1R6U - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AN ACTIVE FRAGMENT OF HUMAN TRYPTOPHANYL-TRNA SYNTHETASE WITH CYTOKINE ACTIVITY

Authors :   X. -L. Yang, F. J. Otero, R. J. Skene, D. E. Mcree, L. Ribas De Pouplana, P. Schimmel

Date :   16 Oct 03 (Deposition) - 06 Jan 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Class Ic Trna Synthetase, Rossmann Fold Catalytic Domain, Anticodon Recognition Domain, Bound Trp-Amp, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. -L. Yang, M. Guo, M. Kapoor, K. L. Ewalt, F. J. Otero, R. J. Skene, D. E. Mcree, P. Schimmel
Functional And Crystal Structure Analysis Of Active Site Adaptations Of A Potent Anti-Angiogenic Human Trna Synthetase
Structure V. 15 793 2007
PubMed-ID: 17637340 | Reference-DOI: 10.1016/J.STR.2007.05.009

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET20B+
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	WARS
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TRYPTOPHAN-TRNA LIGASE, TRPRS, IFP53, HWRS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 22)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	19	Mod. Amino Acid	SELENOMETHIONINE
3	TYM	1	Ligand/Ion	TRYPTOPHANYL-5'AMP

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:159 , THR A:160 , GLY A:161 , ARG A:162 , GLY A:163 , GLY A:172 , HIS A:173 , PRO A:176 , GLN A:194 , GLU A:199 , GLN A:284 , ILE A:307 , CYS A:309 , ALA A:310 , ASP A:312 , GLN A:313 , PHE A:317 , PHE A:340 , LYS A:349 , MSE A:350 , HOH A:1012 , HOH A:1046	BINDING SITE FOR RESIDUE TYM A 501
2	AC2	SOFTWARE	TYR A:201 , THR A:207 , LEU A:208 , LYS B:253	BINDING SITE FOR RESIDUE GOL A 601
3	AC3	SOFTWARE	HIS A:129 , ILE A:178 , LYS A:181 , TRP A:182 , ASP A:185	BINDING SITE FOR RESIDUE GOL A 602

(no "SS Bond" information available for 1R6U)

(no "Cis Peptide Bond" information available for 1R6U)

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036466	E	455	D	SYWC_HUMAN	Unclassified	---	A/B	E	455	D

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_I	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.	SYWC_HUMAN	164-174	2	A:164-174 B:164-174

Asymmetric/Biological Unit (9, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000392882	2a	ENSE00001513471	chr14:100841927-100841620	308	SYWC_HUMAN	-	0	0	-	-
1.3	ENST00000392882	3	ENSE00002192528	chr14:100835595-100835424	172	SYWC_HUMAN	1-33	33	0	-	-
1.4	ENST00000392882	4	ENSE00001607458	chr14:100828258-100828045	214	SYWC_HUMAN	34-105	72	2	A:82-105 B:97-105	24 9
1.5	ENST00000392882	5	ENSE00000941372	chr14:100826999-100826891	109	SYWC_HUMAN	105-141	37	2	A:105-141 B:105-141	37 37
1.6	ENST00000392882	6	ENSE00000941373	chr14:100820903-100820784	120	SYWC_HUMAN	141-181	41	2	A:141-181 B:141-181	41 41
1.7	ENST00000392882	7	ENSE00000941374	chr14:100820206-100820024	183	SYWC_HUMAN	181-242	62	2	A:181-242 B:181-242	62 62
1.8	ENST00000392882	8	ENSE00000941375	chr14:100813183-100813083	101	SYWC_HUMAN	242-276	35	2	A:242-276 B:242-276	35 35
1.9	ENST00000392882	9	ENSE00000941376	chr14:100809724-100809612	113	SYWC_HUMAN	276-313	38	2	A:276-313 B:276-313	38 38
1.10	ENST00000392882	10	ENSE00000941377	chr14:100808908-100808735	174	SYWC_HUMAN	314-371	58	2	A:314-371 B:314-371 (gaps)	58 58
1.11	ENST00000392882	11	ENSE00000941378	chr14:100803539-100803399	141	SYWC_HUMAN	372-418	47	2	A:372-418 B:372-418	47 47
1.12b	ENST00000392882	12b	ENSE00001314927	chr14:100801373-100800125	1249	SYWC_HUMAN	419-471	53	2	A:419-469 B:419-467	51 49

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:388
 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 d1r6ua_ A: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1r6uA01 A:82-339 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                            1r6uA02 A:340-469 Tyrosyl-Transfer RNA Synthetase                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee..........hhhhhh..ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhh....eeeeeee.......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhh.eeeeehhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhh....eeeee...ee..eeeee..............hhhhhhhhhhhh.......hhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D-------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------AA_TRNA_LIG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:82-105 -----------------------------------Exon 1.6  PDB: A:141-181 UniProt: 141-181------------------------------------------------------------Exon 1.8  PDB: A:242-276           -------------------------------------Exon 1.10  PDB: A:314-371 UniProt: 314-371                Exon 1.11  PDB: A:372-418 UniProt: 372-418     Exon 1.12b  PDB: A:419-469 UniProt: 419-471         Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.5  PDB: A:105-141             ---------------------------------------Exon 1.7  PDB: A:181-242 UniProt: 181-242                     ---------------------------------Exon 1.9  PDB: A:276-313              ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1r6u A  82 EDFVDPWTVQTSSAKGIDYDKLIVRFGSSKIDKELINRIERATGQRPHHFLRRGIFFSHRDmNQVLDAYENKKPFYLYTGRGPSSEAmHVGHLIPFIFTKWLQDVFNVPLVIQmTDDEKYLWKDLTLDQAYGDAVENAKDIIACGFDINKTFIFSDLDYmGmSSGFYKNVVKIQKHVTFNQVKGIFGFTDSDCIGKISFPAIQAAPSFSNSFPQIFRDRTDIQCLIPCAIDQDPYFRmTRDVAPRIGYPKPALLHSTFFPALQGAQTKmSASDPNSSIFLTDTAKQIKTKVNKHAFSGGRDTIEEHRQFGGNCDVDVSFmYLTFFLEDDDKLEQIRKDYTSGAmLTGELKKALIEVLQPLIAEHQARRKEVTDEIVKEFmTPRKLSFD 469
                                    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        
                                                                                       143-MSE                   169-MSE                   195-MSE                                       241-MSE                                                                       319-MSE                        350-MSE                                            401-MSE                 425-MSE                             461-MSE    
                                                                                                                                                                                           243-MSE

Chain B from PDB  Type:PROTEIN  Length:362
 aligned with SYWC_HUMAN | P23381 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:371
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466 
           SYWC_HUMAN    97 GIDYDKLIVRFGSSKIDKELINRIERATGQRPHHFLRRGIFFSHRDMNQVLDAYENKKPFYLYTGRGPSSEAMHVGHLIPFIFTKWLQDVFNVPLVIQMTDDEKYLWKDLTLDQAYSYAVENAKDIIACGFDINKTFIFSDLDYMGMSSGFYKNVVKIQKHVTFNQVKGIFGFTDSDCIGKISFPAIQAAPSFSNSFPQIFRDRTDIQCLIPCAIDQDPYFRMTRDVAPRIGYPKPALLHSTFFPALQGAQTKMSASDPNSSIFLTDTAKQIKTKVNKHAFSGGRDTIEEHRQFGGNCDVDVSFMYLTFFLEDDDKLEQIRKDYTSGAMLTGELKKALIEVLQPLIAEHQARRKEVTDEIVKEFMTPRKLS 467
               SCOP domains d1r6ub_ B: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1r6uB01 B:97-345 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                   ---------1r6uB02 B:355-467 Tyrosyl-Transfer RNA Synthetase                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh.ee.hhhhhhhhhhhhh.............eeehhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhh.....eeeee........---------.........hhhhhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------AA_TRNA_LIG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4 -----------------------------------Exon 1.6  PDB: B:141-181 UniProt: 141-181------------------------------------------------------------Exon 1.8  PDB: B:242-276           -------------------------------------Exon 1.10  PDB: B:314-371 (gaps) UniProt: 314-371         Exon 1.11  PDB: B:372-418 UniProt: 372-418     Exon 1.12b  PDB: B:419-467 UniProt: 419-471       Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.5  PDB: B:105-141             ---------------------------------------Exon 1.7  PDB: B:181-242 UniProt: 181-242                     ---------------------------------Exon 1.9  PDB: B:276-313              ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1r6u B  97 GIDYDKLIVRFGSSKIDKELINRIERATGQRPHHFLRRGIFFSHRDmNQVLDAYENKKPFYLYTGRGPSSEAmHVGHLIPFIFTKWLQDVFNVPLVIQmTDDEKYLWKDLTLDQAYGDAVENAKDIIACGFDINKTFIFSDLDYmGmSSGFYKNVVKIQKHVTFNQVKGIFGFTDSDCIGKISFPAIQAAPSFSNSFPQIFRDRTDIQCLIPCAIDQDPYFRmTRDVAPRIGYPKPALLHSTFFPALQG---------PNSSIFLTDTAKQIKTKVNKHAFSGGRDTIEEHRQFGGNCDVDVSFmYLTFFLEDDDKLEQIRKDYTSGAmLTGELKKALIEVLQPLIAEHQARRKEVTDEIVKEFmTPRKLS 467
                                   106       116       126       136      |146       156       166  |    176       186       196       206       216       226       236    | |246       256       266       276       286       296       306       316  |    326       336        |-       356       366       376       386       396    |  406       416       426       436       446       456    |  466 
                                                                        143-MSE                   169-MSE                   195-MSE                                       241-MSE                                                                       319-MSE                   345       355                                           401-MSE                 425-MSE                             461-MSE  
                                                                                                                                                                            243-MSE

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Adenine nucleotide alpha hydrolase-like (440)

Superfamily: Nucleotidylyl transferase (325)

Family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain (137)

Protein domain: Tryptophanyl-tRNA synthetase (TrpRS) (28)

Human (Homo sapiens) [TaxId: 9606] (11)

1a	d1r6ua_	A:
1b	d1r6ub_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1 (328)

Human (Homo sapiens) (27)

1a	1r6uB01	B:97-345
1b	1r6uA01	A:82-339

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Tyrosyl-Transfer RNA Synthetase (70)

Homologous Superfamily: Tyrosyl-Transfer RNA Synthetase (70)

Human (Homo sapiens) (11)

2a	1r6uB02	B:355-467
2b	1r6uA02	A:340-469

(no "Pfam Domain" information available for 1R6U)

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.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 1r6u)

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	1r6u
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	SYWC_HUMAN \| P23381	:	1o5t 1r6t 1ulh 2ake 2azx 2dr2 2quh 2qui 2quj 2quk

1n3l	CRYSTAL STRUCTURE OF AN ACTIVE FRAGMENT OF HUMAN TYROSYL- TRNA SYNTHETASE WITH CYTOKINE ACTIVITY
1ntg	CRYSTAL STRUCTURE OF AN EMAP-II LIKE CYTOKINE RELEASED FROM HUMAN TYROSYL-TRNA SYNTHETASE
1r6t	CRYSTAL STRUCTURE OF THE FULL-LENGTH HUMAN TRYPTOPHANYL- TRNA SYNTHETASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 22)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (1, 2)

Exons (9, 18)

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