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(-) Description

Title :  A SHORT PEPTIDE INSERTION CRUCIAL FOR ANGIOSTATIC ACTIVITY OF HUMAN TRYPTOPHANYL-TRNA SYNTHETASE
 
Authors :  Y. Kise, T. Sengoku, R. Ishii, S. Yokoyama, S. G. Park, S. W. Lee, S. Kim, O. Nureki, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  12 Sep 03  (Deposition) - 03 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoacylation, Angiostatic Cytokine, Apoptosis, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kise, S. W. Lee, S. G. Park, S. Fukai, T. Sengoku, R. Ishii, S. Yokoyama, S. Kim, O. Nureki
A Short Peptide Insertion Crucial For Angiostatic Activity Of Human Tryptophanyl-Trna Synthetase
Nat. Struct. Mol. Biol. V. 11 149 2004
PubMed-ID: 14730354  |  Reference-DOI: 10.1038/NSMB722
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET26B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 35-424
    Gene: TRPS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRYPTOPHAN--TRNA LIGASE, TRPRS, IFP53, HWRS, MINI TRPRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1ULH)

(-) Sites  (0, 0)

(no "Site" information available for 1ULH)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ULH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ULH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036466E455DSYWC_HUMANUnclassified  ---A/BE408D
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYWC_HUMAN164-174
 		  2A:117-127
B:117-127

(-) Exons   (9, 18)

Asymmetric/Biological Unit (9, 18)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003928822aENSE00001513471chr14:100841927-100841620308SYWC_HUMAN-00--
1.3ENST000003928823ENSE00002192528chr14:100835595-100835424172SYWC_HUMAN1-33330--
1.4ENST000003928824ENSE00001607458chr14:100828258-100828045214SYWC_HUMAN34-105722A:53-58
B:35-58		6
24
1.5ENST000003928825ENSE00000941372chr14:100826999-100826891109SYWC_HUMAN105-141372A:58-94
B:58-94		37
37
1.6ENST000003928826ENSE00000941373chr14:100820903-100820784120SYWC_HUMAN141-181412A:94-134
B:94-134		41
41
1.7ENST000003928827ENSE00000941374chr14:100820206-100820024183SYWC_HUMAN181-242622A:134-195
B:134-195		62
62
1.8ENST000003928828ENSE00000941375chr14:100813183-100813083101SYWC_HUMAN242-276352A:195-229
B:195-229		35
35
1.9ENST000003928829ENSE00000941376chr14:100809724-100809612113SYWC_HUMAN276-313382A:229-266
B:229-266		38
38
1.10ENST0000039288210ENSE00000941377chr14:100808908-100808735174SYWC_HUMAN314-371582A:267-324 (gaps)
B:267-324		58
58
1.11ENST0000039288211ENSE00000941378chr14:100803539-100803399141SYWC_HUMAN372-418472A:325-371
B:325-371 (gaps)		47
47
1.12bENST0000039288212bENSE00001314927chr14:100801373-1008001251249SYWC_HUMAN419-471532A:372-424
B:372-422		53
51

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:364
 aligned with SYWC_HUMAN | P23381 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:372
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469  
           SYWC_HUMAN   100 YDKLIVRFGSSKIDKELINRIERATGQRPHHFLRRGIFFSHRDMNQVLDAYENKKPFYLYTGRGPSSEAMHVGHLIPFIFTKWLQDVFNVPLVIQMTDDEKYLWKDLTLDQAYSYAVENAKDIIACGFDINKTFIFSDLDYMGMSSGFYKNVVKIQKHVTFNQVKGIFGFTDSDCIGKISFPAIQAAPSFSNSFPQIFRDRTDIQCLIPCAIDQDPYFRMTRDVAPRIGYPKPALLHSTFFPALQGAQTKMSASDPNSSIFLTDTAKQIKTKVNKHAFSGGRDTIEEHRQFGGNCDVDVSFMYLTFFLEDDDKLEQIRKDYTSGAMLTGELKKALIEVLQPLIAEHQARRKEVTDEIVKEFMTPRKLSFDFQ 471
               SCOP domains d1ulha_ A: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1ulhA01 A:53-299 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                 --------1ulhA02 A:308-424 Tyrosyl-Transfer RNA Synthetase                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh.ee...hhhhhhhhhhh...hhhhhhh...eeehhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeeehhhhh....hhhhhhhhhhhh.hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..........eeeeeee..hhhhhhhhhhhhhhh.....eeeee.........--------..........hhhhhhhhhhh..........hhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D---------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------AA_TRNA_LIG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.4   -----------------------------------Exon 1.6  PDB: A:94-134 UniProt: 141-181 ------------------------------------------------------------Exon 1.8  PDB: A:195-229           -------------------------------------Exon 1.10  PDB: A:267-324 (gaps) UniProt: 314-371         Exon 1.11  PDB: A:325-371 UniProt: 372-418     Exon 1.12b  PDB: A:372-424 UniProt: 419-471           Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.5  PDB: A:58-94               ---------------------------------------Exon 1.7  PDB: A:134-195 UniProt: 181-242                     ---------------------------------Exon 1.9  PDB: A:229-266              -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1ulh A  53 YDKLIVRFGSSKIDKELINRIERATGQRPHHFLRRGIFFSHRDMNQVLDAYENKKPFYLYTGRGPSSEAMHVGHLIPFIFTKWLQDVFNVPLVIQMTDDEKYLWKDLTLDQAYSYAVENAKDIIACGFDINKTFIFSDLDYMGMSSGFYKNVVKIQKHVTFNQVKGIFGFTDSDCIGKISFPAIQAAPSFSNSFPQIFRDRTDIQCLIPCAIDQDPYFRMTRDVAPRIGYPKPALLHSTFFPALQGA--------PNSSIFLTDTAKQIKTKVNKHAFSGGRDTIEEHRQFGGNCDVDVSFMYLTFFLEDDDKLEQIRKDYTSGAMLTGELKKALIEVLQPLIAEHQARRKEVTDEIVKEFMTPRKLSFDFQ 424
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292      |  -     | 312       322       332       342       352       362       372       382       392       402       412       422  
                                                                                                                                                                                                                                                                                299      308                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:379
 aligned with SYWC_HUMAN | P23381 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:388
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461        
           SYWC_HUMAN    82 EDFVDPWTVQTSSAKGIDYDKLIVRFGSSKIDKELINRIERATGQRPHHFLRRGIFFSHRDMNQVLDAYENKKPFYLYTGRGPSSEAMHVGHLIPFIFTKWLQDVFNVPLVIQMTDDEKYLWKDLTLDQAYSYAVENAKDIIACGFDINKTFIFSDLDYMGMSSGFYKNVVKIQKHVTFNQVKGIFGFTDSDCIGKISFPAIQAAPSFSNSFPQIFRDRTDIQCLIPCAIDQDPYFRMTRDVAPRIGYPKPALLHSTFFPALQGAQTKMSASDPNSSIFLTDTAKQIKTKVNKHAFSGGRDTIEEHRQFGGNCDVDVSFMYLTFFLEDDDKLEQIRKDYTSGAMLTGELKKALIEVLQPLIAEHQARRKEVTDEIVKEFMTPRKLSFD 469
               SCOP domains d1ulhb_ B: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1ulhB01 B:35-292 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                            1ulhB02 B:293-422 Tyrosyl-Transfer RNA Syn         thetase                                                                         CATH domains
           Pfam domains (1) ---------------------------------------------------------------------tRNA-synt_1b-1ulhB01 B:104-396                                                                                                                                                                                                                                                                       -------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------tRNA-synt_1b-1ulhB02 B:104-396                                                                                                                                                                                                                                                                       -------------------------- Pfam domains (2)
         Sec.struct. author ..ee....ee.......hhhhhhhhhh.ee...hhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhh..eeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhh.......eeeeehhhhhh...hhhhhhhhhhhh.hhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhh....eeeee...ee..eeeee..............hhhhhhhhhhhhh.....---------......hhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D-------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------AA_TRNA_LIG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: B:35-58  -----------------------------------Exon 1.6  PDB: B:94-134 UniProt: 141-181 ------------------------------------------------------------Exon 1.8  PDB: B:195-229           -------------------------------------Exon 1.10  PDB: B:267-324 UniProt: 314-371                Exon 1.11  PDB: B:325-371 (gaps)               Exon 1.12b  PDB: B:372-422 UniProt: 419-471         Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.5  PDB: B:58-94               ---------------------------------------Exon 1.7  PDB: B:134-195 UniProt: 181-242                     ---------------------------------Exon 1.9  PDB: B:229-266              ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1ulh B  35 EDFVDPWTVQTSSAKGIDYDKLIVRFGSSKIDKELINRIERATGQRPHHFLRRGIFFSHRDMNQVLDAYENKKPFYLYTGRGPSSEAMHVGHLIPFIFTKWLQDVFNVPLVIQMTDDEKYLWKDLTLDQAYSYAVENAKDIIACGFDINKTFIFSDLDYMGMSSGFYKNVVKIQKHVTFNQVKGIFGFTDSDCIGKISFPAIQAAPSFSNSFPQIFRDRTDIQCLIPCAIDQDPYFRMTRDVAPRIGYPKPALLHSTFFPALQGAQTKMSASDPNSSIFLTDTAKQIKTKVNKHAFSGGR---------GGNCDVDVSFMYLTFFLEDDDKLEQIRKDYTSGAMLTGELKKALIEVLQPLIAEHQARRKEVTDEIVKEFMTPRKLSFD 422
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414        
                                                                                                                                                                                                                                                                                                                                     334       344
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYWC_HUMAN | P23381)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004812    aminoacyl-tRNA ligase activity    Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004830    tryptophan-tRNA ligase activity    Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp).
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0045765    regulation of angiogenesis    Any process that modulates the frequency, rate or extent of angiogenesis.
    GO:0006418    tRNA aminoacylation for protein translation    The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006436    tryptophanyl-tRNA aminoacylation    The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SYWC_HUMAN | P23381: 1o5t 1r6t 1r6u 2ake 2azx 2dr2 2quh 2qui 2quj 2quk

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