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PR00478

Identifier
PHRIBLKINASE  [View Relations]  [View Alignment]  
Accession
PR00478
No. of Motifs
4
Creation Date
20-FEB-1996  (UPDATE 07-JUN-1999)
Title
Phosphoribulokinase family signature
Database References

PROSITE; PS00567 PHOSPHORIBULOKINASE
PFAM; PF00485 PRK
INTERPRO; IPR001324
Literature References
1. KLINTWORTH, R., HUSEMANN, M., SALNIKOW, J. AND BOWIEN, B.
Chromosomal and plasmid locations for phosphoribulokinase genes in 
Alcaligenes eutrophus.
J.BACTERIOL. 164 954-956 (1985).
 
2. GIBSON, J.L., CHEN, J.H., TOWER, P.A. AND TABITA, F.R.
The form II fructose-1,6-bisphosphatase and phosphoribulokinase genes form
part of a large operon in Rhobacter sphaeroides: primary structure and
insertional mutagenesis analysis.
BIOCHEMISTRY 29 8085-8093 (1990).
 
3. POTER, M.A., STRINGER, C.D. AND HARTMAN, F.C.
Characterization of the regulatory thioredoxin site of phosphoribulokinase.
J.BIOL.CHEM. 263 123-129 (1988).

Documentation
Phosphoribulokinase (PRK) catalyses the ATP-dependent phosphorylation of
ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose
phosphate pathway [1-3], where carbon dioxide is assimilated by
autotrophic organisms [2]. In general, plant enzymes are light-activated
by the thioredoxin/ferredoxin system, while those from photosynthetic
bacteria are regulated by a system that has an absolute requirement for
NADH [2]. Thioredoxin/ferredoxin regulation is mediated by the reversible
oxidation/reduction of sulphydryl and disulphide groups. In the spinach
enzyme (KPPR_SPIOL) [3], the participating residues are Cys-16 and Cys-55.
Sequence analysis shows the first of these cysteines to be present in the
ATP-binding site [3]; neither is found in the bacterial sequences.
 
PHRIBLKINASE is a 4-element fingerprint that provides a signature for
phosphoribulokinases. The fingerprint was derived from an initial alignment
of 8 sequences: the motifs were drawn from conserved regions spanning the
N-terminal half of the alignment - motif 1 contains a putative ATP-binding
site, and motif 3 includes the region encoded by PROSITE pattern
PHOSPHORIBULOKINASE (PS00567). Two iterations on OWL27.0 were required to
reach convergence, at which point a true set comprising 17 sequences was
identified. A single partial match (URK_HAEIN) was also found, a uridine
kinase that shows slight similarity to motifs 3 and 4.
 
An update on SPTR37_9f identified a true set of 15 sequences.
Summary Information
15 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
415151515
30000
20000
1234
True Positives
KPP1_RHOSH    KPP2_RHOSH    KPPP_ALCEU    KPPR_ALCEU    
KPPR_ARATH KPPR_CHLRE KPPR_ECOLI KPPR_MESCR
KPPR_NITVU KPPR_SPIOL KPPR_SYNY3 KPPR_WHEAT
KPPR_XANFL O34012 Q95033
Sequence Titles
KPP1_RHOSH  PHOSPHORIBULOKINASE 1 (EC 2.7.1.19) (PHOSPHOPENTOKINASE) (PRK I) - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES). 
KPP2_RHOSH PHOSPHORIBULOKINASE 2 (EC 2.7.1.19) (PHOSPHOPENTOKINASE) (PRK II) - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
KPPP_ALCEU PHOSPHORIBULOKINASE, PLASMID (EC 2.7.1.19) (PHOSPHOPENTOKINASE) (PRK) - ALCALIGENES EUTROPHUS.
KPPR_ALCEU PHOSPHORIBULOKINASE, CHROMOSOMAL (EC 2.7.1.19) (PHOSPHOPENTOKINASE) (PRK) - ALCALIGENES EUTROPHUS.
KPPR_ARATH PHOSPHORIBULOKINASE PRECURSOR (EC 2.7.1.19) (PHOSPHOPENTOKINASE) (PRKASE) (PRK) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
KPPR_CHLRE PHOSPHORIBULOKINASE PRECURSOR (EC 2.7.1.19) (PHOSPHOPENTOKINASE) (PRKASE) (PRK) - CHLAMYDOMONAS REINHARDTII.
KPPR_ECOLI PROBABLE PHOSPHORIBULOKINASE (EC 2.7.1.19) (PHOSPHOPENTOKINASE) (PRK) - ESCHERICHIA COLI.
KPPR_MESCR PHOSPHORIBULOKINASE PRECURSOR (EC 2.7.1.19) (PHOSPHOPENTOKINASE) (PRKASE) (PRK) - MESEMBRYANTHEMUM CRYSTALLINUM (COMMON ICE PLANT).
KPPR_NITVU PHOSPHORIBULOKINASE (EC 2.7.1.19) (PHOSPHOPENTOKINASE) (PRK) - NITROBACTER VULGARIS.
KPPR_SPIOL PHOSPHORIBULOKINASE PRECURSOR (EC 2.7.1.19) (PHOSPHOPENTOKINASE) (PRKASE) (PRK) - SPINACIA OLERACEA (SPINACH).
KPPR_SYNY3 PHOSPHORIBULOKINASE (EC 2.7.1.19) (PHOSPHOPENTOKINASE) (PRK) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
KPPR_WHEAT PHOSPHORIBULOKINASE PRECURSOR (EC 2.7.1.19) (PHOSPHOPENTOKINASE) (PRKASE) (PRK) - TRITICUM AESTIVUM (WHEAT).
KPPR_XANFL PHOSPHORIBULOKINASE (EC 2.7.1.19) (PHOSPHOPENTOKINASE) (PRKASE) (PRK) - XANTHOBACTER FLAVUS.
O34012 PHOSPHORIBULOKINASE (EC 2.7.1.19) - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
Q95033 PHOSPHORIBULOKINASE PRECURSOR (EC 2.7.1.19) (PHOSPHOPENTOKINASE) - ODONTELLA SINENSIS.
Scan History
OWL27_0    2  50   NSINGLE    
SPTR37_9f 2 16 NSINGLE
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
ADSGCGKSTFMRRLTSVF KPPR_MESCR 58 58 -
ADSGCGKSTFMRRLTSVF KPPR_WHEAT 65 65 -
GSSGAGTTSVKRTFEQIF KPPR_XANFL 12 12 -
GSSGAGTTSVKRTFEQIF KPPR_NITVU 12 12 -
GSSGAGTSTVKNFEEQIF KPP2_RHOSH 12 12 -
GSSGAGTTSVTRTFENIF KPPP_ALCEU 11 11 -
ADSGCGKSTFMRRMTSIF KPPR_CHLRE 43 43 -
GSSGAGTTTTSLAFRKIF KPPR_ECOLI 12 12 -

Motif 2 width=19
Element Seqn Id St Int Rpt
ILVIEGLHPMFDSRVRDLL KPPR_MESCR 167 91 -
IFVIEGLHPMYDERVRELL KPPR_WHEAT 174 91 -
ILFYEGLHGAVVTDELNLA KPPR_XANFL 127 97 -
LLFYEGLHGAVVTDKVNVA KPPR_NITVU 127 97 -
LLFYEGLHGCVVNDEVNLV KPP2_RHOSH 127 97 -
LLFYEGLHGGVVTDEVNVA KPPP_ALCEU 126 97 -
ILVIEGLHPFYDKRVAELL KPPR_CHLRE 152 91 -
VLFYEGLHGGVVTPQHNVA KPPR_ECOLI 126 96 -

Motif 3 width=18
Element Seqn Id St Int Rpt
KIQRDMAERGHSLESIKA KPPR_MESCR 202 16 -
KIQRDMAERGHSLESIKA KPPR_WHEAT 209 16 -
KIHRDKATRGYTTEDVTD KPPR_XANFL 165 19 -
KLHRDRNARGYSTEAVTD KPPR_NITVU 165 19 -
KIHRDRAQRGYTTEAVTD KPP2_RHOSH 165 19 -
KLWRDKKQRGYSTEAVTD KPPP_ALCEU 164 19 -
KIQRDMAERGHSLESIKS KPPR_CHLRE 187 16 -
KLIRDTSERGHSREAVMD KPPR_ECOLI 164 19 -

Motif 4 width=24
Element Seqn Id St Int Rpt
SIEARKPDFDAYIDPQKQYADAVI KPPR_MESCR 220 0 -
SIEARKPDFDAFIDPQKQYADAVI KPPR_WHEAT 227 0 -
TIMRRMPDYVRYICPQFTETDINF KPPR_XANFL 183 0 -
TILRRMPDYVNYICPQFAETDINF KPPR_NITVU 183 0 -
VILRRMYAYVGCIVPQFSETDINF KPP2_RHOSH 183 0 -
TILRRMPDYVNYICPQFSRTHVNF KPPP_ALCEU 182 0 -
SIAARKPDFDAYIDPQKKDADMII KPPR_CHLRE 205 0 -
SVVRSMEDYINYITPQFSRTHLNF KPPR_ECOLI 182 0 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
ADSGCGKSTFMRRLTSVF KPPR_MESCR 58 58 -
ADSGCGKSTFMRRLTSVF KPPR_ARATH 57 57 -
ADSGCGKSTFMRRLTSVF KPPR_SPIOL 63 63 -
ADSGCGKSTFMRRLTSVF KPPR_WHEAT 65 65 -
GSSGAGTTSVKRTFEQIF KPPR_XANFL 12 12 -
GSSGAGTTSVKRTFEQIF KPPR_NITVU 12 12 -
GSSGAGTSTVKNFEEQIF KPP2_RHOSH 12 12 -
GSSGAGTTSVTRTFENIF KPPP_ALCEU 11 11 -
ADSGCGKSTFMRRMTSIF KPPR_CHLRE 43 43 -
GSSGAGTTSVTRTFENIF KPPR_ALCEU 11 11 -
ADSGCGKSTFMRRLTSIF Q95033 57 57 -
GSSGAGTSTVKHTFDQIF KPP1_RHOSH 12 12 -
GSSGAGTSTVKATFDQIF O34012 12 12 -
GDSGCGKSTFLRRLTDLF KPPR_SYNY3 15 15 -
GSSGAGTTTTSLAFRKIF KPPR_ECOLI 12 12 -

Motif 2 width=19
Element Seqn Id St Int Rpt
ILVIEGLHPMFDSRVRDLL KPPR_MESCR 167 91 -
ILVIEGLHPMFDERVRDLL KPPR_ARATH 166 91 -
ILVIEGLHPMYDARVRELL KPPR_SPIOL 172 91 -
IFVIEGLHPMYDERVRELL KPPR_WHEAT 174 91 -
ILFYEGLHGAVVTDELNLA KPPR_XANFL 127 97 -
LLFYEGLHGAVVTDKVNVA KPPR_NITVU 127 97 -
LLFYEGLHGCVVNDEVNLV KPP2_RHOSH 127 97 -
LLFYEGLHGGVVTDEVNVA KPPP_ALCEU 126 97 -
ILVIEGLHPFYDKRVAELL KPPR_CHLRE 152 91 -
LLFYEGLHGGVVTDSVNVA KPPR_ALCEU 126 97 -
IVIIEGLHPMYDERVRDLL Q95033 170 95 -
LLFYEGLHGAVVNSEVNIA KPP1_RHOSH 127 97 -
LLFYEGLHGCVTNDQVNIA O34012 127 97 -
VVVIEGLHPLYDERVRELV KPPR_SYNY3 107 74 -
VLFYEGLHGGVVTPQHNVA KPPR_ECOLI 126 96 -

Motif 3 width=18
Element Seqn Id St Int Rpt
KIQRDMAERGHSLESIKA KPPR_MESCR 202 16 -
KIQRDMAERGHSLESIKA KPPR_ARATH 201 16 -
KIQRDMKERGHSLESIKA KPPR_SPIOL 207 16 -
KIQRDMAERGHSLESIKA KPPR_WHEAT 209 16 -
KIHRDKATRGYTTEDVTD KPPR_XANFL 165 19 -
KLHRDRNARGYSTEAVTD KPPR_NITVU 165 19 -
KIHRDRAQRGYTTEAVTD KPP2_RHOSH 165 19 -
KLWRDKKQRGYSTEAVTD KPPP_ALCEU 164 19 -
KIQRDMAERGHSLESIKS KPPR_CHLRE 187 16 -
KLWRDKKQRGYSTEAVTD KPPR_ALCEU 164 19 -
KIQRDMEERGHSLESILA Q95033 205 16 -
KIHRDRATRGYTTEAVTD KPP1_RHOSH 165 19 -
KIHRDRAQRGYTTEAVTD O34012 165 19 -
KIQRDMAERGHTYEDILA KPPR_SYNY3 142 16 -
KLIRDTSERGHSREAVMD KPPR_ECOLI 164 19 -

Motif 4 width=24
Element Seqn Id St Int Rpt
SIEARKPDFDAYIDPQKQYADAVI KPPR_MESCR 220 0 -
SIEARKPDFDAFIDPQKQYADAVI KPPR_ARATH 219 0 -
SIESRKPDFDAYIDPQKQHADVVI KPPR_SPIOL 225 0 -
SIEARKPDFDAFIDPQKQYADAVI KPPR_WHEAT 227 0 -
TIMRRMPDYVRYICPQFTETDINF KPPR_XANFL 183 0 -
TILRRMPDYVNYICPQFAETDINF KPPR_NITVU 183 0 -
VILRRMYAYVGCIVPQFSETDINF KPP2_RHOSH 183 0 -
TILRRMPDYVNYICPQFSRTHVNF KPPP_ALCEU 182 0 -
SIAARKPDFDAYIDPQKKDADMII KPPR_CHLRE 205 0 -
TILRRMPDYVNYICPQFSRTHVNF KPPR_ALCEU 182 0 -
SIEARKPDFDAYIAPQKEFADLTI Q95033 223 0 -
VILRRMHAYVHCIVPQFSQTDINF KPP1_RHOSH 183 0 -
VILRRMHAYVHCIVPQFSQTDINF O34012 183 0 -
SINARKPDFTAYIEPQKQYADVVI KPPR_SYNY3 160 0 -
SVVRSMEDYINYITPQFSRTHLNF KPPR_ECOLI 182 0 -