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PR00981

Identifier
TRNASYNTHSER  [View Relations]  [View Alignment]  
Accession
PR00981
No. of Motifs
5
Creation Date
16-SEP-1998  (UPDATE 07-JUN-1999)
Title
Seryl-tRNA synthetase signature
Database References
PRINTS; PR90000 TRNASYNTH; PR90002 TRNASYNTHCLII
PROSITE; PS00179 AA_TRNA_LIGASE_II_1; PS00339 AA_TRNA_LIGASE_II_2
PFAM; PF00152 TRNA-SYNT_2B
INTERPRO; IPR002317
PDB; 1TRN; 1SRY; 1SET; 1SER; 1SES
SCOP; 1SRY; 1SET; 1SER; 1SES
CATH; 1TRN; 1SRY; 1SET; 1SER; 1SES
Literature References
1. LODISH, H., BALTIMORE, D., BERK, A., ZIPURSKY, S.L., MATSUDAIRA, P. 
AND DARNELL, J.
Nucleic Acids, the Genetic Code, and Protein Synthesis. 
IN MOLECULAR CELL BIOLOGY, SCIENTIFIC AMERICAN BOOKS (NEW YORK), 1995,
PP.126-128.
 
2. DELARUE, M.
Aminoacyl-tRNA synthetases.
CURR.OPIN.STRUCT.BIOL. 5 48-55 (1995).
 
3. PERONA, J.J., ROULD, M. AND STEITZ, T.A.
Structural Basis for Transfer RNA Aminoacylation by Escherichia coli
Glutaminyl-tRNA Synthetase.
BIOCHEMISTRY 32 8758-8771 (1993).

Documentation
Appropriate attachment of an amino acid to its cognate tRNA is the key to
faithful translation of the genetic code. The family of enzymes responsible
for this is the aminoacyl-tRNA synthetases (AATRSs) (EC 6.1.1.-).
 
AATRSs catalyse a two-step reaction:
 
(1) Enzyme + amino acid + ATP ---> Enzyme(aminoacyl-AMP) + PPi
 
(2) tRNA + Enzyme(aminoacyl-AMP) ---> aminoacyl-tRNA + AMP + Enzyme
 
In the first step, they form an aminoacyl-adenylate, in which the carboxyl
of the amino acid is linked to the alpha-phosphate of ATP, by displacing
the pyrophosphate. When the correct tRNA is bound, the aminoacyl group is
transferred to the 2'- or 3'-terminal OH of the tRNA at the expense of AMP
[1].
 
Based on structural and sequence comparisons, this group of at least 20
proteins (in prokaryotes there are approximately 20, but in eukaryotes
there are usually 2 forms for each amino acid; namely, the cytosolic and
mitochondrial forms) can be divided into two classes.
 
Class I AATRSs contain a characteristic Rossman fold and are mostly
monomeric. At the primary structure level, two highly-conserved motifs
are observed `HIGH' and `KMSKS' [2,3]; these are associated with the ATP-
binding site.
 
Class II AATRSs share an anti-parallel beta-sheet formation, flanked by
alpha-helices [3], and are mostly dimeric or multimeric.
 
Further distinction between the two classes is evident when the reaction
mechanisms are investigated. In reactions catalysed by the class I AATRSs,
the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in
class II reactions, the 3'-hydroxyl site is preferred.
 
Seryl-tRNA synthetase (EC 6.1.1.11) is specific to serine and belongs to 
Class II.
 
TRNASYNTHSER is a 5-element fingerprint that provides a signature for 
seryl-tRNA synthetases. The fingerprint was derived from an initial
alignment of 6 sequences: the motifs were drawn from conserved regions 
within the C-terminal portion of the alignment - motifs 1 and 2 span part
of the region encoded by PROSITE pattern AA_TRNA_LIGASE_II_1 (PS00179), 
motif 2 including the N_terminal residues of beta-strand 8; motif 3 encodes
beta-strand 9; motif 4 spans the C-terminal residues of strand 10 and the 
N-terminus of strand 11; and motif 5 spans the C-terminus of strand 11,
helix 15 and the N-terminus of strand 12. Four iterations on OWL30.2 were 
required to reach convergence, at which point a true set comprising 22 
sequences was identified. Two partial matches were also found, SYS_CRIGR
and DMSURF41, both of which are AATRS fragments.
 
An update on SPTR37_9f identified a true set of 27 sequences, and 2
partial matches.
Summary Information
  27 codes involving  5 elements
1 codes involving 4 elements
1 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
52727272727
411011
301011
200000
12345
True Positives
O81983        O82108        O84734        SYSC_SCHPO    
SYSC_YEAST SYS_AQUAE SYS_ARATH SYS_ARCFU
SYS_BACSU SYS_BORBU SYS_BUCAP SYS_CAEEL
SYS_COXBU SYS_ECOLI SYS_HAEIN SYS_HALMA
SYS_HELPY SYS_HUMAN SYS_MYCGE SYS_MYCPN
SYS_MYCTU SYS_PYRHO SYS_STAAU SYS_SYNY3
SYS_THETH SYS_TREPA YHH1_YEAST
True Positive Partials
Codes involving 4 elements
O65395
Codes involving 3 elements
O45887
Sequence Titles
O81983      SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - HELIANTHUS ANNUUS (COMMON SUNFLOWER). 
O82108 SERYL-TRNA SYNTHETASE (EC 6.1.1.11) - ZEA MAYS (MAIZE).
O84734 SERYL TRNA SYNTHETASE - CHLAMYDIA TRACHOMATIS.
SYSC_SCHPO SERYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
SYSC_YEAST SERYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
SYS_AQUAE SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - AQUIFEX AEOLICUS.
SYS_ARATH SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
SYS_ARCFU SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - ARCHAEOGLOBUS FULGIDUS.
SYS_BACSU SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - BACILLUS SUBTILIS.
SYS_BORBU SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
SYS_BUCAP SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - BUCHNERA APHIDICOLA.
SYS_CAEEL PROBABLE SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - CAENORHABDITIS ELEGANS.
SYS_COXBU SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - COXIELLA BURNETII.
SYS_ECOLI SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - ESCHERICHIA COLI.
SYS_HAEIN SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - HAEMOPHILUS INFLUENZAE.
SYS_HALMA SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - HALOARCULA MARISMORTUI (HALOBACTERIUM MARISMORTUI).
SYS_HELPY SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
SYS_HUMAN SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - HOMO SAPIENS (HUMAN).
SYS_MYCGE SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - MYCOPLASMA GENITALIUM.
SYS_MYCPN SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - MYCOPLASMA PNEUMONIAE.
SYS_MYCTU SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - MYCOBACTERIUM TUBERCULOSIS.
SYS_PYRHO SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - PYROCOCCUS HORIKOSHII.
SYS_STAAU SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - STAPHYLOCOCCUS AUREUS.
SYS_SYNY3 SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
SYS_THETH SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - THERMUS AQUATICUS (SUBSP. THERMOPHILUS).
SYS_TREPA SERYL-TRNA SYNTHETASE (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - TREPONEMA PALLIDUM.
YHH1_YEAST PUTATIVE SERYL-TRNA SYNTHETASE YHR011W (EC 6.1.1.11) (SERINE--TRNA LIGASE) (SERRS) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).

O65395 F12F1.29 PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).

O45887 W03B1.4 PROTEIN - CAENORHABDITIS ELEGANS.
Scan History
OWL30_2    4  50   NSINGLE    
SPTR37_9f 2 30 NSINGLE
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
EAGSAGRDTRGLI SYS_STAAU 264 264 -
EAGSYGRDTRGLI SYS_HAEIN 268 268 -
EAGSAGRDTRGLI SYS_BACSU 264 264 -
EAGSYGRDTRGLI SYS_ECOLI 270 270 -
EAGSAGKQTKGTI SYS_MYCPN 258 258 -
EAGSAGKQTKGTI SYS_MYCGE 258 258 -

Motif 2 width=14
Element Seqn Id St Int Rpt
IRLHQFDKVEMVRF SYS_STAAU 276 -1 -
IRMHQFDKVEMVQI SYS_HAEIN 280 -1 -
IRQHQFNKVELVKF SYS_BACSU 276 -1 -
IRMHQFDKVEMVQI SYS_ECOLI 282 -1 -
IRLHQFQKVELVKF SYS_MYCPN 270 -1 -
IRLHQFQKTELVKF SYS_MYCGE 270 -1 -

Motif 3 width=14
Element Seqn Id St Int Rpt
PYRRVILCTGDIGF SYS_STAAU 316 26 -
PYRKVLLCTGDMGF SYS_HAEIN 320 26 -
PYRVMSMCTGDLGF SYS_BACSU 316 26 -
PYRKIILCTGDMGF SYS_ECOLI 322 26 -
PFRRLLLCSGDMGF SYS_MYCPN 310 26 -
PFRRLLLCTGDMGF SYS_MYCGE 310 26 -

Motif 4 width=17
Element Seqn Id St Int Rpt
KTYDLEVWLPSYNDYKE SYS_STAAU 333 3 -
KTYDLEVWVPAQNTYRE SYS_HAEIN 337 3 -
KKYDIEVWIPSQDTYRE SYS_BACSU 333 3 -
KTYDLEVWIPAQNTYRE SYS_ECOLI 339 3 -
KTYDLEVWMAGCNEYRE SYS_MYCPN 327 3 -
KTYDLEVWMAASNEYRE SYS_MYCGE 327 3 -

Motif 5 width=17
Element Seqn Id St Int Rpt
SSCSNCTDFQARRANIR SYS_STAAU 351 1 -
SSCSNMWDFQARRMQAR SYS_HAEIN 355 1 -
SSCSNFEAFQARRANIR SYS_BACSU 351 1 -
SSCSNVWDFQARRMQAR SYS_ECOLI 357 1 -
SSCSSCGDFQARRAMIR SYS_MYCPN 345 1 -
SSCSSCGDFQARRAMIR SYS_MYCGE 345 1 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
EAGSYGRDTKGLI SYS_SYNY3 271 271 -
EAGAYGKDIRGII SYS_AQUAE 264 264 -
EAGSAGRDTRGLI SYS_STAAU 264 264 -
EAGSYGKDVRGMI SYS_COXBU 264 264 -
EAGSYGRDTRGLI SYS_HAEIN 268 268 -
EAGTAGKDTKGIF SYS_PYRHO 290 290 -
EAGSAGRDTRGLI SYS_BACSU 264 264 -
EAGAHGKDTKGIF SYS_ARCFU 282 282 -
EAGSYGRDTRGLI SYS_ECOLI 270 270 -
EAGSHGRDTLGIF O81983 268 268 -
EAGSHGRDTLGIF SYS_ARATH 271 271 -
EASSYGRDSKGLI SYS_BUCAP 266 266 -
EAGSAGKDTRGMI SYS_HELPY 264 264 -
EVGSHGRDTRGIF SYS_CAEEL 304 304 -
EVGSHGRDTRGIF SYS_HUMAN 304 304 -
EAGSAGKQTKGTI SYS_MYCPN 258 258 -
EAGSHGRDTAGIF O82108 269 269 -
EAGSHGKDTRGII SYS_MYCTU 259 259 -
EAGSHGRDAWGIF SYSC_SCHPO 273 273 -
EAGSAGKQTKGTI SYS_MYCGE 258 258 -
EAGSHGKDAWGVF SYSC_YEAST 281 281 -
EAGEHGTETRGYV SYS_HALMA 275 275 -
EAGAYGQLSKGLY SYS_BORBU 261 261 -
EAGSFGKDVRGLM SYS_THETH 258 258 -
EAGARGKDTKGLY YHH1_YEAST 286 286 -
EAGAAGQFSRGLY SYS_TREPA 262 262 -
EAGAGGAHERGLV O84734 264 264 -

Motif 2 width=14
Element Seqn Id St Int Rpt
IRLHQFNKVELVKL SYS_SYNY3 283 -1 -
IRQHQFDKVELVKI SYS_AQUAE 276 -1 -
IRLHQFDKVEMVRF SYS_STAAU 276 -1 -
IRQHQFQKVELVQL SYS_COXBU 276 -1 -
IRMHQFDKVEMVQI SYS_HAEIN 280 -1 -
FRVHQFHKVEQFVY SYS_PYRHO 302 -1 -
IRQHQFNKVELVKF SYS_BACSU 276 -1 -
FRVHQFNKVEQFVF SYS_ARCFU 294 -1 -
IRMHQFDKVEMVQI SYS_ECOLI 282 -1 -
FRVHQFEKVEQFCL O81983 280 -1 -
FRVHQFEKIEQFCI SYS_ARATH 283 -1 -
IRLHQFDKVELVQI SYS_BUCAP 278 -1 -
IRQHQFDKVELVAI SYS_HELPY 276 -1 -
FRVHQFEKIEQFVL SYS_CAEEL 316 -1 -
FRVHQFEKIEQFVY SYS_HUMAN 316 -1 -
IRLHQFQKVELVKF SYS_MYCPN 270 -1 -
FRVHQFEKIEQFCI O82108 281 -1 -
IRVHQFDKVEGFVY SYS_MYCTU 271 -1 -
FRVHAFEKIEQFVL SYSC_SCHPO 285 -1 -
IRLHQFQKTELVKF SYS_MYCGE 270 -1 -
FRVHAFEKIEQFVI SYSC_YEAST 293 -1 -
VRVHQFHKVELVNF SYS_HALMA 287 -1 -
YRVHQFSKVEMFCF SYS_BORBU 273 -1 -
MRVHQFHKVEQYVL SYS_THETH 270 -1 -
YRVHEFTKVELFCW YHH1_YEAST 298 -1 -
YRVHQFTKLEMFAY SYS_TREPA 274 -1 -
VRVHQFHKVEMFAF O84734 276 -1 -

Motif 3 width=14
Element Seqn Id St Int Rpt
PYRVVELCTGDLGF SYS_SYNY3 323 26 -
PYRVVELCTGDLGF SYS_AQUAE 316 26 -
PYRRVILCTGDIGF SYS_STAAU 316 26 -
PYRVVELCAGDLGF SYS_COXBU 316 26 -
PYRKVLLCTGDMGF SYS_HAEIN 320 26 -
PYRVVNICTGDLGY SYS_PYRHO 342 26 -
PYRVMSMCTGDLGF SYS_BACSU 316 26 -
PYRIVNICTGDLGI SYS_ARCFU 334 26 -
PYRKIILCTGDMGF SYS_ECOLI 322 26 -
PYQVVSIVSGALND O81983 322 28 -
PYQIVSIVSGALND SYS_ARATH 325 28 -
PYRKVLLCGGEMGF SYS_BUCAP 318 26 -
PHRFVQLCSGDLGF SYS_HELPY 316 26 -
PYQVVNIVSGELNN SYS_CAEEL 358 28 -
PYHIVNIVSGSLNH SYS_HUMAN 358 28 -
PFRRLLLCSGDMGF SYS_MYCPN 310 26 -
PYQVVSIVSGALND O82108 323 28 -
PYRVIDVAAGDLGS SYS_MYCTU 311 26 -
PYRIVAIVSGALNN SYSC_SCHPO 325 26 -
PFRRLLLCTGDMGF SYS_MYCGE 310 26 -
PYRIVGIVSGELNN SYSC_YEAST 333 26 -
PYRVLDMCTGDMGF SYS_HALMA 327 26 -
PYRVLNICSFDLGS SYS_BORBU 313 26 -
PYRLVEVATGDMGP SYS_THETH 312 28 -
PAKVLNMPSNDLGN YHH1_YEAST 338 26 -
PFRVVEVCAGDLGA SYS_TREPA 314 26 -
PYQLSLLSTGDMSF O84734 316 26 -

Motif 4 width=17
Element Seqn Id St Int Rpt
KCYDLEVWLPSANTYRE SYS_SYNY3 340 3 -
KTYDIEVWFPSQNKYRE SYS_AQUAE 333 3 -
KTYDLEVWLPSYNDYKE SYS_STAAU 333 3 -
KTYDLEVWLPSQNKYRE SYS_COXBU 333 3 -
KTYDLEVWVPAQNTYRE SYS_HAEIN 337 3 -
KKYDIEAWMPGQGKFRE SYS_PYRHO 359 3 -
KKYDIEVWIPSQDTYRE SYS_BACSU 333 3 -
KKYDLEAWMPAQAKYRE SYS_ARCFU 351 3 -
KTYDLEVWIPAQNTYRE SYS_ECOLI 339 3 -
KKYDLEAWFPASKTYRE O81983 339 3 -
KKYDLEAWFPSSETFRE SYS_ARATH 342 3 -
KTYDLEVWFPSQKKYRE SYS_BUCAP 335 3 -
NTIDIEVWLPGQNCYRE SYS_HELPY 333 3 -
KKFDLEAWFPGSGAYRE SYS_CAEEL 375 3 -
KKLDLEAWFPGSGAFRE SYS_HUMAN 375 3 -
KTYDLEVWMAGCNEYRE SYS_MYCPN 327 3 -
KKYDLEAWFPASKTFRE O82108 340 3 -
RKFDCEAWIPTQGAYRE SYS_MYCTU 328 3 -
KKYDLEAWFPFQGEYKE SYSC_SCHPO 342 3 -
KTYDLEVWMAASNEYRE SYS_MYCGE 327 3 -
KKYDLEAWFPYQKEYKE SYSC_YEAST 350 3 -
KKYDIEVWAPGDDMEDG SYS_HALMA 344 3 -
KKYDIEAWMPGRDGKGG SYS_BORBU 330 3 -
RQVDIEVYLPSEGRYRE SYS_THETH 329 3 -
KKYDIEAWMPGRGKFGE YHH1_YEAST 355 3 -
RKWDLEAWMPGRQGGSW SYS_TREPA 331 3 -
KTIDAEVWLPGQKAFYE O84734 333 3 -

Motif 5 width=17
Element Seqn Id St Int Rpt
SSCSNFHDFQARRANIR SYS_SYNY3 358 1 -
SSCSNCEDFQARRMNTR SYS_AQUAE 351 1 -
SSCSNCTDFQARRANIR SYS_STAAU 351 1 -
SSCSNCEDFQARRIQAR SYS_COXBU 351 1 -
SSCSNMWDFQARRMQAR SYS_HAEIN 355 1 -
VSASNCTDWQARRLNIR SYS_PYRHO 377 1 -
SSCSNFEAFQARRANIR SYS_BACSU 351 1 -
VSCSNCTDWQSYRLDIR SYS_ARCFU 369 1 -
SSCSNVWDFQARRMQAR SYS_ECOLI 357 1 -
VSCSNCTDYQSRKLEIR O81983 357 1 -
VSCSNCTDYQARRLEIR SYS_ARATH 360 1 -
SSCSNMSDFQARRMKTR SYS_BUCAP 353 1 -
SSVSNTRDFQARRAKIR SYS_HELPY 351 1 -
VSCSNCLDYQSRRLKVR SYS_CAEEL 393 1 -
VSCSNCTDYQARRLRIR SYS_HUMAN 393 1 -
SSCSSCGDFQARRAMIR SYS_MYCPN 345 1 -
VSCSNCTDFSQRRLGIG O82108 358 1 -
TSTSNCTTFQARRLATR SYS_MYCTU 346 1 -
VSCSNCTDYQSRNLEIR SYSC_SCHPO 360 1 -
SSCSSCGDFQARRAMIR SYS_MYCGE 345 1 -
VSCSNCTDYQSRNLEIR SYSC_YEAST 368 1 -
SSVSNFEDFQARRAGLR SYS_HALMA 371 10 -
TSTSNCTDYQSRRLKIR SYS_BORBU 351 4 -
HSCSALLDWQARRANLR SYS_THETH 347 1 -
SSASNCTDFQSRRLNTK YHH1_YEAST 373 1 -
TSASNCTDYQARRLNVR SYS_TREPA 351 3 -
SSISKCGDFQARRSETR O84734 351 1 -