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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL TYROSYL-TRNA SYNTHETASE IN COMPLEX WITH AN ADENYLATE ANALOG

Authors :   L. Bonnefond, M. Frugier, E. Touze, B. Lorber, C. Florentz, R. Giege, C. J. Rudinger-Thirion

Date :   13 Apr 07 (Deposition) - 23 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Aminoacyl-Trna Synthetase, Protein-Substrate Complex, Atp-Binding, Ligase, Mitochondrion, Nucleotide-Binding, Protein Biosynthesis, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Bonnefond, M. Frugier, E. Touze, B. Lorber, C. Florentz, R. Giege, C. Sauter, J. Rudinger-Thirion
Crystal Structure Of Human Mitochondrial Tyrosyl-Trna Synthetase Reveals Common And Idiosyncratic Features.
Structure V. 15 1505 2007
PubMed-ID: 17997975 | Reference-DOI: 10.1016/J.STR.2007.09.018
(for further references see the PDB file header)

Molecule 1 - TYROSYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE70-MT-TYRRS-[DELTA]S4
	Expression System Strain	:	TOP10
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 28-375
	Gene	:	YARS2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TYROSINE-TRNA LIGASE, TYRRS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	YSA	2	Ligand/Ion	5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:77 , GLY A:79 , ASP A:81 , GLY A:90 , HIS A:91 , LEU A:111 , THR A:116 , ASP A:121 , TYR A:221 , GLN A:225 , ASP A:228 , GLN A:241 , GLY A:243 , GLY A:244 , ASP A:246 , GLN A:247 , PRO A:272 , LEU A:273 , ILE A:274 , HOH A:388 , HOH A:400 , HOH A:403	BINDING SITE FOR RESIDUE YSA A 384
2	AC2	SOFTWARE	TYR B:77 , GLY B:79 , ASP B:81 , GLY B:90 , HIS B:91 , ALA B:94 , LEU B:111 , THR B:116 , ASP B:121 , TYR B:221 , GLN B:225 , ASP B:228 , GLN B:241 , GLY B:243 , GLY B:244 , ASP B:246 , GLN B:247 , PRO B:272 , LEU B:273 , ILE B:274 , HOH B:397	BINDING SITE FOR RESIDUE YSA B 384

(no "SS Bond" information available for 2PID)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:52	-	Pro A:53
2	Phe B:52	-	Pro B:53
3	Phe B:72	-	Pro B:73

Asymmetric/Biological Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068646	G	46	D	SYYM_HUMAN	Disease (MLASA2)	587777213	A/B	G	46	D
2	UniProt	VAR_064188	F	52	L	SYYM_HUMAN	Disease (MLASA2)	267607180	A/B	F	52	L
3	UniProt	VAR_034534	G	191	V	SYYM_HUMAN	Polymorphism	11539445	A/B	G	191	V

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.	SYYM_HUMAN	82-92	2	A:82-92 B:82-92

Asymmetric/Biological Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000324868	1	ENSE00000936513	chr12:32908874-32908030	845	SYYM_HUMAN	1-260	260	2	A:37-260 (gaps) B:37-260	224 224
1.2	ENST00000324868	2	ENSE00000936514	chr12:32907019-32906852	168	SYYM_HUMAN	260-316	57	2	A:260-316 (gaps) B:260-316 (gaps)	57 57
1.3	ENST00000324868	3	ENSE00000936515	chr12:32903808-32903653	156	SYYM_HUMAN	316-368	53	2	A:316-368 B:316-368	53 53
1.4	ENST00000324868	4	ENSE00000936516	chr12:32903041-32902871	171	SYYM_HUMAN	368-425	58	2	A:368-373 B:368-373	6 6
1.5	ENST00000324868	5	ENSE00001266823	chr12:32900297-32899479	819	SYYM_HUMAN	425-477	53	0	-	-

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:317
 aligned with SYYM_HUMAN | Q9Y2Z4 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:337
                                    46        56        66        76        86        96       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       
           SYYM_HUMAN    37 GLLAAQKARGLFKDFFPETGTKIELPELFDRGTASFPQTIYCGFDPTADSLHVGHLLALLGLFHLQRAGHNVIALVGGATARLGDPSGRTKEREALETERVRANARALRLGLEALAANHQQLFTDGRSWGSFTVLDNSAWYQKQHLVDFLAAVGGHFRMGTLLSRQSVQLRLKSPEGMSLAEFFYQVLQAYDFYYLFQRYGCRVQLGGSDQLGNIMSGYEFINKLTGEDVFGITVPLITSTTGAKLGKSAGNAVWLNRDKTSPFELYQFFVRQPDDSVERYLKLFTFLPLPEIDHIMQLHVKEPERRGPQKRLAAEVTKLVHGREGLDSAKRCTQAL 373
               SCOP domains d2pida_ A: automated matches                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2pidA01 A:37-273 Tyrosyl-Tran       sfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                2p             idA02 A:274-373 Tyrosyl-Transfer RNA Synthetase                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh...eee.......hhhhhh-------..eeeeee.......hhhhhhhhhhhhhhhhh..eeeeee..hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh....eeeee....-------------.........hhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------D-----L------------------------------------------------------------------------------------------------------------------------------------------V-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------AA_TRNA_LIG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:37-260 (gaps) UniProt: 1-260 [INCOMPLETE]                                                                                                                                                                      -------------------------------------------------------Exon 1.3  PDB: A:316-368 UniProt: 316-368            ----- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.2  PDB: A:260-316 (gaps) UniProt: 260-316         ---------------------------------------------------1.4    Transcript 1 (2)
                 2pid A  37 GLLAAQKARGLFKDFFPETGTKIELPELF-------PQTIYCGFDPTADSLHVGHLLALLGLFHLQRAGHNVIALVGGATARLGDPSGRTKEREALETERVRANARALRLGLEALAANHQQLFTDGRSWGSFTVLDNSAWYQKQHLVDFLAAVGGHFRMGTLLSRQSVQLRLKSPEGMSLAEFFYQVLQAYDFYYLFQRYGCRVQLGGSDQLGNIMSGYEFINKLTGEDVFGITVPLIT-------------AVWLNRDKTSPFELYQFFVRQPDDSVERYLKLFTFLPLPEIDHIMQLHVKEPERRGPQKRLAAEVTKLVHGREGLDSAKRCTQAL 373
                                    46        56        |-      | 76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266        |-         -  |    296       306       316       326       336       346       356       366       
                                                       65      73                                                                                                                                                                                                       275           289

Chain B from PDB  Type:PROTEIN  Length:324
 aligned with SYYM_HUMAN | Q9Y2Z4 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:337
                                    46        56        66        76        86        96       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       
           SYYM_HUMAN    37 GLLAAQKARGLFKDFFPETGTKIELPELFDRGTASFPQTIYCGFDPTADSLHVGHLLALLGLFHLQRAGHNVIALVGGATARLGDPSGRTKEREALETERVRANARALRLGLEALAANHQQLFTDGRSWGSFTVLDNSAWYQKQHLVDFLAAVGGHFRMGTLLSRQSVQLRLKSPEGMSLAEFFYQVLQAYDFYYLFQRYGCRVQLGGSDQLGNIMSGYEFINKLTGEDVFGITVPLITSTTGAKLGKSAGNAVWLNRDKTSPFELYQFFVRQPDDSVERYLKLFTFLPLPEIDHIMQLHVKEPERRGPQKRLAAEVTKLVHGREGLDSAKRCTQAL 373
               SCOP domains d2pidb_ B: automated matches                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2pidB01 B:37-273 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                       2p             idB02 B:274-373 Tyrosyl-Transfer RNA Synthetase                                       CATH domains
           Pfam domains (1) ---------------------------------tRNA-synt_1b-2pidB01 B:70-373                                                                                                                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) ---------------------------------tRNA-synt_1b-2pidB02 B:70-373                                                                                                                                                                                                                                                                                    Pfam domains (2)
         Sec.struct. author hhhhhhhhh....eee.......hhhhhhh........eeeeee.......hhhhhhhhhhhhhhhhh..eeeeee..hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeehhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh...eeeee....-------------.........hhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------D-----L------------------------------------------------------------------------------------------------------------------------------------------V-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------AA_TRNA_LIG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:37-260 UniProt: 1-260 [INCOMPLETE]                                                                                                                                                                             -------------------------------------------------------Exon 1.3  PDB: B:316-368 UniProt: 316-368            ----- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.2  PDB: B:260-316 (gaps) UniProt: 260-316         ---------------------------------------------------1.4    Transcript 1 (2)
                 2pid B  37 GLLAAQKARGLFKDFFPETGTKIELPELFDRGTASFPQTIYCGFDPTADSLHVGHLLALLGLFHLQRAGHNVIALVGGATARLGDPSGRTKEREALETERVRANARALRLGLEALAANHQQLFTDGRSWGSFTVLDNSAWYQKQHLVDFLAAVGGHFRMGTLLSRQSVQLRLKSPEGMSLAEFFYQVLQAYDFYYLFQRYGCRVQLGGSDQLGNIMSGYEFINKLTGEDVFGITVPLIT-------------AVWLNRDKTSPFELYQFFVRQPDDSVERYLKLFTFLPLPEIDHIMQLHVKEPERRGPQKRLAAEVTKLVHGREGLDSAKRCTQAL 373
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266        |-         -  |    296       306       316       326       336       346       356       366       
                                                                                                                                                                                                                                                                        275           289

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: automated matches (67)

Protein domain: automated matches (67)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d2pida_	A:
1b	d2pidb_	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	2pidA01	A:37-273
1b	2pidB01	B:37-273

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	2pidA02	A:274-373
2b	2pidB02	B:274-373

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HUP (230)

Family: tRNA-synt_1b (51)

Homo sapiens (Human) (10)

1a	tRNA-synt_1b-2pidB01	B:70-373
1b	tRNA-synt_1b-2pidB02	B:70-373

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SYYM_HUMAN | Q9Y2Z4)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	GO:0072545	tyrosine binding	Interacting selectively and non-covalently with2-amino-3-(4-hydroxyphenyl)propanoic acid.
	GO:0004831	tyrosine-tRNA ligase activity	Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H(+).
biological process
	GO:0070184	mitochondrial tyrosyl-tRNA aminoacylation	The process of coupling tyrosine to tyrosyl-tRNA in a mitochondrion, catalyzed by tyrosyl-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.
	GO:0043039	tRNA aminoacylation	The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.
	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:0006437	tyrosyl-tRNA aminoacylation	The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-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:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric/Biological Unit
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	SYYM_HUMAN \| Q9Y2Z4	:	3zxi

1vbm	TYROSYL-TRNA SYNTHETASE FROM ESCHERICHIA COLI
3ts1	TYROSYL-TRNA SYNTHETASE FROM BACILLUS STEAROTHERMOPHILUS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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