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PR01181

Identifier
DAPDCRBXLASE  [View Relations]  [View Alignment]  
Accession
PR01181
No. of Motifs
4
Creation Date
18-SEP-1999
Title
Diaminopimelate decarboxylase signature
Database References
PRINTS; PR01179 ODADCRBXLASE
INTERPRO; IPR002986
Literature References
1. MARTIN, C., CAMI, B., YEH, P., STRAGIER, P., PARSOT, C. AND PATTE, J.-C.
Pseudomonas aeruginosa diaminopimelate decarboxylase: evolutionary 
relationship with other amino acid decarboxylases.
MOL.BIOL.EVOL. 5 549-559 (1988).
 
2. SANDMEIER, E., HALE, T.I. AND CHRISTEN, P.
Multiple evolutionary origin of pyridoxal-5'-phosphate-dependent amino acid
decarboxylases. 
EUR.J.BIOCHEMISTRY 221 997-1002 (1994).
 
3. MILLS, D.A. AND FLICKINGER, M.C.
Cloning and sequence analysis of the meso-diaminopimelate decarboxylase gene
from Bacillus methanolicus MGA3 and comparison to other decarboxylase genes.
APPL.ENVIRON.MICROBIOL. 59 2927-2937( 1993). 
 
4. POULIN, R., LU, L., ACKERMANN, B., BEY, P. AND PEGG, A.E.
Mechanism of the irreversible inactivation of mouse ornithine decarboxylase
by alpha-difluoromethylornithine. Characterization of sequences at the
inhibitor and coenzyme binding sites.
J.BIOL.CHEM. 267 150-158 (1992).

Documentation
Pyridoxal-dependent decarboxylases that act on ornithine-, lysine-, 
arginine- and related substrates can be classified into different families
on the basis of sequence similarity [1,2]. One of these families includes:
eukaryotic ornithine decarboxylase (ODC), which catalyses the transformation
of ornithine into putrescine; prokaryotic diaminopimelic acid decarboxylase
(DAPDC), which catalyses the conversion of diaminopimelic acid into lysine,
the final step of lysine biosynthesis; Pseudomonas syringae pv. tabaci
protein, tabA, which is probably involved in tabtoxin biosynthesis and
is similar to DAPDC; and bacterial and plant biosynthetic arginine
decarboxylase (ADC), which catalyses the transformation of arginine 
into agmatine, the first step in putrescine synthesis from arginine.
 
Although these proteins, which are known collectively as group IV
decarboxylases [2], probably share a common evolutionary origin, their
levels of sequence similarity are low, being confined to a few short
conserved regions. These conserved motifs suggest a common structural
arrangement for positioning of substrate and the cofactor pyridoxal
5'-phosphate among bacterial DAP decarboxylases, eukaryotic ornithine
decarboxylases and arginine decarboxylases [3]. 
 
DAPDCRBXLASE is a 4-element fingerprint that provides a signature for
diaminopimelate decarboxylases. The fingerprint was derived from an initial
alignment of 6 sequences: the motifs were drawn from conserved regions
spanning virtually the full alignment length, focusing on those sections
that characterise the diaminopimelate decarboxylases but distinguish them
from the rest of the ODA family. Four iterations on SPTR37_10f were required
to reach convergence, at which point a true set comprising 19 sequences was
identified. A single partial match was found, TABA_PSESZ, Pseudomonas
syringae tabA protein, which matches motifs 3 and 4.
Summary Information
  19 codes involving  4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
419191919
30000
20000
1234
True Positives
DCDA_BACMT    DCDA_BACSU    DCDA_CORGL    DCDA_ECOLI    
DCDA_HAEIN DCDA_HELPY DCDA_METJA DCDA_MYCTU
DCDA_PSEAE DCDA_PSEFL DCDA_SYNY3 O27390
O29458 O67262 O69203 Q50140
Q9Z661 Q9ZBH5 Q9ZME5
True Positive Partials
Codes involving 2 elements
TABA_PSESZ
Sequence Titles
DCDA_BACMT  DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) (DAP DECARBOXYLASE) - BACILLUS METHA 
DCDA_BACSU DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) (DAP DECARBOXYLASE) - BACILLUS SUBTI
DCDA_CORGL DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) (DAP DECARBOXYLASE) - CORYNEBACTERIU
DCDA_ECOLI DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) (DAP DECARBOXYLASE) - ESCHERICHIA CO
DCDA_HAEIN DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) (DAP DECARBOXYLASE) - HAEMOPHILUS IN
DCDA_HELPY DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) (DAP DECARBOXYLASE) - HELICOBACTER P
DCDA_METJA DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) (DAP DECARBOXYLASE) - METHANOCOCCUS
DCDA_MYCTU DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) (DAP DECARBOXYLASE) - MYCOBACTERIUM
DCDA_PSEAE DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) (DAP DECARBOXYLASE) - PSEUDOMONAS AE
DCDA_PSEFL DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) (DAP DECARBOXYLASE) - PSEUDOMONAS FL
DCDA_SYNY3 DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) (DAP DECARBOXYLASE) - SYNECHOCYSTIS
O27390 DIAMINOPIMELATE DECARBOXYLASE - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O29458 DIAMINOPIMELATE DECARBOXYLASE (LYSA) - ARCHAEOGLOBUS FULGIDUS.
O67262 DIAMINOPIMELATE DECARBOXYLASE - AQUIFEX AEOLICUS.
O69203 DIAMINOPIMELATE DECARBOXYLASE - ACTINOSYNNEMA PRETIOSUM AURANTICUM.
Q50140 LYSA - MYCOBACTERIUM LEPRAE.
Q9Z661 DIAMINOPIMELATE DECARBOXYLASE - ZYMOMONAS MOBILIS.
Q9ZBH5 DIAMINOPIMELATE DECARBOXYLASE - STREPTOMYCES COELICOLOR.
Q9ZME5 DIAMINOPIMELATE DECARBOXYLASE - HELICOBACTER PYLORI J99.

TABA_PSESZ TABA PROTEIN - PSEUDOMONAS SYRINGAE (PV. TABACI).
Scan History
SPTR37_10f 4  20   NSINGLE    
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
GLSLDVVSGGELYTALVA DCDA_BACMT 81 81 -
GSGFDIVSQGELERVLAA DCDA_HAEIN 75 75 -
GAGFDIVSRGELERVLAA DCDA_PSEAE 75 75 -
GVKVDSVSLGEIERALAA DCDA_ECOLI 69 69 -
GLGFDVVSGGELFTTVSA DCDA_SYNY3 108 108 -
GLALDIASINELGIALAA DCDA_CORGL 90 90 -

Motif 2 width=10
Element Seqn Id St Int Rpt
TGQEDSKFGF DCDA_BACMT 170 71 -
TGLKENKFGV DCDA_HAEIN 164 71 -
TGLKENKFGI DCDA_PSEAE 164 71 -
TGGENSKHGI DCDA_ECOLI 157 70 -
TGHLDSKFGF DCDA_SYNY3 204 78 -
TSHEDQKFGF DCDA_CORGL 179 71 -

Motif 3 width=19
Element Seqn Id St Int Rpt
RHYVAVDGGMSDNIRPALY DCDA_BACMT 316 136 -
RNFAITDTGMNDMIRPALY DCDA_HAEIN 299 125 -
KDFAIVDAAMNDLIRPALY DCDA_PSEAE 298 124 -
RHFVLVDAGFNDLMRPAMY DCDA_ECOLI 293 126 -
RTYISVDGGMSDNPRPITY DCDA_SYNY3 347 133 -
RRYIAVDGGMSDNIRPALY DCDA_CORGL 329 140 -

Motif 4 width=23
Element Seqn Id St Int Rpt
YNRIPRPAVVFVENGESMLVVKR DCDA_BACMT 398 63 -
YNSRARTAEVLVDGDQSYLIRRR DCDA_HAEIN 380 62 -
YNTRGRAAEVLVDGQQTHEVRRR DCDA_PSEAE 378 61 -
YNSRPLLPEVLFDNGQARLIRRR DCDA_ECOLI 386 74 -
YNRLGRPAAVLVNQGQANLILQR DCDA_SYNY3 429 63 -
YNAFTRPAVVSVRAGSSRLMLRR DCDA_CORGL 412 64 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
GLSLDVVSGGELYTAVAA DCDA_BACSU 83 83 -
GLSLDVVSGGELYTALVA DCDA_BACMT 81 81 -
GAGFDIVSGGELERVLAA DCDA_PSEFL 75 75 -
GSGFDIVSQGELERVLAA DCDA_HAEIN 75 75 -
GAGFDIVSRGELERVLAA DCDA_PSEAE 75 75 -
GAGADIVSGGELYLAKKA O67262 80 80 -
GSGIDAVSPGEIYTALMA O27390 79 79 -
GSGADCVSIGEIQRALKA Q9ZME5 61 61 -
GLSLDVCSGGELAVALHA Q50140 135 135 -
GVKVDSVSLGEIERALAA DCDA_ECOLI 69 69 -
GFGADVFSDGELYLASLA O29458 71 71 -
ESGADCVSIGEIYRALKA DCDA_HELPY 61 61 -
GVHVDAVSEGEIERALAA Q9ZBH5 76 76 -
GLGADVVSAGEIRRAVHA Q9Z661 78 78 -
GLCLDVCTGGELAVALHA DCDA_MYCTU 87 87 -
GLGFDVVSGGELFTTVSA DCDA_SYNY3 108 108 -
GLSLDVCSAGELAIARSV O69203 96 96 -
GLALDIASINELGIALAA DCDA_CORGL 90 90 -
GCGADVVSGGELYIAKLS DCDA_METJA 88 88 -

Motif 2 width=10
Element Seqn Id St Int Rpt
TGQEDSKFGF DCDA_BACSU 172 71 -
TGQEDSKFGF DCDA_BACMT 170 71 -
TGLKENKFGI DCDA_PSEFL 165 72 -
TGLKENKFGV DCDA_HAEIN 164 71 -
TGLKENKFGI DCDA_PSEAE 164 71 -
TGMQKSKFGV O67262 169 71 -
TGGEMSKFGV O27390 164 67 -
TGLKENKFGV Q9ZME5 150 71 -
TAHEDQKFGL Q50140 224 71 -
TGGENSKHGI DCDA_ECOLI 157 70 -
TGLRESKFGI O29458 159 70 -
TGLKENKFGV DCDA_HELPY 150 71 -
TGGEHSKHGI Q9ZBH5 164 70 -
TGKADTKFGI Q9Z661 167 71 -
TAHEDQKFGL DCDA_MYCTU 176 71 -
TGHLDSKFGF DCDA_SYNY3 204 78 -
TGVEDQKFGF O69203 182 68 -
TSHEDQKFGF DCDA_CORGL 179 71 -
TGLKKNKFGL DCDA_METJA 177 71 -

Motif 3 width=19
Element Seqn Id St Int Rpt
RQYVAVDGGMNDNIRPALY DCDA_BACSU 318 136 -
RHYVAVDGGMSDNIRPALY DCDA_BACMT 316 136 -
KDFAIVDAAMNDLIRPALY DCDA_PSEFL 299 124 -
RNFAITDTGMNDMIRPALY DCDA_HAEIN 299 125 -
KDFAIVDAAMNDLIRPALY DCDA_PSEAE 298 124 -
KHFIIVDAGMNDLIRPSIY O67262 304 125 -
RKFAGVDAGFNTLLRPAMY O27390 305 131 -
KRFVIVDAGMNDFLRPSLY Q9ZME5 284 124 -
RRYVSIDGGMSDNIRTALY Q50140 378 144 -
RHFVLVDAGFNDLMRPAMY DCDA_ECOLI 293 126 -
KNFVAVDAGFNVLIRPAMY O29458 298 129 -
KRFVVVDAGMNDFLRPSLY DCDA_HELPY 284 124 -
NYFVLVDAGFNDLMRPAMY Q9ZBH5 300 126 -
ARFVILDAAMNDLVRPTLY Q9Z661 303 126 -
RRYVSVDGGMSDNIRTALY DCDA_MYCTU 330 144 -
RTYISVDGGMSDNPRPITY DCDA_SYNY3 347 133 -
RVFVAVDGGMSDNPRPALY O69203 323 131 -
RRYIAVDGGMSDNIRPALY DCDA_CORGL 329 140 -
TKWVMIDAGMNDMMRPAMY DCDA_METJA 319 132 -

Motif 4 width=23
Element Seqn Id St Int Rpt
YNRIPRPAVVFVENGEAHLVVKR DCDA_BACSU 400 63 -
YNRIPRPAVVFVENGESMLVVKR DCDA_BACMT 398 63 -
YNTRGRCAEVLVDGDQAFEVRRR DCDA_PSEFL 379 61 -
YNSRARTAEVLVDGDQSYLIRRR DCDA_HAEIN 380 62 -
YNTRGRAAEVLVDGQQTHEVRRR DCDA_PSEAE 378 61 -
YNMRPRAAEVLVENGSVKLIRKR O67262 385 62 -
YNSRPRPAEVLVREGKVDVVRER O27390 387 63 -
YNSRPKLLELALEDHKIRVIRKR Q9ZME5 366 63 -
YNMLGRPAVVAVCAGQARLILRR Q50140 461 64 -
YNSRPLLPEVLFDNGQARLIRRR DCDA_ECOLI 386 74 -
YNGRPRCAEVLVSGDRWDVIREK O29458 380 63 -
YNSRPKLLELALEDHKIRVIRKR DCDA_HELPY 366 63 -
YNSRPLIPEVLVDGAETRLIRRR Q9ZBH5 392 73 -
YNSRPLVAEVMVSGNKSALIRKR Q9Z661 383 61 -
YNMVGRPAVVAVHAGNARLVLRR DCDA_MYCTU 413 64 -
YNRLGRPAAVLVNQGQANLILQR DCDA_SYNY3 429 63 -
YNAVGRPPVVGVRDGVARVLVRR O69203 404 62 -
YNAFTRPAVVSVRAGSSRLMLRR DCDA_CORGL 412 64 -
YNARGRPRMVLTSKKGVFLIRER DCDA_METJA 399 61 -