 158 14 -
TSWADLWKPEFKGKV POT2_HAEIN 155 9 -
TSWADLWKPEYKGSL POTD_ECOLI 149 9 -

Motif 7 width=20
Element Seqn Id St Int Rpt
DDAREVFNIALLKLGKNPNT PHU25682 183 3 -
DDAREVFNIALLKIGQDPNT POT1_HAEIN 179 3 -
DDAREVFQMALRKLGYSGNT POTD_ECOLI 167 3 -
SDAREVFHVALLLDGKSPNT POT2_HAEIN 173 3 -
DAPEEVFATVLNYLGKDPNS POTF_ECOLI 181 8 -

Motif 8 width=20
Element Seqn Id St Int Rpt
PNVATFNSDSPEVPYVQGEV POT2_HAEIN 210 17 -
PNIRYFHSSQYINDLANGDI POTF_ECOLI 219 18 -
PNVLSFTSDNPANSFIAGEV PHU25682 220 17 -
PNVLSFNSDNPANSFISGEV POT1_HAEIN 216 17 -
PNVAAFNSDNPANPYMEGEV POTD_ECOLI 204 17 -

Motif 9 width=20
Element Seqn Id St Int Rpt
PKEGAIFWMDNYAIPTTAKN POT2_HAEIN 254 24 -
PKEGPVLWVDTLAIPANAKN PHU25682 264 24 -
PKEGPVLWVDTLAIPATAKN POT1_HAEIN 260 24 -
PKEGGIFWMDSLAIPANAKN POTD_ECOLI 248 24 -
PKEGAMAFFDVFAMPADAKN POTF_ECOLI 269 30 -

Motif 10 width=27
Element Seqn Id St Int Rpt
YPTSNIEAKKALPKEITEDPAIYPSAD POT1_HAEIN 305 25 -
YANANKAATPLVSAEVRENPGIYPPAD POTF_ECOLI 314 25 -
FSMPNNGAKTLLSAEVANDPKLFPPAE POT2_HAEIN 299 25 -
YPTPNLAARKLLSPEVANDKTLYPDAE POTD_ECOLI 293 25 -
YPTSNVEALKVLPKEITEDTAIYPSAE PHU25682 309 25 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
YTWTEYVPDGLLDEFTK POT1_HAEIN 43 43 -
YTWTEYVPDGLLDEFTK O85821 48 48 -
YTWTEYVPEGLLDEFTK Q51848 47 47 -
YNWTEYVPPGLLEQFTK POTD_ECOLI 32 32 -
YNWTDYVPSDLVAQFSK POT2_HAEIN 36 36 -
YNWSDYIAPDTVANFEK POTF_ECOLI 35 35 -
YNWYDYIGPTTLQDFKR O69760 43 43 -

Motif 2 width=22
Element Seqn Id St Int Rpt
KETGIKVIVSSLESNETMYAKL POT1_HAEIN 59 -1 -
KETGIKVIVSSLESNETMYAKI O85821 64 -1 -
KETGIKVEVSSLESNETMYAKL Q51848 63 -1 -
KETGIKVIYSTYESNETMYAKL POTD_ECOLI 48 -1 -
KETGIEVIYSTFESNEEMYAKL POT2_HAEIN 52 -1 -
KETGIKVVYDVFDSNEVLEGKL POTF_ECOLI 51 -1 -
RETGIEPVYDTFDSGEVLEAKL O69760 59 -1 -

Motif 3 width=15
Element Seqn Id St Int Rpt
GYDVIAPSNYFVSKM POT1_HAEIN 88 7 -
GYDVIAPSNYFVSKM O85821 93 7 -
GYDVIAPSNYFVSKM Q51848 92 7 -
AYDLVVPSTYYVDKM POTD_ECOLI 76 6 -
GYDLVFPSSYYVNKM POT2_HAEIN 82 8 -
GFDLVVPSASFLERQ POTF_ECOLI 78 5 -
GYDVVVASNFILPAL O69760 86 5 -

Motif 4 width=14
Element Seqn Id St Int Rpt
REGMLKELDHSKLP POT1_HAEIN 104 1 -
REGMLKELDHSKLP O85821 109 1 -
KEGMLAELDHAQLP Q51848 108 1 -
KEGMIQKIDKSKLT POTD_ECOLI 92 1 -
KEKMLQPIDQSKLT POT2_HAEIN 98 1 -
TAGVFQPLDKSKLP POTF_ECOLI 94 1 -
KAGALQKLDRSQLP O69760 102 1 -

Motif 5 width=17
Element Seqn Id St Int Rpt
NKYSLPQLLGAPGIAFN POT1_HAEIN 135 17 -
NKYSLPQLLGAPGIAFN O85821 140 17 -
NKYSLPQLLGAPGIAFN Q51848 139 17 -
NDYSIPYIWGATAIGVN POTD_ECOLI 123 17 -
NKYSLPYVYGLTGIEVN POT2_HAEIN 129 17 -
NKFAMPYMWATTGIGYN POTF_ECOLI 127 19 -
NQYAIPYLWGTDGIGYN O69760 135 19 -

Motif 6 width=15
Element Seqn Id St Int Rpt
TSWADLWKPEFANKV POT1_HAEIN 161 9 -
TSWGDLWKPEFANKV O85821 166 9 -
TSWGDLWKPEFAGKV Q51848 165 9 -
TSWADLWKPEYKGSL POTD_ECOLI 149 9 -
TSWADLWKPEFKGKV POT2_HAEIN 155 9 -
DSWDLILKPENLEKL POTF_ECOLI 158 14 -
NSWDLLFKEENLAKL O69760 166 14 -

Motif 7 width=20
Element Seqn Id St Int Rpt
DDAREVFNIALLKIGQDPNT POT1_HAEIN 179 3 -
DDAREVFNIALLKIGQDPNT O85821 184 3 -
DDAREVFNIALLKLGKNPNT Q51848 183 3 -
DDAREVFQMALRKLGYSGNT POTD_ECOLI 167 3 -
SDAREVFHVALLLDGKSPNT POT2_HAEIN 173 3 -
DAPEEVFATVLNYLGKDPNS POTF_ECOLI 181 8 -
DAPAEIMPIALHYLGLPPNS O69760 189 8 -

Motif 8 width=20
Element Seqn Id St Int Rpt
PNVLSFNSDNPANSFISGEV POT1_HAEIN 216 17 -
PNVLSFNSDNPANSFISGEV O85821 221 17 -
PNVLSFTSDNPANSFIAGEV Q51848 220 17 -
PNVAAFNSDNPANPYMEGEV POTD_ECOLI 204 17 -
PNVATFNSDSPEVPYVQGEV POT2_HAEIN 210 17 -
PNIRYFHSSQYINDLANGDI POTF_ECOLI 219 18 -
PYITYFNSSKIGSDLANGDI O69760 226 17 -

Motif 9 width=20
Element Seqn Id St Int Rpt
PKEGPVLWVDTLAIPATAKN POT1_HAEIN 260 24 -
PKEGPVLWVDTLAIPVTSKN O85821 265 24 -
PKEGPVLWVDTLAIPANAKN Q51848 264 24 -
PKEGGIFWMDSLAIPANAKN POTD_ECOLI 248 24 -
PKEGAIFWMDNYAIPTTAKN POT2_HAEIN 254 24 -
PKEGAMAFFDVFAMPADAKN POTF_ECOLI 269 30 -
PVEGAPLWSDNLVLVKDGSH O69760 276 30 -

Motif 10 width=27
Element Seqn Id St Int Rpt
YPTSNIEAKKALPKEITEDPAIYPSAD POT1_HAEIN 305 25 -
YPTANLEAKKALPKEITEDSAIYPSAD O85821 310 25 -
YPTSNVEALKVLPKEITEDTAIYPSAE Q51848 309 25 -
YPTPNLAARKLLSPEVANDKTLYPDAE POTD_ECOLI 293 25 -
FSMPNNGAKTLLSAEVANDPKLFPPAE POT2_HAEIN 299 25 -
YANANKAATPLVSAEVRENPGIYPPAD POTF_ECOLI 314 25 -
TANANKDATALVSAEVNDNPNIYPTAQ O69760 321 25 -