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PR00982

Identifier
TRNASYNTHLYS  [View Relations]  [View Alignment]  
Accession
PR00982
No. of Motifs
5
Creation Date
16-SEP-1998  (UPDATE 07-JUN-1999)
Title
Lysyl-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_2
INTERPRO; IPR002313
PDB; IKRS; IKRT; 1LYL
SCOP; 1LYL
CATH; IKRS; IKRT; 1LYL
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.
 
Lysyl-tRNA synthetase (EC 6.1.1.6) is specific to lysine and belongs to 
class II.
 
TRNASYNTHLYS is a 5-element fingerprint that provides a signature for 
lysyl-tRNA synthetases. The fingerprint was derived from an initial
alignment of 7 sequences: the motifs were drawn from conserved regions 
within the C-terminal portion of the alignment - motifs 1 and 2 each
include a short beta-strand (6 and 8 respectively); motif 3 encodes the 
C-terminal residues of helix 9 and the N-terminus of strand 10; motif 4 
encodes the C-terminal residues of strand 11, and includes the region 
encoded by PROSITE pattern AA_TRNA_LIGASE_II_1 (PS00179); and motif 5 spans
strand 15 and helix 16. Four iterations on OWL30.2 were required to reach 
convergence, at which point a true set comprising 28 sequences was 
identified. Several partial matches were also found, all 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
0 codes involving 4 elements
1 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
52727272727
400000
310011
210010
12345
True Positives
O67258        O74858        O84786        O87821        
P94974 SYK1_ECOLI SYK2_ECOLI SYKC_YEAST
SYKM_YEAST SYK_ACICA SYK_BACSU SYK_CAEEL
SYK_CAMJE SYK_CRILO SYK_HAEIN SYK_HELPY
SYK_HUMAN SYK_LYCES SYK_MYCFE SYK_MYCGE
SYK_MYCHO SYK_MYCPN SYK_MYCTU SYK_STAAU
SYK_SULSO SYK_SYNY3 SYK_THETH
True Positive Partials
Codes involving 3 elements
SYK3_ECOLI
Codes involving 2 elements
SYK3_HAEIN
Sequence Titles
O67258      LYSYL-TRNA SYNTHETASE - AQUIFEX AEOLICUS.     
O74858 LYSYL-TRNA SYNTHETASE - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
O84786 LYSYL TRNA SYNTHETASE - CHLAMYDIA TRACHOMATIS.
O87821 LYSYL-TRNA SYNTHETASE - SINORHIZOBIUM MELILOTI.
P94974 HYPOTHETICAL 128.2 KD PROTEIN - MYCOBACTERIUM TUBERCULOSIS.
SYK1_ECOLI LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - ESCHERICHIA COLI.
SYK2_ECOLI LYSYL-TRNA SYNTHETASE, HEAT INDUCIBLE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - ESCHERICHIA COLI.
SYKC_YEAST LYSYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
SYKM_YEAST LYSYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
SYK_ACICA LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - ACINETOBACTER CALCOACETICUS.
SYK_BACSU LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - BACILLUS SUBTILIS.
SYK_CAEEL PROBABLE LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - CAENORHABDITIS ELEGANS.
SYK_CAMJE LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - CAMPYLOBACTER JEJUNI.
SYK_CRILO LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - CRICETULUS LONGICAUDATUS (LONG-TAILED HAMSTER) (CHINESE HAMSTER).
SYK_HAEIN LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - HAEMOPHILUS INFLUENZAE.
SYK_HELPY LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
SYK_HUMAN LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) (KIAA0070) - HOMO SAPIENS (HUMAN).
SYK_LYCES LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - LYCOPERSICON ESCULENTUM (TOMATO).
SYK_MYCFE LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - MYCOPLASMA FERMENTANS.
SYK_MYCGE LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - MYCOPLASMA GENITALIUM.
SYK_MYCHO LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - MYCOPLASMA HOMINIS.
SYK_MYCPN LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - MYCOPLASMA PNEUMONIAE.
SYK_MYCTU LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - MYCOBACTERIUM TUBERCULOSIS.
SYK_STAAU LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - STAPHYLOCOCCUS AUREUS.
SYK_SULSO LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - SULFOLOBUS SOLFATARICUS.
SYK_SYNY3 LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
SYK_THETH LYSYL-TRNA SYNTHETASE (EC 6.1.1.6) (LYSINE--TRNA LIGASE) (LYSRS) - THERMUS AQUATICUS (SUBSP. THERMOPHILUS).

SYK3_ECOLI HYPOTHETICAL LYSYL-TRNA SYNTHETASE HOMOLOG (EC 6.1.1.6) (GX) - ESCHERICHIA COLI.

SYK3_HAEIN HYPOTHETICAL LYSYL-TRNA SYNTHETASE HOMOLOG (EC 6.1.1.6) (GX) - HAEMOPHILUS INFLUENZAE.
Scan History
OWL30_2    4  70   NSINGLE    
SPTR37_9f 2 45 NSINGLE
Initial Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
NNKGFLEVETP SYK_STAAU 191 191 -
DDHGYLEVETP SYK_BACSU 195 195 -
ISKGFMEVETP SYK_HAEIN 195 195 -
EMEGFLEVETP SYK_HELPY 188 188 -
TNQRFMEVETP SYK_ACICA 201 201 -
NEAGFLEVETP SYK_MYCPN 184 184 -
DQNGFIEVETP SYK_MYCGE 185 185 -

Motif 2 width=17
Element Seqn Id St Int Rpt
AGGAAARPFVTHHNALD SYK_STAAU 207 5 -
PGGASARPFITHHNALD SYK_BACSU 211 5 -
PGGASARPFVTHHNALD SYK_HAEIN 211 5 -
PGGANARPFITYHNALE SYK_HELPY 204 5 -
PGGASAQPFVTHHNALD SYK_ACICA 217 5 -
LGGANAKPFKTHYNALK SYK_MYCPN 200 5 -
LGGANAKPFKTHYNALK SYK_MYCGE 201 5 -

Motif 3 width=14
Element Seqn Id St Int Rpt
LKRLIVGGLEKVYE SYK_STAAU 236 12 -
LKRLIVGGLEKVYE SYK_BACSU 240 12 -
LKRLVVGGFERVFE SYK_HAEIN 240 12 -
LKRLIVGGFEAVFE SYK_HELPY 233 12 -
LKRLVVGGFERVFE SYK_ACICA 246 12 -
LKKLIVGGLPKVYE SYK_MYCPN 229 12 -
LKKLIIGGFNKVYE SYK_MYCGE 230 12 -

Motif 4 width=18
Element Seqn Id St Int Rpt
FRNEGVSTRHNPEFTMIE SYK_STAAU 254 4 -
FRNEGVSTRHNPEFTMIE SYK_BACSU 258 4 -
FRNEGVSVRHNPEFTMLE SYK_HAEIN 258 4 -
FRNEGMDHSHNPEFTMIE SYK_HELPY 251 4 -
FRNEGVSTRHNPEFTMIE SYK_ACICA 264 4 -
FRNEGVDTTHNPEFTSIE SYK_MYCPN 247 4 -
FRNEGVDTTHNPEFTSIE SYK_MYCGE 248 4 -

Motif 5 width=17
Element Seqn Id St Int Rpt
QPTFIYGHPTEISPLAK SYK_STAAU 377 105 -
QPTFIYGHPVEISPLAK SYK_BACSU 381 105 -
QPTFLNGSPAEISPLAR SYK_HAEIN 384 108 -
NPTFVTQYPIEISPLAR SYK_HELPY 373 104 -
QPTFITEYPAETSPLAR SYK_ACICA 389 107 -
QPTFVTHYPKAVSPLAK SYK_MYCPN 370 105 -
EPTFVTHYPKAVSPLAK SYK_MYCGE 371 105 -
Final Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
NNKGFLEVETP SYK_STAAU 191 191 -
VNRGFMEVETP SYK1_ECOLI 198 198 -
DDHGYLEVETP SYK_BACSU 195 195 -
VARGFMEVETP SYK2_ECOLI 198 198 -
ISKGFMEVETP SYK_HAEIN 195 195 -
DNLGFLEVETP SYK_CAEEL 238 238 -
DNLEFLEVETP SYK_LYCES 273 273 -
DKQGFIEIETP SYK_SYNY3 199 199 -
EMEGFLEVETP SYK_HELPY 188 188 -
TNQRFMEVETP SYK_ACICA 201 201 -
DQRKFIEVETP SYKC_YEAST 261 261 -
EAKGFLEVETP SYK_THETH 182 182 -
NEAGFLEVETP SYK_MYCPN 184 184 -
ENKGFLEVETP SYK_CAMJE 189 189 -
DELGFLEIETP SYK_CRILO 259 259 -
DELGFLEIETP SYK_HUMAN 259 259 -
DQNGFIEVETP SYK_MYCGE 185 185 -
EMHGFIEVETP O67258 285 285 -
FAKGFVEVETP P94974 857 857 -
QRRGFLEVETP SYK_MYCTU 193 193 -
NKLDYLEAETP SYK_MYCFE 185 185 -
YSKGFIEVETP SYK_SULSO 184 184 -
SERGFLEVETP O74858 219 219 -
DSLNYIEVDTP SYK_MYCHO 185 185 -
DQQSFLEVETP O84786 207 207 -
EDEGFMEVETP O87821 191 191 -
DDRNFVEVETP SYKM_YEAST 242 242 -

Motif 2 width=17
Element Seqn Id St Int Rpt
AGGAAARPFVTHHNALD SYK_STAAU 207 5 -
PGGAAARPFITHHNALD SYK1_ECOLI 214 5 -
PGGASARPFITHHNALD SYK_BACSU 211 5 -
PGGASARPFITHHNALD SYK2_ECOLI 214 5 -
PGGASARPFVTHHNALD SYK_HAEIN 211 5 -
AGGATAKPFITHHNDLD SYK_CAEEL 254 5 -
AGGASARPFITHHNELD SYK_LYCES 289 5 -
SGGAEARPFITHHNTLG SYK_SYNY3 215 5 -
PGGANARPFITYHNALE SYK_HELPY 204 5 -
PGGASAQPFVTHHNALD SYK_ACICA 217 5 -
AGGATAKPFITHHNDLD SYKC_YEAST 277 5 -
TGGAEARPFKTYHNALD SYK_THETH 198 5 -
LGGANAKPFKTHYNALK SYK_MYCPN 200 5 -
AGGANAKPFVTFHNSLG SYK_CAMJE 205 5 -
PGGAVAKPFITYHNELD SYK_CRILO 275 5 -
PGGAVAKPFITYHNELD SYK_HUMAN 275 5 -
LGGANAKPFKTHYNALK SYK_MYCGE 201 5 -
ASGANARPFVTYHNFLE O67258 301 5 -
HGGATARPFVTHINTYS P94974 873 5 -
AGGAAARPFATHSNALD SYK_MYCTU 209 5 -
LSGAAAKPFTTHHNSLN SYK_MYCFE 201 5 -
YGGALAKPFKTHVNYLN SYK_SULSO 200 5 -
FGGATARPFITSDIHKL O74858 235 5 -
LGGAAAKPFITFYNATN SYK_MYCHO 201 5 -
YGGAEATPFVTTLQALH O84786 223 5 -
YGGATAEPFKTHHNTLK O87821 207 5 -
SNGAMAKPFITSSKDFD SYKM_YEAST 258 5 -

Motif 3 width=14
Element Seqn Id St Int Rpt
LKRLIVGGLEKVYE SYK_STAAU 236 12 -
LKRLVVGGFERVFE SYK1_ECOLI 243 12 -
LKRLIVGGLEKVYE SYK_BACSU 240 12 -
LKRLVVGGFERVFE SYK2_ECOLI 243 12 -
LKRLVVGGFERVFE SYK_HAEIN 240 12 -
HKMLVVGGIDRVYE SYK_CAEEL 283 12 -
LKKLVVGGFDRVYE SYK_LYCES 318 12 -
LKRLVVGGFEKVFE SYK_SYNY3 244 12 -
LKRLIVGGFEAVFE SYK_HELPY 233 12 -
LKRLVVGGFERVFE SYK_ACICA 246 12 -
LKQLVVGGLDRVYE SYKC_YEAST 306 12 -
LKRLLVGGYEKVFE SYK_THETH 227 12 -
LKKLIVGGLPKVYE SYK_MYCPN 229 12 -
LKRLIVGGFEAVFE SYK_CAMJE 234 12 -
HKMLVVGGIDRVYE SYK_CRILO 304 12 -
HKMLVVGGIDRVYE SYK_HUMAN 304 12 -
LKKLIIGGFNKVYE SYK_MYCGE 230 12 -
LKRLIVGGFPRVYE O67258 330 12 -
LKRLCVGGVERVFE P94974 902 12 -
LKRCIVGGFDKVFE SYK_MYCTU 238 12 -
LKKLVVGGFERVYE SYK_MYCFE 230 12 -
LKRYIIGGFNKVFE SYK_SULSO 229 12 -
LKQLVIGGMNRVFE O74858 263 11 -
LKKLIVGGLDRVYE SYK_MYCHO 230 12 -
LKKLLVGGMSRVYE O84786 252 12 -
NAILVSGLTDKVFE O87821 237 13 -
LKRLIISGLQKVYE SYKM_YEAST 286 11 -

Motif 4 width=18
Element Seqn Id St Int Rpt
FRNEGVSTRHNPEFTMIE SYK_STAAU 254 4 -
FRNEGISVRHNPEFTMME SYK1_ECOLI 261 4 -
FRNEGVSTRHNPEFTMIE SYK_BACSU 258 4 -
FRNEGISVRHNPEFTMME SYK2_ECOLI 261 4 -
FRNEGVSVRHNPEFTMLE SYK_HAEIN 258 4 -
FRNEGIDLTHNPEFTTCE SYK_CAEEL 301 4 -
FRNEGMDLTHSPEFTMCE SYK_LYCES 336 4 -
FRNEGVSTRHNPEFTSIE SYK_SYNY3 262 4 -
FRNEGMDHSHNPEFTMIE SYK_HELPY 251 4 -
FRNEGVSTRHNPEFTMIE SYK_ACICA 264 4 -
FRNEGIDMTHNPEFTTCE SYKC_YEAST 324 4 -
FRNEGIDHNHNPEFTMLE SYK_THETH 245 4 -
FRNEGVDTTHNPEFTSIE SYK_MYCPN 247 4 -
FRNEGMDLTHNPEFTTIE SYK_CAMJE 252 4 -
FRNEGIDLTHNPEFTTCE SYK_CRILO 322 4 -
FRNEGIDLTHNPEFTTCE SYK_HUMAN 322 4 -
FRNEGVDTTHNPEFTSIE SYK_MYCGE 248 4 -
FRNESVDRTHNPEFTMVE O67258 348 4 -
FRNEGVDFSHNPEFTLLE P94974 920 4 -
FRNEGADSTHSPEFSMLE SYK_MYCTU 256 4 -
FRNEGYDTTHNPEFTTIE SYK_MYCFE 248 4 -
FRNEDIDVTHNPEFTLLE SYK_SULSO 247 4 -
FRNEGIDATHNPEFTSCE O74858 281 4 -
FRNEGVDTTHNPEFTSIE SYK_MYCHO 248 4 -
FRNEGIDRTHNPEFTMIE O84786 270 4 -
FRNEGVSTRHNPEFTMME O87821 255 4 -
FRNEGIDSTHNAEFSTLE SYKM_YEAST 304 4 -

Motif 5 width=17
Element Seqn Id St Int Rpt
QPTFIYGHPTEISPLAK SYK_STAAU 377 105 -
QPTFITEYPAEVSPLAR SYK1_ECOLI 385 106 -
QPTFIYGHPVEISPLAK SYK_BACSU 381 105 -
QPTFITEYPAEVSPLAR SYK2_ECOLI 385 106 -
QPTFLNGSPAEISPLAR SYK_HAEIN 384 108 -
SPTFLIGHPQIMSPLAK SYK_CAEEL 438 119 -
NPTFIINHPEIMSPLAK SYK_LYCES 470 116 -
QPTFIIDFPVEISPLAK SYK_SYNY3 386 106 -
NPTFVTQYPIEISPLAR SYK_HELPY 373 104 -
QPTFITEYPAETSPLAR SYK_ACICA 389 107 -
NPTFIFGHPQMMSPLAK SYKC_YEAST 460 118 -
DPTFVFDFPLAISPLAK SYK_THETH 366 103 -
QPTFVTHYPKAVSPLAK SYK_MYCPN 370 105 -
NPTFVIDFPISISPLSR SYK_CAMJE 375 105 -
NPTFICDHPQIMSPLAK SYK_CRILO 458 118 -
NPTFICDHPQIMSPLAK SYK_HUMAN 458 118 -
EPTFVTHYPKAVSPLAK SYK_MYCGE 371 105 -
QPTFVIDFPKILSPLAK O67258 472 106 -
QPTFYIDFPTSVSPLTR P94974 1055 117 -
APTFVKDFPVQTTPLTR SYK_MYCTU 386 112 -
QPTFLYGHPIEISPLSA SYK_MYCFE 369 103 -
NPTFITDYPIETTPLCK SYK_SULSO 370 105 -
SPKFVINHPEVMSPLAK O74858 407 108 -
EPTFVYGHPIEISPTAA SYK_MYCHO 369 103 -
APHHITDHPLETTPLCK O84786 401 113 -
QPAHVIHFPKDISPFAK O87821 378 105 -
LPTVIYHQPAILSPLAK SYKM_YEAST 451 129 -