WORKLIST ENTRIES (1):
CARBMTKINASE View alignment View Structure Bacterial carbamate kinase signature
Type of fingerprint: COMPOUND with 7 elements
Links:
PRINTS; PR00102 OTCASE
PDB; 1B7B 3Dinfo
SCOP; 1B7B
CATH; 1B7B
Creation date 09-JAN-2001
1. BROWN, D.M., UPCROFT, J.A., EDWARDS, M.R. AND UPCROFT, P.
Anaerobic bacterial metabolism in the ancient eukaryote Giardia duodenalis.
INT.J.PARASITOL. 28 149-64 (1998).
2. BAUR, H., LUETHI, E., STALON, V., MERCENIER, A. AND HAAS, D.
Sequence analysis and expression of the arginine-deiminase and carbamate-
kinase genes of Pseudomonas aeruginosa.
EUR.J.BIOCHEM. 179 53-60 (1989).
3. MAGHNOUJ, A., DE SOUSA CABRAL, T.F., STALON, V. AND VANDER WAUVEN, C.
The arcABDC gene cluster, encoding the arginine deiminase pathway of
Bacillus licheniformis, and its activation by the arginine repressor argR.
J.BACTERIOL. 180 6468-6475 (1998).
4. MARINA, A., ALZARI, P.M., BRAVO, J., URIARTE, M., BARCELONA, B., FITA, I.
AND RUBIO, V.
Carbamate kinase: New structural machinery for making carbamoyl phosphate,
the common precursor of pyrimidines and arginine.
PROTEIN SCI. 8 934-940 (1999).
The arginine dihydrolase (AD) pathway is found in many prokaryotes and some
primitive eukaryotes, an example of the latter being Giardia [1}. The three-
enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon
dioxide and ammonia. In simpler bacteria, the first enzyme, arginine
deiminase, can account for up to 10% of total cell protein [1].
Carbamate kinase is involved in the last step of the AD pathway, converting
carbamoyl phosphate and ADP into ammonia, carbon dioxide and ATP [2]. The
second step of the pathway involves the degradation of L-citrulline to
carbamoyl phosphate and L-ornithine, using ornithine carbamoyltransferase [3].
The crystal structure of Enterococcus (Streptococcus) faecium carbamate
kinase has been determined to 2.8A resolution [4]. The enzyme exists as a
homodimer of two 33kDa subunits. The hallmark of the dimer is a 16-stranded
beta-sheet, surrounded by alpha-helices [4]. Each subunit contains an active
site within a large crevice.
CARBMTKINASE is a 7-element fingerprint that provides a signature for the
bacterial carbamate kinases. The fingerprint was derived from an initial
alignment of 3 sequences: the motifs were drawn from conserved regions
spanning the full alignment length (~220 amino acids) - motif 1 spans beta-
strand 3 and the N-terminus of alpha-helix 3 of the E.faecium carbamate
kinase structure; motif 2 encodes the N-terminus of helix 4; motif 3 spans
the C-terminus of strand 4, strand 5 and helix 5; motif 4 spans the
C-terminus of strand 8, strand 9 and the N-terminus of helix 7; motif 5
spans strands 10 and 11, and helix 8; motif 6 encodes helix 9; and motif
7 encodes helix 11. Two iterations on SPTR37_10f were required to reach
convergence, at which point a true set comprising 17 sequences was
identified. A single partial match was also found, ARGB_BACST, a Bacillus
stearothermophilus acetylglutamate kinase that matched motifs 1 and 7.
SUMMARY INFORMATION
17 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
1 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
7| 17 17 17 17 17 17 17
6| 0 0 0 0 0 0 0
5| 0 0 0 0 0 0 0
4| 0 0 0 0 0 0 0
3| 0 0 0 0 0 0 0
2| 1 0 0 0 0 0 1
--+------------------------------------
| 1 2 3 4 5 6 7
True positives..
P95474 O59023 ARCC_PSEAE ARCC_HAEIN
ARCC_CLOPE ARCC_HALSA O31019 ARCC_SYNY3
ARCL_ECOLI O54531 O86134 O53090
ARCM_ECOLI O96432 O97438 ARCC_ECOLI
ARCL_MYCPN
Subfamily: Codes involving 2 elements
Subfamily True positives..
ARGB_BACST
PROTEIN TITLES
P95474 CARBAMATE KINASE-LIKE CARBAMOYLPHOSPHATE SYNTHETASE - PYROCO
O59023 314AA LONG HYPOTHETICAL CARBAMATE KINASE (FUCOXANTHIN CHLORO
ARCC_PSEAE CARBAMATE KINASE (EC 2.7.2.2) - PSEUDOMONAS AERUGINOSA.
ARCC_HAEIN CARBAMATE KINASE (EC 2.7.2.2) - HAEMOPHILUS INFLUENZAE.
ARCC_CLOPE CARBAMATE KINASE (EC 2.7.2.2) - CLOSTRIDIUM PERFRINGENS.
ARCC_HALSA CARBAMATE KINASE (EC 2.7.2.2) - HALOBACTERIUM SALINARIUM.
O31019 ARCC (EC 2.7.2.2) (CARBAMATE KINASE) - RHIZOBIUM ETLI.
ARCC_SYNY3 CARBAMATE KINASE (EC 2.7.2.2) - SYNECHOCYSTIS SP. (STRAIN PC
ARCL_ECOLI CARBAMATE KINASE-LIKE PROTEIN 1 - ESCHERICHIA COLI.
O54531 CARBAMATE KINASE (EC 2.7.2.2) - ENTEROCOCCUS FAECALIS (STREP
O86134 CARBAMATE KINASE (EC 2.7.2.2) - BACILLUS LICHENIFORMIS.
O53090 CARBAMATE KINASE (EC 2.7.2.2) - LACTOBACILLUS SAKE.
ARCM_ECOLI CARBAMATE KINASE-LIKE PROTEIN 2 - ESCHERICHIA COLI.
O96432 CARBAMATE KINASE (EC 2.7.2.2) - TRICHOMONAS VAGINALIS.
O97438 CARBAMATE KINASE (EC 2.7.2.2) - GIARDIA LAMBLIA (GIARDIA INT
ARCC_ECOLI CARBAMATE KINASE (EC 2.7.2.2) - ESCHERICHIA COLI.
ARCL_MYCPN CARBAMATE KINASE-LIKE PROTEIN - MYCOPLASMA PNEUMONIAE.
ARGB_BACST ACETYLGLUTAMATE KINASE (EC 2.7.2.8) (NAG KINASE) (AGK) (N-AC
SCAN HISTORY
SPTR37_10f 2 75 NSINGLE
INITIAL MOTIF SETS
CARBMTKINASE1 Length of motif = 20 Motif number = 1
Bacterial carbamate kinase motif I - 1
PCODE ST INT
GHELVFTHGNGPQVGQLLLQ ARCC_HALSA 42 42
GHEVIVTHGNGPQVGMINQA ARCL_ECOLI 39 39
GNELVIAHGNGPQVGLLALQ ARCC_PSEAE 41 41
CARBMTKINASE2 Length of motif = 19 Motif number = 2
Bacterial carbamate kinase motif II - 1
PCODE ST INT
PLDVLGAESQAQIGYLLQQ ARCC_HALSA 72 10
PMSVCVALSQGYIGYDLQN ARCL_ECOLI 73 14
PLDVLGAETEGMIGYMIEQ ARCC_PSEAE 71 10
CARBMTKINASE3 Length of motif = 20 Motif number = 3
Bacterial carbamate kinase motif III - 1
PCODE ST INT
TVITQTIVDEDDPAFDDPTK ARCC_HALSA 102 11
TLVTQVEVDANDPAFLNPTK ARCL_ECOLI 108 16
TILTQVEVDGKDPAFQNPTK ARCC_PSEAE 103 13
CARBMTKINASE4 Length of motif = 20 Motif number = 4
Bacterial carbamate kinase motif IV - 1
PCODE ST INT
YRRVVPSPKPVDIVEAEHIK ARCC_HALSA 151 29
YRRVVASPKPVDIIEKETVK ARCL_ECOLI 156 28
FRRVVPSPRPKRIFEIRPVK ARCC_PSEAE 151 28
CARBMTKINASE5 Length of motif = 19 Motif number = 5
Bacterial carbamate kinase motif V - 1
PCODE ST INT
ETGKPVISSGGGGVPVVED ARCC_HALSA 174 3
DAGQVVITVGGGGIPVIRE ARCL_ECOLI 179 3
EKGTIVICAGGGGIPTMYD ARCC_PSEAE 174 3
CARBMTKINASE6 Length of motif = 16 Motif number = 6
Bacterial carbamate kinase motif VI - 1
PCODE ST INT
DKDRAAQSLATDIGAD ARCC_HALSA 204 11
DKDWASARLAEMIDAD ARCL_ECOLI 209 11
DKDLCSSLLAQELVAD ARCC_PSEAE 206 13
CARBMTKINASE7 Length of motif = 16 Motif number = 7
Bacterial carbamate kinase motif VII - 1
PCODE ST INT
FGEGSMAPKVEACIEF ARCC_HALSA 259 39
FAKGSMLPKVEAAASF ARCL_ECOLI 264 39
FAAGSMGPKVQAAIEF ARCC_PSEAE 257 35
FINAL MOTIF SETS
CARBMTKINASE1 Length of motif = 20 Motif number = 1
Bacterial carbamate kinase motif I - 2
PCODE ST INT
GYEVVITHGNGPQVGSLLLH P95474 44 44
GYEVVITHGNGPQVGTILLH O59023 44 44
GNELVIAHGNGPQVGLLALQ ARCC_PSEAE 41 41
NNELVIAHGNGPQVGLLALQ ARCC_HAEIN 41 41
GHEVSIVHGNGPQVGQILAS ARCC_CLOPE 42 42
GHELVFTHGNGPQVGQLLLQ ARCC_HALSA 42 42
DHEIVITHGNGPQVGLLALQ O31019 41 41
HYPVVVTHGNGPQVGLLALQ ARCC_SYNY3 49 49
GHEVIVTHGNGPQVGMINQA ARCL_ECOLI 39 39
GHRLIVSHGNGPQVGNLLLQ O54531 42 42
GAELIITHGNGPQVGNLMIQ O86134 43 43
GDQLIISHGNGPQVGNLLIQ O53090 43 43
DYDIVLTHGNGPQVGLDLRR ARCM_ECOLI 44 44
GNELVMTHGNGPQCGAIFLQ O96432 42 42
GYKVVLTSGNAPQVGAIKLQ O97438 46 46
SYRLAIVHGNGPQVGLLALQ ARCC_ECOLI 42 42
GYQILLGHGNGPQVGMIYNA ARCL_MYCPN 38 38
CARBMTKINASE2 Length of motif = 19 Motif number = 2
Bacterial carbamate kinase motif II - 2
PCODE ST INT
PMDVAGAMSQGWIGYMIQQ P95474 77 13
PMDVAGAMSQGWIGYMIQQ O59023 77 13
PLDVLGAETEGMIGYMIEQ ARCC_PSEAE 71 10
PLDVLGAETAGMIGYMIQQ ARCC_HAEIN 71 10
PFDVVGAFSEGYIGYHLQN ARCC_CLOPE 76 14
PLDVLGAESQAQIGYLLQQ ARCC_HALSA 72 10
PLDVLGAETEGMIGYMLEQ O31019 71 10
PLDVLGAETEGMIGYLLEQ ARCC_SYNY3 79 10
PMSVCVALSQGYIGYDLQN ARCL_ECOLI 73 14
PLDTCVAMTQGSIGYWLSN O54531 74 12
PLETCVSMTQGMIGYWLQN O86134 75 12
PLDTVGAMSQGEIGYWMQN O53090 75 12
PLANCVADTQGGIGYLIQQ ARCM_ECOLI 77 13
PLHVCGAETQGFLGELLQQ O96432 74 12
PLHVCGAMSQGFIGYMMSQ O97438 77 11
PLDVLVAESQGMIGYMLAQ ARCC_ECOLI 72 10
PFAESGAMSQGYIGLHLLT ARCL_MYCPN 72 14
CARBMTKINASE3 Length of motif = 20 Motif number = 3
Bacterial carbamate kinase motif III - 2
PCODE ST INT
TIITQTIVDKNDPAFQNPTK P95474 112 16
TIITQTIVDKKDPAFQNPTK O59023 112 16
TILTQVEVDGKDPAFQNPTK ARCC_PSEAE 103 13
TLLSQVEVDINDPAFKNPTK ARCC_HAEIN 103 13
TITTQVIVDKNDPGFTNPTK ARCC_CLOPE 111 16
TVITQTIVDEDDPAFDDPTK ARCC_HALSA 102 11
TLLTMVEVDADDPGFQNPTK O31019 103 13
TLLTQIVVDRQDPAFLQPTK ARCC_SYNY3 110 12
TLVTQVEVDANDPAFLNPTK ARCL_ECOLI 108 16
TVLTQVVVDPADEAFKNPTK O54531 109 16
TVITRVAVRSDDEAFRNPTK O86134 110 16
TIVTQTIVDAKDEAFQNPTK O53090 110 16
TVVTQVEVDKNDPGFAHPTK ARCM_ECOLI 111 15
SIVTQSFVDPKDPAFQNPTK O96432 109 16
TCVTQTLVDPKDQAFTNPTK O97438 112 16
TVLTRIEVSPDDPAFLQPEK ARCC_ECOLI 103 12
YFLTQTLVEASDPAFQNPNK ARCL_MYCPN 107 16
CARBMTKINASE4 Length of motif = 20 Motif number = 4
Bacterial carbamate kinase motif IV - 2
PCODE ST INT
WRRVVPSPDPKGHVEAETIK P95474 161 29
WRRVVPSPDPKGHVEAETIR O59023 161 29
FRRVVPSPRPKRIFEIRPVK ARCC_PSEAE 151 28
YRRVVPSPLPKRIFEIRPVK ARCC_HAEIN 151 28
YRRVVASPKPVDIVEKEAIK ARCC_CLOPE 160 29
YRRVVPSPKPVDIVEAEHIK ARCC_HALSA 151 29
WRRVVASPVPKRIFEIRPVR O31019 151 28
YRRVVASPEPKRIIELPTIQ ARCC_SYNY3 158 28
YRRVVASPKPVDIIEKETVK ARCL_ECOLI 156 28
WRKVVPSPKPIDIHEAETIN O54531 157 28
WRRVVPSPAPVSILEHDVIN O86134 161 31
WRRVVPSPRPIGIQEAPVIQ O53090 160 30
YRRVVASPEPKRIVEAPAIK ARCM_ECOLI 161 30
YRMIVPSPVPQKFVEKEAIK O96432 158 29
WRVVVPSPRPLEIVEYGVIK O97438 163 31
LRRVVASPQPRKILDSEAIE ARCC_ECOLI 151 28
WRKVVASPKPVDVLGIDAIK ARCL_MYCPN 155 28
CARBMTKINASE5 Length of motif = 19 Motif number = 5
Bacterial carbamate kinase motif V - 2
PCODE ST INT
ERGVIVIASGGGGVPVILE P95474 184 3
ESGIIVIASGGGGVPVIEE O59023 184 3
EKGTIVICAGGGGIPTMYD ARCC_PSEAE 174 3
EKGSIVICAGGGGIPTYYD ARCC_HAEIN 174 3
DSGFIVIACGGGGIPVVED ARCC_CLOPE 183 3
ETGKPVISSGGGGVPVVED ARCC_HALSA 174 3
EQRTIVICAGGGGIPTMYE O31019 174 3
KSGALVVCAGGGGIPVVVN ARCC_SYNY3 181 3
DAGQVVITVGGGGIPVIRE ARCL_ECOLI 179 3
KNDIITISCGGGGIPVVGQ O54531 180 3
EHGHIVIAAGGGGVPVIEN O86134 184 3
EGNVITISAGGGGVPVAKE O53090 183 3
QQGFVVIGAGGGGIPVVRT ARCM_ECOLI 184 3
NSGFIVVCSGGGGIPVILD O96432 181 3
DNNVLVICTNGGGIPCKRE O97438 186 3
KEGHVVICSGGGGVPVTDD ARCC_ECOLI 174 3
NQGNLVIVGGGGGVPTIKT ARCL_MYCPN 178 3
CARBMTKINASE6 Length of motif = 16 Motif number = 6
Bacterial carbamate kinase motif VI - 2
PCODE ST INT
DKDLAGEKLAEEVNAD P95474 214 11
DKDLAGEKLAEEVNAD O59023 214 11
DKDLCSSLLAQELVAD ARCC_PSEAE 206 13
DKDLCSALLAENLDAD ARCC_HAEIN 205 12
DKDFAAEKLAEILDAD ARCC_CLOPE 213 11
DKDRAAQSLATDIGAD ARCC_HALSA 204 11
DKDLCSGLLARELNAD O31019 206 13
DKDLAAALLAQNLQAQ ARCC_SYNY3 212 12
DKDWASARLAEMIDAD ARCL_ECOLI 209 11
DKDFASEKLAELVDAD O54531 208 9
DKDFAACKLAELVQAD O86134 214 11
DKDFASEKLAELVGAD O53090 213 11
DKDLSTALLAREIHAD ARCM_ECOLI 215 12
DKDLGASVLAAATNAD O96432 213 13
DKDLATSLLAKTLNSD O97438 216 11
DKDLAAALLAEQINAD ARCC_ECOLI 201 8
DKDLALSEIAIKVEAD ARCL_MYCPN 208 11
CARBMTKINASE7 Length of motif = 16 Motif number = 7
Bacterial carbamate kinase motif VII - 2
PCODE ST INT
FKAGSMGPKVLAAIRF P95474 269 39
FKAGSMGPKVLAAIRF O59023 269 39
FAAGSMGPKVQAAIEF ARCC_PSEAE 257 35
FASGSMGPKVQAAINF ARCC_HAEIN 256 35
FAPGSMLPKVEACKKF ARCC_CLOPE 268 39
FGEGSMAPKVEACIEF ARCC_HALSA 259 39
FPAGSMGPKVDAACHF O31019 257 35
FAAGSMGPKVEAACRF ARCC_SYNY3 263 35
FAKGSMLPKVEAAASF ARCL_ECOLI 264 39
FAPGSMLPKIEAAIQF O54531 263 39
FAEGSMLPKVKAAIQF O86134 269 39
FAKGSMLPKIQTAIEY O53090 268 39
FPPGSMLPKIIASLTF ARCM_ECOLI 270 39
FIKGSMLPKVQACLRF O96432 268 39
FAAGSMGPKVRAAIEF O97438 271 39
KADGSMGPNVTAVSGY ARCC_ECOLI 252 35
FAKGSMLPKVEACLNF ARCL_MYCPN 263 39
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