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PR00146

Identifier
DHPICSNTHASE  [View Relations]  [View Alignment]  
Accession
PR00146
No. of Motifs
4
Creation Date
09-MAR-1995  (UPDATE 07-JUN-1999)
Title
Dihydrodipicolinate synthase signature
Database References

PROSITE; PS00665 DHDPS_1; PS00666 DHDPS_2
PFAM; PF00701 DHDPS
INTERPRO; IPR002220
Literature References
1. MIRWALDT, C., KORNDORFER, I. AND HUBER, R.
The crystal structure of dihydropicolinate synthase from Escherichia coli
at 2.5A resolution.
J.MOL.BIOL. 246 227-239 (1995).

Documentation
Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis
via the diaminopimelate pathway of prokaryotes, some phycomycetes and
higher plants. The enzyme catalyses the condensation of L-aspartate-beta-
semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong
mechanism in which pyruvate binds to the enzyme by forming a Schiff-base
with a lysine residue [1].
 
The sequences of DHDPS from different sources are well-conserved. The
structure takes the form of a homotetramer, in which 2 monomers are
related by an approximate 2-fold symmetry [1]. Each monomer comprises
2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical
domain. The fold resembles that of N-acetylneuraminate lyase. The active
site lysine is located in the barrel domain, and has access via 2 channels
on the C-terminal side of the barrel.
 
DHPICSNTHASE is a 4-element fingerprint that provides a signature for
dihydropicolinate synthases. The fingerprint was derived from an initial
alignment of 6 sequences: the motifs were drawn from conserved regions
spanning virtually the full alignment length, motif 1 including the region
encoded by PROSITE pattern DHDPS_1 (PS00665) (the region containing the
active site lysine was not sufficiently well conserved to form part of
the fingerprint - cf. PROSITE pattern DHDPS_2 (PS00666)). Two iterations
on OWL25.2 were required to reach convergence, at which point a true
set comprising 10 sequences was identified.
 
An update on SPTR37_9f identified a true set of 30 sequences, and 3
partial matches.
Summary Information
  30 codes involving  4 elements
1 codes involving 3 elements
2 codes involving 2 elements
Composite Feature Index
430303030
31101
22101
1234
True Positives
DAP1_WHEAT    DAP2_WHEAT    DAPA_BACSU    DAPA_BRELA    
DAPA_COILA DAPA_CORGL DAPA_ECOLI DAPA_HAEIN
DAPA_MAIZE DAPA_METJA DAPA_PROMA DAPA_RICPR
DAPA_SYNY3 MOSA_RHIME NPL_ECOLI NPL_HAEIN
O08360 O22129 O25657 O26892
O29352 O33295 O58577 O67216
O86841 Q27818 Q42800 Q42948
YAGE_ECOLI YJHH_ECOLI
True Positive Partials
Codes involving 3 elements
O69782
Codes involving 2 elements
O54288 O85960
Sequence Titles
DAP1_WHEAT  DIHYDRODIPICOLINATE SYNTHASE 1 PRECURSOR (EC 4.2.1.52) (DHDPS) - TRITICUM AESTIVUM (WHEAT). 
DAP2_WHEAT DIHYDRODIPICOLINATE SYNTHASE 2 PRECURSOR (EC 4.2.1.52) (DHDPS) - TRITICUM AESTIVUM (WHEAT).
DAPA_BACSU DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52) (DHDPS) (VEGETATIVE PROTEIN 81) (VEG81) - BACILLUS SUBTILIS.
DAPA_BRELA DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52) (DHDPS) - BREVIBACTERIUM LACTOFERMENTUM.
DAPA_COILA DIHYDRODIPICOLINATE SYNTHASE PRECURSOR (EC 4.2.1.52) (DHDPS) - COIX LACHRYMA-JOBI (JOBS'TEARS).
DAPA_CORGL DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52) (DHDPS) - CORYNEBACTERIUM GLUTAMICUM (BREVIBACTERIUM FLAVUM).
DAPA_ECOLI DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52) (DHDPS) - ESCHERICHIA COLI.
DAPA_HAEIN DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52) (DHDPS) - HAEMOPHILUS INFLUENZAE.
DAPA_MAIZE DIHYDRODIPICOLINATE SYNTHASE PRECURSOR (EC 4.2.1.52) (DHDPS) - ZEA MAYS (MAIZE).
DAPA_METJA DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52) (DHDPS) - METHANOCOCCUS JANNASCHII.
DAPA_PROMA DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52) (DHDPS) - PROCHLOROCOCCUS MARINUS.
DAPA_RICPR DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52) (DHDPS) - RICKETTSIA PROWAZEKII.
DAPA_SYNY3 DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52) (DHDPS) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
MOSA_RHIME MOSA PROTEIN (EC 4.1.-.-) - RHIZOBIUM MELILOTI.
NPL_ECOLI N-ACETYLNEURAMINATE LYASE SUBUNIT (EC 4.1.3.3) (N-ACETYLNEURAMINIC ACID ALDOLASE) (N-ACETYLNEURAMINATE PYRUVATE LYASE) (NALASE) - ESCHERICHIA COLI.
NPL_HAEIN PROBABLE N-ACETYLNEURAMINATE LYASE SUBUNIT (EC 4.1.3.3) (N- ACETYLNEURAMINIC ACID ALDOLASE) (N-ACETYLNEURAMINATE PYRUVATE LYASE) (NALASE) - HAEMOPHILUS INFLUENZAE.
O08360 N-ACETYLNEURAMINATE LYASE (EC 4.1.3.3) (N-ACETYLNEURAMINIC ACID ALDOLASE) - CLOSTRIDIUM PERFRINGENS.
O22129 PUTATIVE DIHYDRODIPICOLINATE SYNTHASE - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O25657 DIHYDRODIPICOLINATE SYNTHETASE (DAPA) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
O26892 DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52) (DHDPS) - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O29352 DIHYDRODIPICOLINATE SYNTHASE (EC 4.2.1.52) (DHDPS) - ARCHAEOGLOBUS FULGIDUS.
O33295 DIHYDRODIPICOLINATE SYNTHASE - MYCOBACTERIUM TUBERCULOSIS.
O58577 287AA LONG HYPOTHETICAL DIHYDRODIPICOLINE SYNTHASE - PYROCOCCUS HORIKOSHII.
O67216 DIHYDRODIPICOLINATE SYNTHASE - AQUIFEX AEOLICUS.
O86841 PUTATIVE DIHYDRODIPICOLINATE SYNTHASE - STREPTOMYCES COELICOLOR.
Q27818 N-ACETYLNEURAMINATE LYASE (EC 4.1.3.3) (N-ACETYLNEURAMINIC ACID ALDOLASE) - TRICHOMONAS VAGINALIS.
Q42800 DIHYDRODIPICOLINATE SYNTHASE PRECURSOR (EC 4.2.1.52) (DHDPS) - GLYCINE MAX (SOYBEAN).
Q42948 DIHYDRODIPICOLINATE SYNTHASE PRECURSOR (EC 4.2.1.52) (DHDPS) - NICOTIANA TABACUM (COMMON TOBACCO).
YAGE_ECOLI HYPOTHETICAL 33.3 KD PROTEIN IN PERR-ARGF INTERGENIC REGION - ESCHERICHIA COLI.
YJHH_ECOLI HYPOTHETICAL 34.9 KD PROTEIN IN FECI-FIMB INTERGENIC REGION (F319) - ESCHERICHIA COLI.

O69782 DAPA - SINORHIZOBIUM MELILOTI.

O54288 2-KETO-3-DEOXY GLUCONATE ALDOLASE - SULFOLOBUS SOLFATARICUS.
O85960 1, 2-DIHYDROXYBENZYLPYRUVATE ALDOLASE - SPHINGOMONAS AROMATICIVORANS.
Scan History
OWL25_2    2  50   NSINGLE    
SPTR37_9f 2 36 NSINGLE
Initial Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
GAEGVIVGGTTGEGHLMSWDEH DAP2_WHEAT 110 110 -
GAEGVIVGGTTGEGHLMSWDEH DAP1_WHEAT 121 121 -
GAEGVIVGGTTGEGHLMSWDEH DAPA_MAIZE 113 113 -
GTDSLVVAGTTGESPTLSTEEK DAPA_BACSU 36 36 -
GTSAIVSVGTTGESATLNHDEH DAPA_ECOLI 35 35 -
GLDSLVLAGTTGESPTTTAAEK DAPA_CORGL 47 47 -

Motif 2 width=19
Element Seqn Id St Int Rpt
IKVIGNTGSNSTREAIHAS DAP2_WHEAT 146 14 -
IKVIGNTGSNSTREAVHAT DAP1_WHEAT 157 14 -
IKVIGNTGSNSTREAVHAT DAPA_MAIZE 149 14 -
VPVIAGTGSNNTKDSIKLT DAPA_BACSU 72 14 -
IPVIAGTGANATAEAISLT DAPA_ECOLI 71 14 -
AKLIAGVGTNNTRTSVELA DAPA_CORGL 83 14 -

Motif 3 width=17
Element Seqn Id St Int Rpt
VNPYYGKTSTAGLISHF DAP2_WHEAT 178 13 -
VNPYYGKTSTEGLISHF DAP1_WHEAT 189 13 -
INPYYGKTSAEGMISHF DAPA_MAIZE 181 13 -
VTPYYNKPSQEGMYQHF DAPA_BACSU 104 13 -
VTPYYNRPSQEGLYQHF DAPA_ECOLI 103 13 -
VTPYYSKPSQEGLLAHF DAPA_CORGL 115 13 -

Motif 4 width=18
Element Seqn Id St Int Rpt
GPTIIYNVPSRTGQDIPP DAP2_WHEAT 201 6 -
GPTIIYNVPSRTSQDIPP DAP1_WHEAT 212 6 -
GPTIIYNVPSRSAQDIPP DAPA_MAIZE 204 6 -
LPVMLYNVPGRTVASLAP DAPA_BACSU 129 8 -
LPQILYNVPSRTGCDLLP DAPA_ECOLI 128 8 -
VPICLYDIPGRSGIPIES DAPA_CORGL 140 8 -
Final Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
GAEGVIVGGTTGEGQLMSWDEH Q42948 92 92 -
GAEGVIVGGTTGEGQLMSWDEH O22129 98 98 -
GAEGVIVGGTTGEGHLMSWDEH DAP2_WHEAT 110 110 -
GSDGLVVCGTTGESPTLSWEEE DAPA_SYNY3 43 43 -
GAEGVIVGGTTGEGHLMSWDEH DAP1_WHEAT 121 121 -
GSDGLIVCGTTGESPTLSWEEQ DAPA_PROMA 45 45 -
GAEGVIVGGTTGEGQLMSWEEH Q42800 65 65 -
GAEGVIVGGTTGEGHLMSWDEH DAPA_COILA 110 110 -
GAEGVIVGGTTGEGHLMSWDEH DAPA_MAIZE 113 113 -
GTDSLVVAGTTGESPTLSTEEK DAPA_BACSU 36 36 -
GTSAIVSVGTTGESATLNHDEH DAPA_ECOLI 35 35 -
GVSGIVAVGTTGESPTLSHEEH DAPA_METJA 34 34 -
GTDAILVCGTTGESPTLTFEEH O67216 34 34 -
HVNALVPAGTTGEAATLSYEEH O29352 34 34 -
GSNALVSVGTTGESATLSIEEN DAPA_HAEIN 41 41 -
GSFGLVPCGTTGESPTLSKSEH MOSA_RHIME 34 34 -
GNDGLIINGTTGESPTTSDAEK O86841 44 44 -
GLDSLVLAGTTGESPTTTAAEK DAPA_BRELA 47 47 -
GLDSLVLAGTTGESPTTTAAEK DAPA_CORGL 47 47 -
GVDGLLVAGTTGESATITHEEQ O26892 36 36 -
GCDGLVVSGTTGESPTTTDGEK O33295 45 45 -
GMDACVPVGTTGESATLTHKEH O25657 35 35 -
GVDGLFFLGSGGEFSQLGAEER YAGE_ECOLI 47 47 -
GVDGLFYLGTGGEFSQMNTAQR YJHH_ECOLI 55 55 -
KIDAVLIAGSTGEANSLSFEEY DAPA_RICPR 37 37 -
GIDGLYVGGSTGEAFVQSLSER NPL_ECOLI 37 37 -
KVDGLYVGGSTGENFMLSTEEK NPL_HAEIN 38 38 -
KIDGLYVGGSTGENFELSTEEK Q27818 63 63 -
GVHGIFINSTTGEFTSLSLEER O58577 34 34 -
KIDGLYVGGSTGENFMLSTDEK O08360 35 35 -

Motif 2 width=19
Element Seqn Id St Int Rpt
IKVIGNTGSNSTREAIHAT Q42948 128 14 -
IKVIGNTGSNSTREAIHAT O22129 134 14 -
IKVIGNTGSNSTREAIHAS DAP2_WHEAT 146 14 -
GSVIAGTGSNCTREAMEAT DAPA_SYNY3 79 14 -
IKVIGNTGSNSTREAVHAT DAP1_WHEAT 157 14 -
AKVLPGTGSNSTSEAIHAT DAPA_PROMA 81 14 -
IKVIGNTGSNSTREAIHAT Q42800 101 14 -
IKVIGNTGSNSTREAVHAT DAPA_COILA 146 14 -
IKVIGNTGSNSTREAVHAT DAPA_MAIZE 149 14 -
VPVIAGTGSNNTKDSIKLT DAPA_BACSU 72 14 -
IPVIAGTGANATAEAISLT DAPA_ECOLI 71 14 -
VQVIAGAGSNCTEEAIELS DAPA_METJA 70 14 -
IKVIAGTGGNATHEAVHLT O67216 70 14 -
LPVIGGAGSNSTREAIWLA O29352 68 12 -
IPIIAGAGANATSEAITMT DAPA_HAEIN 77 14 -
VPVIAGAGSNSTAEAIAFV MOSA_RHIME 70 14 -
AHVVAGVGTNNTQHSIELA O86841 80 14 -
AKLIAGVGTNNTRTSVELA DAPA_BRELA 83 14 -
AKLIAGVGTNNTRTSVELA DAPA_CORGL 83 14 -
VRTVAGAGSNSSREAMGLV O26892 72 14 -
ARVIAGAGTYDTAHSIRLA O33295 81 14 -
MKVLAGVGSNATSESLSLA O25657 78 21 -
VPVLIGTGGTNARETIELS YAGE_ECOLI 83 14 -
VPVLIGVGSPSTDEAVKLA YJHH_ECOLI 91 14 -
MPIISGCSSNNTAYAIELA DAPA_RICPR 73 14 -
IKLIAHVGCVSTAESQQLA NPL_ECOLI 73 14 -
IALIAQVGSVNLKEAVELG NPL_HAEIN 74 14 -
VALIAQVGSINIHESIELG Q27818 99 14 -
RTYLVGTGSTSTFEVIELT O58577 68 12 -
VKLIAQVGSVNLKEAVELA O08360 71 14 -

Motif 3 width=17
Element Seqn Id St Int Rpt
INPYYGKTSLEGLISHF Q42948 160 13 -
INPYYGKTSIEGLIAHF O22129 166 13 -
VNPYYGKTSTAGLISHF DAP2_WHEAT 178 13 -
VVPYYNKPPQEGLLAHF DAPA_SYNY3 111 13 -
VNPYYGKTSTEGLISHF DAP1_WHEAT 189 13 -
VVPYYNKPPQAGLESHF DAPA_PROMA 113 13 -
INPYYGKTSLDGMVAHF Q42800 133 13 -
INPYYGKTSTEGMISHF DAPA_COILA 178 13 -
INPYYGKTSAEGMISHF DAPA_MAIZE 181 13 -
VTPYYNKPSQEGMYQHF DAPA_BACSU 104 13 -
VTPYYNRPSQEGLYQHF DAPA_ECOLI 103 13 -
ITPYYNKPTQEGLRKHF DAPA_METJA 102 13 -
VVPYYNKPTQRGLYEHF O67216 102 13 -
VTPYYNKPNAEGLYQHY O29352 100 13 -
VVPYYNKPTQEGMYQHF DAPA_HAEIN 109 13 -
VSPYYNKPTQEGIYQHF MOSA_RHIME 102 13 -
VTPYYNKPPQEGLYLHF O86841 112 13 -
VTPYYSKPSQEGLLAHF DAPA_BRELA 115 13 -
VTPYYSKPSQEGLLAHF DAPA_CORGL 115 13 -
ITPYYNKPQPHGLIEHY O26892 104 13 -
VTPYYSKPPQRGLQAHF O33295 113 13 -
VSPYYNRPTQQGLFEHY O25657 110 13 -
INPYYWKVSEANLIRYF YAGE_ECOLI 115 13 -
INPYYWKVAPRNLDDYY YJHH_ECOLI 123 13 -
SPPSYVKPTQHGIYKHF DAPA_RICPR 105 13 -
VTPFYYPFSFEEHCDHY NPL_ECOLI 105 13 -
VTPFYYKFSFPEIKHYY NPL_HAEIN 106 13 -
VTPFYYKFTFPEIKNYY Q27818 131 13 -
VSPYYCRLKEDAIFKHF O58577 100 13 -
VTPFYYKFDFNEIKHYY O08360 103 13 -

Motif 4 width=18
Element Seqn Id St Int Rpt
GPTIIYNVPSRTGQDIPP Q42948 183 6 -
GPTIIYNVPGRTGQDIPP O22129 189 6 -
GPTIIYNVPSRTGQDIPP DAP2_WHEAT 201 6 -
LPLMLYNIPGRTGQSLAP DAPA_SYNY3 137 9 -
GPTIIYNVPSRTSQDIPP DAP1_WHEAT 212 6 -
LPLMLYNIPGRTGCSISP DAPA_PROMA 139 9 -
GPTIIYNVPARTGQDIPP Q42800 156 6 -
GPTIIYNVPSRSAQDIPP DAPA_COILA 201 6 -
GPTIIYNVPSRSAQDIPP DAPA_MAIZE 204 6 -
LPVMLYNVPGRTVASLAP DAPA_BACSU 129 8 -
LPQILYNVPSRTGCDLLP DAPA_ECOLI 128 8 -
LPIVLYNVPSRTAVNLEP DAPA_METJA 127 8 -
IPIIIYNIPSRTCVEISV O67216 127 8 -
IPIIVYNVPSRTGINTTP O29352 125 8 -
LPQILYNVPSRTGSDMKP DAPA_HAEIN 134 8 -
IPIIVYNIPGRSAIEIHV MOSA_RHIME 127 8 -
LPVMLYDIPGRSGVPINT O86841 137 8 -
VPICLYDIPGRSGIPIES DAPA_BRELA 140 8 -
VPICLYDIPGRSGIPIES DAPA_CORGL 140 8 -
IPLIIYNVPSRTGTDIDV O26892 129 8 -
LPMLLYDIPGRSAVPIEP O33295 138 8 -
IPVMLYDVPSRTGVSIEV O25657 135 8 -
LPVMLYNFPALTGQDLTP YAGE_ECOLI 140 8 -
LPVILYNFPDLTGQDLTP YJHH_ECOLI 148 8 -
LPIMLYSAPTRSGVDFSD DAPA_RICPR 130 8 -
LPMVVYNIPALSGVKLTL NPL_ECOLI 131 9 -
NNMIVYSIPFLTGVNMGI NPL_HAEIN 131 8 -
MNMIVYSIPALTGVSMTA Q27818 156 8 -
IPIILYAIPSCANPISLE O58577 125 8 -
NKLIIYSIPFLTGVNMSI O08360 128 8 -