SPRINT Home UMBER Home Contents Standard Search Advanced Search Relation Search

==SPRINT==> PRINTS View



  selected as


PR01043

Identifier
TRNASYNTHGLY  [View Relations]  [View Alignment]  
Accession
PR01043
No. of Motifs
7
Creation Date
14-DEC-1998  (UPDATE 07-JUN-1999)
Title
Glycyl-tRNA synthetase signature
Database References
PRINTS; PR90000 TRNASYNTH; PR90002 TRNASYNTHCLII; PR90003 TRNASYNTHGF

PROSITE; PS00179 AA_TRNA_LIGASE_II_1; PS00339 AA_TRNA_LIGASE_II_2
BLOCKS; BL00179
PFAM; PF00587 tRNA-synt_2b
INTERPRO; IPR002315
PDB; 1ATI
SCOP; 1ATI
CATH; 1ATI
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).
 
4. WEBSTER, T.A., GIBSON, B.W., KENG, T., BIEMANN, K. AND SCHIMMEL, P.
Primary Structures of Both Subunits of Escherichia coli Glycyl-tRNA
Synthetase.
J.BIOL.CHEM. 258(17) 10637-10641 (1983).
 
5. SHIBA, K., SCHIMMEL, P., MOTEGI, H. AND NODA, T.
Human Glycyl-tRNA Synthetase.
J.BIOL.CHEM. 269(47) 30049-30055 (1994).
 
6. WAGAR, E.A., GIESE, M.J., YASIN, B. AND PANG, M.
The Gylcyl-tRNA Synthetase of Chlamydia trachomatis.
J.BACTERIOL. 177(17) 5179-5185 (1995).

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.
 
Glycyl-tRNA synthetase (EC 6.1.1.14) is specific to glycine and belongs to
class II. It is one of the most complex synthetases, existing as either an
alpha(2) dimer or alpha(2)-beta(2) tetramer [4-6]. What is most interesting
is the lack of similarity between the two types: divergence at the sequence
level is so great that it is impossible to infer descent from common genes.
 
TRNASYNTHGLY is a 7-element fingerprint that provides a signature for the
glycyl-tRNA synthetase. The fingerprint was derived from an initial 
alignment of 9 sequences: the motifs were drawn from conserved regions
spanning the full alignment length - motif 1 spans helix 2, beta-strand 2 
and the N-terminus of helix 3; motif 2 includes strands 6 and 7; motif 3 
encodes helix 7 and the N-terminus of helix 8; motifs 4 and 5 span the 
region encoded by PROSITE pattern AA_TRNA_LIGASE_II_1 (PS00179), which 
includes the C-terminus of helix 9 and strands 9 and 10; and motif 7 spans
the region encoded by PROSITE pattern AA_TRNA_LIGASE_II_2 (PS00339), which 
includes helix 17 and strand 21. Two iterations on OWL31.1 were required to
reach convergence, at which point a true set comprising 21 sequences was
identified.
 
An update on SPTR37_9f identified a true set of 18 sequences.
Summary Information
18 codes involving  7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
718181818181818
60000000
50000000
40000000
30000000
20000000
1234567
True Positives
O50551        O51344        O59235        O65932        
Q06817 SYG_ARATH SYG_ARCFU SYG_BOMMO
SYG_CAEEL SYG_HUMAN SYG_METJA SYG_METTH
SYG_MYCGE SYG_MYCPN SYG_SCHPO SYG_THETH
SYG_TREPA SYG_YEAST
Sequence Titles
O50551      GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) - THERMUS AQUATICUS (SUBSP. THERMOPHILUS). 
O51344 GLYCYL-TRNA SYNTHETASE (GLYS) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
O59235 570AA LONG HYPOTHETICAL GLYCYL-TRNA SYNTHETASE - PYROCOCCUS HORIKOSHII.
O65932 GLYS - MYCOBACTERIUM TUBERCULOSIS.
Q06817 SIMILAR TO GLYCYL-TRNA SYNTHETASE - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
SYG_ARATH GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
SYG_ARCFU PROBABLE GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - ARCHAEOGLOBUS FULGIDUS.
SYG_BOMMO GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - BOMBYX MORI (SILK MOTH).
SYG_CAEEL PROBABLE GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - CAENORHABDITIS ELEGANS.
SYG_HUMAN GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - HOMO SAPIENS (HUMAN).
SYG_METJA PROBABLE GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - METHANOCOCCUS JANNASCHII.
SYG_METTH PROBABLE GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - METHANOBACTERIUM THERMOAUTOTROPHICUM.
SYG_MYCGE GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - MYCOPLASMA GENITALIUM.
SYG_MYCPN GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - MYCOPLASMA PNEUMONIAE.
SYG_SCHPO PUTATIVE GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
SYG_THETH GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - THERMUS AQUATICUS (SUBSP. THERMOPHILUS).
SYG_TREPA GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - TREPONEMA PALLIDUM.
SYG_YEAST GLYCYL-TRNA SYNTHETASE (EC 6.1.1.14) (GLYCINE--TRNA LIGASE) (GLYRS) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
Scan History
OWL31_1    2  40   NSINGLE    
SPTR37_9f 2 19 NSINGLE
Initial Motifs
Motif 1  width=15
Element Seqn Id St Int Rpt
LYGGVSGLYDYGPPG SYG_YEAST 36 36 -
IYGGISGLYDYGPPG SYG_SCHPO 31 31 -
IYGGVTGLYDFGPMG SYG_CAEEL 154 154 -
IYSGVAGLFDYGPPG SYG_ARATH 136 136 -
IYGGITGQFDFGPMG SYG_BOMMO 86 86 -
IYGGIAGFVDYGPLG SYG_METJA 25 25 -
IYGGLQGVYDYGPLG SYG_THETH 24 24 -
LYNGLANSWDFGPLG SYG_MYCPN 26 26 -
IYNGLNNSWDFGPLG SYG_MYCGE 26 26 -

Motif 2 width=13
Element Seqn Id St Int Rpt
RAFNLMFETAIGP SYG_YEAST 205 154 -
RQFNLMFETQIGP SYG_SCHPO 198 152 -
IAFNLMFPTQIGP SYG_CAEEL 290 121 -
YPFNLMFQTSIGP SYG_ARATH 273 122 -
IEFNLMFNTQIGP SYG_BOMMO 222 121 -
KKFNLMFVTSIGP SYG_METJA 141 101 -
RYFNMMFQDLRGP SYG_THETH 163 124 -
RDFNLLFQTEIGV SYG_MYCPN 133 92 -
RDFNLLFQTEIGV SYG_MYCGE 133 92 -

Motif 3 width=18
Element Seqn Id St Int Rpt
YLRPETAQGQFLNFNKLL SYG_YEAST 224 6 -
YLRPETAQGQFLNFSRLL SYG_SCHPO 217 6 -
FLRPETAQGIFVNFKRLL SYG_CAEEL 309 6 -
YMRPETAQGIFVNFKDLY SYG_ARATH 292 6 -
FLRPETAQGIFVNFKRLL SYG_BOMMO 241 6 -
YMRPETAQGIFIQFRRLA SYG_METJA 160 6 -
YLRPETAQGIFVNFKNVL SYG_THETH 184 8 -
YLRPETAQGIFINFKQLL SYG_MYCPN 154 8 -
FLRPETAQGSFINFKNIL SYG_MYCGE 154 8 -

Motif 4 width=18
Element Seqn Id St Int Rpt
GKSFRNEISPRAGLLRVR SYG_YEAST 256 14 -
GKAFRNEISPRSGLLRVR SYG_SCHPO 249 14 -
GLGFRNEISPRQGLIRVR SYG_CAEEL 341 14 -
GQAFRNEISPRQGLLRVR SYG_ARATH 324 14 -
GNSFRNEISPRSGLLRVR SYG_BOMMO 273 14 -
GKSYRNEISPRQGVIRLR SYG_METJA 192 14 -
GKAFRNEITPRNFIFRVR SYG_THETH 216 14 -
GKSFRNEVTPGNFLFRVR SYG_MYCPN 186 14 -
GKSFRNEITPGNFLFRTR SYG_MYCGE 186 14 -

Motif 5 width=11
Element Seqn Id St Int Rpt
REFLMAEIEHF SYG_YEAST 273 -1 -
REFLMAEVEHF SYG_SCHPO 266 -1 -
REFTMCEIEHF SYG_CAEEL 358 -1 -
REFTLAEIEHF SYG_ARATH 341 -1 -
REFTMCEIEHF SYG_BOMMO 290 -1 -
REFTQAEIEYF SYG_METJA 209 -1 -
REFEQMEIEYF SYG_THETH 233 -1 -
REFEQFEMEWF SYG_MYCPN 203 -1 -
REFEQFEIEWF SYG_MYCGE 203 -1 -

Motif 6 width=13
Element Seqn Id St Int Rpt
PSVIEPSFGIGRI SYG_YEAST 504 220 -
PNVIEPSFGLGRI SYG_SCHPO 495 218 -
PSVIEPSYGIGRI SYG_CAEEL 586 217 -
PSVIEPSFGIGRI SYG_ARATH 571 219 -
PSVIEPSFGVGRI SYG_BOMMO 516 215 -
PHVIEPSYGIDRI SYG_METJA 443 223 -
PYVIEPSAGVDRG SYG_THETH 355 111 -
PAVVEPSVGIERL SYG_MYCPN 311 97 -
PFIIEPAVGIERL SYG_MYCGE 311 97 -

Motif 7 width=20
Element Seqn Id St Int Rpt
IGKRYARNDELGTPFGVTID SYG_YEAST 586 69 -
IGRRYARNDELGTPFGLTVD SYG_SCHPO 577 69 -
IGRRYARTDEIGIPFGITVD SYG_CAEEL 668 69 -
IGKRYARTDELGVPFAITVD SYG_ARATH 656 72 -
IGRRYARTDELGVPYAVTVD SYG_BOMMO 598 69 -
IGRRYMRADEIGVPFCITVD SYG_METJA 521 65 -
IGKAYRRHDEVGTPFAVTVD SYG_THETH 440 72 -
IGKRYRKADAIGTKFAITFD SYG_MYCPN 391 67 -
IGKRYRKADAIGIKYAVTFD SYG_MYCGE 391 67 -
Final Motifs
Motif 1  width=15
Element Seqn Id St Int Rpt
LYGGVSGLYDYGPPG SYG_YEAST 36 36 -
IYGGVSGLYDFGPVG SYG_HUMAN 86 86 -
IYGGISGLYDYGPPG SYG_SCHPO 31 31 -
IYGGVTGLYDFGPMG SYG_CAEEL 154 154 -
IYSGVAGLFDYGPPG SYG_ARATH 136 136 -
IYGGITGQFDFGPMG SYG_BOMMO 86 86 -
IYGGSRGFYDYGPLG O59235 27 27 -
IYSGVAGFVDYGPLG SYG_METTH 25 25 -
IYGGIAGFVDYGPLG SYG_METJA 25 25 -
IYGGLQGVYDYGPLG SYG_THETH 24 24 -
IYGGVSGLFDLGPPG Q06817 28 28 -
IYGGMAGFIDYAPLG SYG_ARCFU 22 22 -
IYGGTKSAWDYGPLG O65932 28 28 -
VYGGLSGAWDYGPLG O51344 23 23 -
LYNGLANSWDFGPLG SYG_MYCPN 26 26 -
IYGGLQGVYDYGPLG O50551 25 25 -
IYGGQGGVWDYGPMG SYG_TREPA 20 20 -
IYNGLNNSWDFGPLG SYG_MYCGE 26 26 -

Motif 2 width=13
Element Seqn Id St Int Rpt
RAFNLMFETAIGP SYG_YEAST 205 154 -
VSFNLMFKTFIGP SYG_HUMAN 222 121 -
RQFNLMFETQIGP SYG_SCHPO 198 152 -
IAFNLMFPTQIGP SYG_CAEEL 290 121 -
YPFNLMFQTSIGP SYG_ARATH 273 122 -
IEFNLMFNTQIGP SYG_BOMMO 222 121 -
FYFNLMFETYIGP O59235 142 100 -
WSYNLMFQTLIGA SYG_METTH 141 101 -
KKFNLMFVTSIGP SYG_METJA 141 101 -
RYFNMMFQDLRGP SYG_THETH 163 124 -
TSFNLMFETKIGA Q06817 164 121 -
APMNLMFSTTIGP SYG_ARCFU 136 99 -
REFNMMLKTYLGP O65932 140 97 -
RSFNLMFKTHIGV O51344 120 82 -
RDFNLLFQTEIGV SYG_MYCPN 133 92 -
RYFNMMFQDLRGP O50551 164 124 -
RNFNLMFSTHMGP SYG_TREPA 118 83 -
RDFNLLFQTEIGV SYG_MYCGE 133 92 -

Motif 3 width=18
Element Seqn Id St Int Rpt
YLRPETAQGQFLNFNKLL SYG_YEAST 224 6 -
YLRPETAQGIFLNFKRLL SYG_HUMAN 241 6 -
YLRPETAQGQFLNFSRLL SYG_SCHPO 217 6 -
FLRPETAQGIFVNFKRLL SYG_CAEEL 309 6 -
YMRPETAQGIFVNFKDLY SYG_ARATH 292 6 -
FLRPETAQGIFVNFKRLL SYG_BOMMO 241 6 -
YLRPETAQGIFVNFKRLN O59235 161 6 -
YLRPETAQGIFIPFKRLL SYG_METTH 160 6 -
YMRPETAQGIFIQFRRLA SYG_METJA 160 6 -
YLRPETAQGIFVNFKNVL SYG_THETH 184 8 -
FLRPETAQGQFLNFNKLL Q06817 183 6 -
YLRPETAQGMFVDFKRLA SYG_ARCFU 155 6 -
YLRPETAQGIFVNFANVV O65932 161 8 -
YLRPETAQGIFVNFRNVL O51344 141 8 -
YLRPETAQGIFINFKQLL SYG_MYCPN 154 8 -
YLRPETARASSSTSRTVL O50551 185 8 -
YLRPETAQGIYVNYKNVL SYG_TREPA 139 8 -
FLRPETAQGSFINFKNIL SYG_MYCGE 154 8 -

Motif 4 width=18
Element Seqn Id St Int Rpt
GKSFRNEISPRAGLLRVR SYG_YEAST 256 14 -
GNSFRNEISPRSGLIRVR SYG_HUMAN 273 14 -
GKAFRNEISPRSGLLRVR SYG_SCHPO 249 14 -
GLGFRNEISPRQGLIRVR SYG_CAEEL 341 14 -
GQAFRNEISPRQGLLRVR SYG_ARATH 324 14 -
GNSFRNEISPRSGLLRVR SYG_BOMMO 273 14 -
GKAYRNEISPRQGMIRLR O59235 193 14 -
GKSYRNEISPRQGVIRLR SYG_METTH 192 14 -
GKSYRNEISPRQGVIRLR SYG_METJA 192 14 -
GKAFRNEITPRNFIFRVR SYG_THETH 216 14 -
GKSFRNEISPRSGLLRVR Q06817 215 14 -
GRAYRNEISPRQGVIRLR SYG_ARCFU 187 14 -
GKSFRNEITPGNFIFRTR O65932 193 14 -
GKAFRNEIVTKNFIFRTC O51344 173 14 -
GKSFRNEVTPGNFLFRVR SYG_MYCPN 186 14 -
ARPSRNEITPRNFIFRVR O50551 217 14 -
GKAFRNEIVTKNFIFRTC SYG_TREPA 171 14 -
GKSFRNEITPGNFLFRTR SYG_MYCGE 186 14 -

Motif 5 width=11
Element Seqn Id St Int Rpt
REFLMAEIEHF SYG_YEAST 273 -1 -
REFTMAEIEHF SYG_HUMAN 290 -1 -
REFLMAEVEHF SYG_SCHPO 266 -1 -
REFTMCEIEHF SYG_CAEEL 358 -1 -
REFTLAEIEHF SYG_ARATH 341 -1 -
REFTMCEIEHF SYG_BOMMO 290 -1 -
REFTQAEAEIF O59235 210 -1 -
REFTQAEAEIF SYG_METTH 209 -1 -
REFTQAEIEYF SYG_METJA 209 -1 -
REFEQMEIEYF SYG_THETH 233 -1 -
REFLMAEIEHF Q06817 232 -1 -
REFNQAELEFF SYG_ARCFU 204 -1 -
REFEQMEMEFF O65932 210 -1 -
CEFEQMEMQFF O51344 190 -1 -
REFEQFEMEWF SYG_MYCPN 203 -1 -
REFEQMEIEYF O50551 234 -1 -
CEFEQMEMQFF SYG_TREPA 188 -1 -
REFEQFEIEWF SYG_MYCGE 203 -1 -

Motif 6 width=13
Element Seqn Id St Int Rpt
PSVIEPSFGIGRI SYG_YEAST 504 220 -
PNVIEPSFGLGRI SYG_HUMAN 518 217 -
PNVIEPSFGLGRI SYG_SCHPO 495 218 -
PSVIEPSYGIGRI SYG_CAEEL 586 217 -
PSVIEPSFGIGRI SYG_ARATH 571 219 -
PSVIEPSFGVGRI SYG_BOMMO 516 215 -
PHVLEPSFGIDRP O59235 435 214 -
PHVIEPSFGIDRI SYG_METTH 432 212 -
PHVIEPSYGIDRI SYG_METJA 443 223 -
PYVIEPSAGVDRG SYG_THETH 355 111 -
PNVIEPSFGLGRI Q06817 462 219 -
PHVIEPSFGLDRI SYG_ARCFU 418 203 -
PYVIEPAAGLTRS O65932 320 99 -
PYVIETSAGLTRS O51344 300 99 -
PAVVEPSVGIERL SYG_MYCPN 311 97 -
PYVIEPSAGVDRG O50551 356 111 -
PCVVETSAGLTRC SYG_TREPA 300 101 -
PFIIEPAVGIERL SYG_MYCGE 311 97 -

Motif 7 width=20
Element Seqn Id St Int Rpt
IGKRYARNDELGTPFGVTID SYG_YEAST 586 69 -
IGRRYARTDEIGVAFGVTID SYG_HUMAN 600 69 -
IGRRYARNDELGTPFGLTVD SYG_SCHPO 577 69 -
IGRRYARTDEIGIPFGITVD SYG_CAEEL 668 69 -
IGKRYARTDELGVPFAITVD SYG_ARATH 656 72 -
IGRRYARTDELGVPYAVTVD SYG_BOMMO 598 69 -
IGKRYMRYDEIGTPYCVTVD O59235 514 66 -
IGRRYARADEIGVPFAVTVD SYG_METTH 510 65 -
IGRRYMRADEIGVPFCITVD SYG_METJA 521 65 -
IGKAYRRHDEVGTPFAVTVD SYG_THETH 440 72 -
IGKKYARNDELGTPFGITID Q06817 544 69 -
IGRRYRRFDEIGTPFCVTVD SYG_ARCFU 500 69 -
IGRRYRRQDEVGTPFCVTVD O65932 406 73 -
IGKRYRRQDEIGTPYCVTID O51344 382 69 -
IGKRYRKADAIGTKFAITFD SYG_MYCPN 391 67 -
IGKAYRRHDEVGTPFAVTVD O50551 441 72 -
IGKRYRRQDEVGTPFCVTVD SYG_TREPA 402 89 -
IGKRYRKADAIGIKYAVTFD SYG_MYCGE 391 67 -