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PR00151

Identifier
PORPHBDMNASE  [View Relations]  [View Alignment]  
Accession
PR00151
No. of Motifs
5
Creation Date
09-MAR-1995  (UPDATE 07-JUN-1999)
Title
Porphobilinogen deaminase signature
Database References

PROSITE; PS00533 PORPHOBILINOGEN_DEAM
BLOCKS; BL00533
PFAM; PF01379 Porphobil_deam
INTERPRO; IPR000860
PDB; 1PDA
SCOP; 1PDA
CATH; 1PDA
Literature References
1. LOUIE, G.V.
Porphobilinogen deaminase and its structural similarity to the bidomain
binding proteins.
CURR.OPIN.STRUCT.BIOL. 3 401-408 (1993).

Documentation
Porphobilinogen deaminase (PBGD), or hydroxymethylbilane synthase, is the
third enzyme in the biosynthetic pathway of tetrapyrroles, which include
the vitally important macrocyles haem, chlorophyll and corrin [1]. PBGD
catalyses the head-to-tail polymerisation of 4 molecules of porpho-
bilinogen to assemble the open chain tetrapyrole, hydroxymethylbilane.
 
PBGD is a ubiquitously occurring, monomeric protein, showing high sequence
conservation among proteins from bacteria, fungi, plants and mammals. The
protein contains a dipyrromethane cofactor, which is covalently attached
to a cysteine side chain. The structure of PBGD shows the same chain fold
as proteins from 2 classes of binding protein: the transferrins and the
group-II periplasmic receptors (the sulphate-, phosphate-, maltodextrin-
and lysine/arginine/ornithine-binding proteins). Despite structural
similarities, there is no significant identity between their sequences.
 
PORPHBDMNASE is a 5-element fingerprint that provides a signature for
porphobilinogen deaminases. The fingerprint was derived from an initial
alignment of 6 sequences: the motifs were drawn from conserved regions
spanning the full alignment length, motif 5 including the region encoded
by PROSITE pattern PORPHOBILINOGEN_DEAM (PS00533), which contains the
conserved Cys residue responsible for cofactor binding. Two iterations
on OWL25.2 were required to reach convergence, at which point a true
set comprising 16 sequences was identified. Two partial matches were
also found, NRL_1PDA2 and HEM3_YERIN, both PBGD fragments, lacking the
first and final motifs respectively. 
 
An update on SPTR37_9f identified a true set of 21 sequences, and 4
partial matches.
Summary Information
  21 codes involving  5 elements
3 codes involving 4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
52121212121
403333
300000
200110
12345
True Positives
HEM3_ARATH    HEM3_BACSU    HEM3_CHLVI    HEM3_CLOJO    
HEM3_ECOLI HEM3_EUGGR HEM3_HELPY HEM3_HUMAN
HEM3_METJA HEM3_MOUSE HEM3_PEA HEM3_PROMI
HEM3_PSEAE HEM3_RAT HEM3_SYNY3 HEM3_YEAST
O26960 O29026 O34090 O66621
O69110
True Positive Partials
Codes involving 4 elements
HEM3_MYCTU P78887 Q49808
Codes involving 2 elements
O84301
Sequence Titles
HEM3_ARATH  PORPHOBILINOGEN DEAMINASE PRECURSOR (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS). 
HEM3_BACSU PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - BACILLUS SUBTILIS.
HEM3_CHLVI PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - CHLOROBIUM VIBRIOFORME.
HEM3_CLOJO PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - CLOSTRIDIUM JOSUI.
HEM3_ECOLI PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - ESCHERICHIA COLI.
HEM3_EUGGR PORPHOBILINOGEN DEAMINASE PRECURSOR (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - EUGLENA GRACILIS.
HEM3_HELPY PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
HEM3_HUMAN PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - HOMO SAPIENS (HUMAN).
HEM3_METJA PROBABLE PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - METHANOCOCCUS JANNASCHII.
HEM3_MOUSE PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - MUS MUSCULUS (MOUSE).
HEM3_PEA PORPHOBILINOGEN DEAMINASE PRECURSOR (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - PISUM SATIVUM (GARDEN PEA).
HEM3_PROMI PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - PROTEUS MIRABILIS.
HEM3_PSEAE PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - PSEUDOMONAS AERUGINOSA.
HEM3_RAT PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - RATTUS NORVEGICUS (RAT).
HEM3_SYNY3 PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
HEM3_YEAST PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
O26960 PORPHOBILINOGEN DEAMINASE - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O29026 PORPHOBILINOGEN DEAMINASE (HEMC) - ARCHAEOGLOBUS FULGIDUS.
O34090 PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) - STAPHYLOCOCCUS AUREUS.
O66621 PORPHOBILINOGEN DEAMINASE - AQUIFEX AEOLICUS.
O69110 PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) - PAENIBACILLUS MACERANS (BACILLUS MACERANS).

HEM3_MYCTU PORPHOBILINOGEN DEAMINASE (EC 4.3.1.8) (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE) - MYCOBACTERIUM TUBERCULOSIS.
P78887 FISSION YEAST - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
Q49808 HEM3B - MYCOBACTERIUM LEPRAE.

O84301 PORPHOBILINOGEN DEAMINASE - CHLAMYDIA TRACHOMATIS.
Scan History
OWL25_2    2  100  NSINGLE    
SPTR37_9f 2 33 NSINGLE
Initial Motifs
Motif 1  width=21
Element Seqn Id St Int Rpt
GDKILDSPLAKVGGKGLFVKE HEM3_EUGGR 191 191 -
GDKILDTALSKIGEKSLFTKE HEM3_HUMAN 60 60 -
GDKIVDTALSKIGEKSLFTKE HEM3_MOUSE 60 60 -
GDVILDTPLAKVGGKGLFVKE HEM3_ECOLI 45 45 -
GDRIVDVTLSKVGGKGLFVKE HEM3_BACSU 44 44 -
GDQIQFKPLYSFGGKALWTKE HEM3_YEAST 45 45 -

Motif 2 width=20
Element Seqn Id St Int Rpt
DIAVHSTKDVPMELPEGLVL HEM3_EUGGR 222 10 -
DLVVHSLKDLPTVLPPGFTI HEM3_HUMAN 91 10 -
DLVVHSLKDVPTILPPGFTI HEM3_MOUSE 91 10 -
DIAVHSMKDVPVEFPQGLGL HEM3_ECOLI 76 10 -
DMAVHSMKDMPAVLPEGLVI HEM3_BACSU 75 10 -
DLIVHSLKDMPTLLPEGFEL HEM3_YEAST 80 14 -

Motif 3 width=18
Element Seqn Id St Int Rpt
RVGTSSLRRQCQLLLKRP HEM3_EUGGR 273 31 -
VVGTSSLRRAAQLQRKFP HEM3_HUMAN 142 31 -
AVGTSSLRRVAQLQRKFP HEM3_MOUSE 142 31 -
IVGTSSLRRQCQLAERRP HEM3_ECOLI 124 28 -
VIGTSSLRRSAQLLIERP HEM3_BACSU 123 28 -
IVGTSSVRRSAQLKRKYP HEM3_YEAST 131 31 -

Motif 4 width=18
Element Seqn Id St Int Rpt
LKFLELRGNVNTRLAKLD HEM3_EUGGR 292 1 -
LEFRSIRGNLNTRLRKLD HEM3_HUMAN 161 1 -
LEFKSIRGNLNTRLRKLD HEM3_MOUSE 161 1 -
LIIRSLRGNVGTRLSKLD HEM3_ECOLI 143 1 -
LTIKWIRGNIDTRLQKLE HEM3_BACSU 142 1 -
LKFESVRGNIQTRLQKLD HEM3_YEAST 150 1 -

Motif 5 width=18
Element Seqn Id St Int Rpt
CERAMNRRLNGGCQVPIS HEM3_EUGGR 383 73 -
AERAFLRHLEGGCSVPVA HEM3_HUMAN 249 70 -
AERAFLRHLEGGCSVPVA HEM3_MOUSE 249 70 -
AERAMNTRLEGACQVPIG HEM3_ECOLI 230 69 -
AERAFLNAMEGGCQVPIA HEM3_BACSU 230 70 -
SERALMRTLEGGCSVPIG HEM3_YEAST 239 71 -
Final Motifs
Motif 1  width=21
Element Seqn Id St Int Rpt
GDIILDTPLAKVGGKGLFVKE HEM3_PROMI 45 45 -
GDKILDSPLAKVGGKGLFVKE HEM3_EUGGR 191 191 -
GDKILDTALSKIGEKSLFTKE HEM3_RAT 60 60 -
GDKILDTALSKIGEKSLFTKE HEM3_HUMAN 60 60 -
GDKILDVALAKIGDKGLFTQE HEM3_SYNY3 49 49 -
GDKIVDTALSKIGEKSLFTKE HEM3_MOUSE 60 60 -
GDVILDTPLAKVGGKGLFVKE HEM3_ECOLI 45 45 -
GDKLLDAPLAKIGGKGLFVKE HEM3_PSEAE 46 46 -
GDRIVDVTLSKVGGKGLFVKE HEM3_BACSU 44 44 -
GDKITDVPLAKIGGKGLFVKE O66621 60 60 -
GDRILDVTLSKIGGKGLFVKE O69110 49 49 -
GDRIVDKQLSKVGGKGLFVKE O34090 43 43 -
GDKILDTPLNKIGGKGLFTKE HEM3_HELPY 42 42 -
GDQIQFKPLYSFGGKALWTKE HEM3_YEAST 45 45 -
GDKILSQPLADIGGKGLFTKE HEM3_ARATH 118 118 -
GDKILSQPLADIGGKGLFTKE HEM3_PEA 105 105 -
GDVLLDSPLSKIGDMGLFTKD HEM3_CHLVI 12 12 -
GDKILDKTLDKIEGKGLFVKE HEM3_CLOJO 47 47 -
GDIMKDKPLYEFKGMGAFVRA O29026 39 39 -
GDRVLDKKLSDIGIGVFTKEL HEM3_METJA 39 39 -
GDRIRDSQLYSMDSRGLFTRE O26960 39 39 -

Motif 2 width=20
Element Seqn Id St Int Rpt
DIAVHSMKDVPIDFPEGLGL HEM3_PROMI 76 10 -
DIAVHSTKDVPMELPEGLVL HEM3_EUGGR 222 10 -
DLVVHSLKDVPTILPPGFTI HEM3_RAT 91 10 -
DLVVHSLKDLPTVLPPGFTI HEM3_HUMAN 91 10 -
DLAVHSLKDLPTNLPAGLML HEM3_SYNY3 80 10 -
DLVVHSLKDVPTILPPGFTI HEM3_MOUSE 91 10 -
DIAVHSMKDVPVEFPQGLGL HEM3_ECOLI 76 10 -
DIAVHSMKDVPMDFPEGLGL HEM3_PSEAE 77 10 -
DMAVHSMKDMPAVLPEGLVI HEM3_BACSU 75 10 -
DLAVHSLKDVPMVIPKGLKL O66621 91 10 -
DMAVHSMKDMPSVLPEGLIN O69110 80 10 -
DMAIHSLKDVPSVIPEGLTL O34090 74 10 -
DLAVHSLKDVPVVFEKGLDL HEM3_HELPY 73 10 -
DLIVHSLKDMPTLLPEGFEL HEM3_YEAST 80 14 -
DIAVHSMKDVPTYLPEKTIL HEM3_ARATH 149 10 -
DIAVHSMKDVPTYLPEETIL HEM3_PEA 136 10 -
DLAVHSLKDVPTVRRKAWLS HEM3_CHLVI 43 10 -
DITVHSYKDMPLEENPELPV HEM3_CLOJO 78 10 -
DVAVHSFKDVPSQRVEGTVV O29026 70 10 -
DIAVHSLKDIPTIWNENLMV HEM3_METJA 69 9 -
DLAVHSLKDVPSDLDPDLAI O26960 70 10 -

Motif 3 width=18
Element Seqn Id St Int Rpt
VVGTSSLRRQCQLKALRP HEM3_PROMI 124 28 -
RVGTSSLRRQCQLLLKRP HEM3_EUGGR 273 31 -
AVGTSSLRRVAQLQRKFP HEM3_RAT 142 31 -
VVGTSSLRRAAQLQRKFP HEM3_HUMAN 142 31 -
VIGTSSLRRLAQLRYHFP HEM3_SYNY3 131 31 -
AVGTSSLRRVAQLQRKFP HEM3_MOUSE 142 31 -
IVGTSSLRRQCQLAERRP HEM3_ECOLI 124 28 -
VVGTSRLGRQAQLLARRP HEM3_PSEAE 125 28 -
VIGTSSLRRSAQLLIERP HEM3_BACSU 123 28 -
VIGTSSLRRQVQIKKRRR O66621 139 28 -
RVGTSTLRRSSQLLAYRP O69110 128 28 -
IIGTSSLRRGAQILSKYP O34090 122 28 -
KVGTTSLRRSMQIKLKRQ HEM3_HELPY 121 28 -
IVGTSSVRRSAQLKRKYP HEM3_YEAST 131 31 -
VVGTASLRRKSQILHKYP HEM3_ARATH 197 28 -
VIGTASLRRKSQILHRYP HEM3_PEA 184 28 -
KMATSSLRRMSQLLSLRP HEM3_CHLVI 90 27 -
PIGSSSLRRQLQLKELFP HEM3_CLOJO 121 23 -
VVGTSSLRRRAQLSRLRG O29026 118 28 -
VIGTSSMRRRAFLKFIYP HEM3_METJA 116 27 -
KLGTSSLRREAFCNHHQK O26960 116 26 -

Motif 4 width=18
Element Seqn Id St Int Rpt
LIIRDLRGNVGTRLSKLD HEM3_PROMI 143 1 -
LKFLELRGNVNTRLAKLD HEM3_EUGGR 292 1 -
LEFKSIRGNLNTRLRKLD HEM3_RAT 161 1 -
LEFRSIRGNLNTRLRKLD HEM3_HUMAN 161 1 -
LTFKDVRGNVNTRLAKLD HEM3_SYNY3 150 1 -
LEFKSIRGNLNTRLRKLD HEM3_MOUSE 161 1 -
LIIRSLRGNVGTRLSKLD HEM3_ECOLI 143 1 -
LQIRFLRGNVNTRLAKLD HEM3_PSEAE 144 1 -
LTIKWIRGNIDTRLQKLE HEM3_BACSU 142 1 -
LKVEVLRGNVDTRMRKLK O66621 158 1 -
LVLEPVRGNIDSRLRKLE O69110 147 1 -
LEIKWIRGNIDTRLEKLQ O34090 141 1 -
LDTESLRGNVQTRLKKLE HEM3_HELPY 140 1 -
LKFESVRGNIQTRLQKLD HEM3_YEAST 150 1 -
HVEENFRGNVQTRLSKLQ HEM3_ARATH 217 2 -
TVQDNFRGNVQTRLRKLS HEM3_PEA 204 2 -
LEIMDIRGNLNTRFKKFD HEM3_CHLVI 109 1 -
CKTAPIRGNVQTRLKKLD HEM3_CLOJO 140 1 -
LRFENLRGNLDTRLRKLR O29026 137 1 -
AKFELLRGNVDTRLRKLK HEM3_METJA 135 1 -
FKMEPLRGNIDTRIRKVM O26960 135 1 -

Motif 5 width=18
Element Seqn Id St Int Rpt
AERAMNTRLEGGCQVPIG HEM3_PROMI 230 69 -
CERAMNRRLNGGCQVPIS HEM3_EUGGR 383 73 -
AERAFLRHLEGGCSVPVA HEM3_RAT 249 70 -
AERAFLRHLEGGCSVPVA HEM3_HUMAN 249 70 -
AERAFLRQLEGGCQVPIG HEM3_SYNY3 237 69 -
AERAFLRHLEGGCSVPVA HEM3_MOUSE 249 70 -
AERAMNTRLEGACQVPIG HEM3_ECOLI 230 69 -
AERALNKRLNGGCQVPIA HEM3_PSEAE 231 69 -
AERAFLNAMEGGCQVPIA HEM3_BACSU 230 70 -
AERTFLRRLEGGCQVPVG O66621 243 67 -
AERRFLAVLNGGCQVPIA O69110 234 69 -
AERTFLAEMDGSCQVPIA O34090 229 70 -
LEREFIKGLNGGCQIPIG HEM3_HELPY 227 69 -
SERALMRTLEGGCSVPIG HEM3_YEAST 239 71 -
CERAFLETLDGSCRTPIA HEM3_ARATH 304 69 -
CERAFLTTLDGSCRTPIA HEM3_PEA 291 69 -
AERALLRHLQGGCQIPIG HEM3_CHLVI 196 69 -
AERTFVREMNGGCSTPIA HEM3_CLOJO 225 67 -
VERAVIKELGVGCAVPVG O29026 222 67 -
CERTALNEFGGGCSVPFG HEM3_METJA 221 68 -
AEKTLLRELGAGCQCPLG O26960 221 68 -