2YY5 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE FROM MYCOPLASMA PNEUMONIAE

Authors :   T. Ishii, Y. Bessho, S. Yokoyama, Riken Structural Genomics/Proteo Initiative (Rsgi)

Date :   27 Apr 07 (Deposition) - 29 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Aminoaccyl Trna Synthetase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Ishii, Y. Bessho, S. Yokoyama
Crystal Structure Of Tryptophanyl-Trna Synthetase From Mycoplasma Pneumoniae
To Be Published
PubMed: search

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
	Chains	:	A, B, C, D
	EC Number	:	6.1.1.2
	Engineered	:	YES
	Expression System	:	CELL FREE SYSTEM
	Expression System Plasmid	:	PUC18
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	MYCOPLASMA PNEUMONIAE
	Organism Taxid	:	272634
	Strain	:	M129
	Synonym	:	TRYPTOPHAN--TRNA LIGASE, TRPRS

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION
2	WSA	4	Ligand/Ion	5'-O-[(L-TRYPTOPHYLAMINO)SULFONYL]ADENOSINE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION
2	WSA	2	Ligand/Ion	5'-O-[(L-TRYPTOPHYLAMINO)SULFONYL]ADENOSINE

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION
2	WSA	2	Ligand/Ion	5'-O-[(L-TRYPTOPHYLAMINO)SULFONYL]ADENOSINE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS B:16 , ASN B:19 , LYS B:200 , SER B:202 , LYS B:203 , HOH B:1411 , HOH B:1471	BINDING SITE FOR RESIDUE SO4 B 1360
02	AC2	SOFTWARE	GLN B:108 , LYS B:112 , TYR B:133 , GLN B:155 , HIS B:158 , HOH B:1368 , HOH B:1471 , HOH B:1474	BINDING SITE FOR RESIDUE SO4 B 1361
03	AC3	SOFTWARE	HIS A:16 , ASN A:19 , LYS A:200 , SER A:202 , LYS A:203 , HOH A:1410 , HOH A:1482	BINDING SITE FOR RESIDUE SO4 A 1362
04	AC4	SOFTWARE	GLN A:108 , TYR A:133 , GLN A:155 , HIS A:158 , HOH A:1368 , HOH A:1482 , HOH A:1483	BINDING SITE FOR RESIDUE SO4 A 1363
05	AC5	SOFTWARE	HIS D:16 , ASN D:19 , LYS D:200 , SER D:202 , LYS D:203 , HOH D:1480	BINDING SITE FOR RESIDUE SO4 D 1364
06	AC6	SOFTWARE	GLN D:10 , GLN D:108 , LYS D:112 , TYR D:133 , GLN D:155 , HIS D:158 , HOH D:1419	BINDING SITE FOR RESIDUE SO4 D 1365
07	AC7	SOFTWARE	GLN C:108 , TYR C:133 , GLN C:155 , HIS C:158 , HOH C:1426	BINDING SITE FOR RESIDUE SO4 C 1366
08	AC8	SOFTWARE	HIS C:16 , ASN C:19 , LYS C:200 , SER C:202 , LYS C:203 , HOH C:1412	BINDING SITE FOR RESIDUE SO4 C 1367
09	AC9	SOFTWARE	GLY A:8 , GLN A:10 , HIS A:16 , GLY A:18 , ASN A:19 , GLY A:22 , PHE A:39 , HIS A:44 , MET A:137 , ASP A:140 , GLY A:152 , ASP A:154 , GLN A:155 , THR A:188 , ASN A:189 , ARG A:190 , ILE A:191 , LYS A:200 , MET A:201 , LYS A:203 , HOH A:1468 , HOH A:1482	BINDING SITE FOR RESIDUE WSA A 1350
10	BC1	SOFTWARE	THR B:7 , GLY B:8 , GLN B:10 , HIS B:16 , GLY B:18 , ASN B:19 , GLY B:22 , HIS B:44 , MET B:137 , ASP B:140 , GLY B:152 , ASP B:154 , GLN B:155 , THR B:188 , ASN B:189 , ARG B:190 , ILE B:191 , LYS B:200 , MET B:201 , LYS B:203 , HOH B:1368 , HOH B:1400 , HOH B:1420 , HOH B:1471	BINDING SITE FOR RESIDUE WSA B 1351
11	BC2	SOFTWARE	GLY C:8 , GLN C:10 , HIS C:16 , GLY C:18 , ASN C:19 , GLY C:22 , PHE C:39 , HIS C:44 , MET C:137 , ASP C:140 , ILE C:141 , GLY C:152 , ASP C:154 , GLN C:155 , THR C:188 , ASN C:189 , ARG C:190 , ILE C:191 , LYS C:200 , MET C:201 , LYS C:203 , HOH C:1369 , HOH C:1419	BINDING SITE FOR RESIDUE WSA C 1352
12	BC3	SOFTWARE	THR D:7 , GLY D:8 , GLN D:10 , HIS D:16 , GLY D:18 , ASN D:19 , GLY D:22 , HIS D:44 , MET D:137 , ASP D:140 , GLY D:152 , ASP D:154 , GLN D:155 , THR D:188 , ASN D:189 , ARG D:190 , ILE D:191 , LYS D:200 , MET D:201 , LYS D:203 , HOH D:1373 , HOH D:1415 , HOH D:1420	BINDING SITE FOR RESIDUE WSA D 1353

(no "SS Bond" information available for 2YY5)

(no "Cis Peptide Bond" information available for 2YY5)

(no "SAP(SNP)/Variant" information available for 2YY5)

(no "PROSITE Motif" information available for 2YY5)

(no "Exon" information available for 2YY5)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:334
 aligned with SYW_MYCPN | P75510 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:345
                                    11        21        31        41        51        61        71        81        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     
            SYW_MYCPN     2 MKRALTGIQASGKQHLGNYLGVMQSLIELQEQCQLFVFVADLHSITVDFQPQALKQNNFDLVRTLLAVGLDPQKACLFLQSDLLEHSMMGYLMMVQSNLGELQRMTQFKAKKAEQTRNPNGTLNIPTGLLTYPALMAGDILLYQPDIVPVGNDQKQHLELTRDLAQRIQKKFKLKLRLPQFVQNKDTNRIMDLFDPTKKMSKSSKNQNGVIYLDDPKEVVVKKIRQATTDSFNKIRFAPKTQPGVTNMLTILKALLKEPVNQSLTNQLGNDLEAYFSTKSYLDLKNALTEATVNLLVNIQRKREQISREQVFNCLQAGKNQAQATARTTLALFYDGFGLGSQNIK 346
               SCOP domains d2yy5a_ A: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2yy5A01 A:2-190,A:310-346 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                              2yy5A02 A:191-309 Tyrosyl-Transfer RNA Synthetase                                                                      2yy5A01 A:2-190,A:310-346             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhh..hhhhhhhhheeeeeehhhhhh....hhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..-----------...hhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhh......eee.......................hhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yy5 A   2 MKRALTGIQASGKQHLGNYLGVMQSLIELQEQCQLFVFVADLHSITVDFQPQALKQNNFDLVRTLLAVGLDPQKACLFLQSDLLEHSMMGYLMMVQSNLGELQRMTQFKAKK-----------NIPTGLLTYPALMAGDILLYQPDIVPVGNDQKQHLELTRDLAQRIQKKFKLKLRLPQFVQNKDTNRIMDLFDPTKKMSKSSKNQNGVIYLDDPKEVVVKKIRQATTDSFNKIRFASKTQPGVTNMLTILKALLKEPVNQSLTNQLGNDLEAYFSTKSYLDLKNALTEATVNLLVNIQRKREQISREQVFNCLQAGKNQAQATARTTLALFYDGFGLGSQNIK 346
                                    11        21        31        41        51        61        71        81        91       101       111 |       -   |   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341     
                                                                                                                                         113         125

Chain B from PDB  Type:PROTEIN  Length:346
 aligned with SYW_MYCPN | P75510 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:346
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340      
            SYW_MYCPN     1 MMKRALTGIQASGKQHLGNYLGVMQSLIELQEQCQLFVFVADLHSITVDFQPQALKQNNFDLVRTLLAVGLDPQKACLFLQSDLLEHSMMGYLMMVQSNLGELQRMTQFKAKKAEQTRNPNGTLNIPTGLLTYPALMAGDILLYQPDIVPVGNDQKQHLELTRDLAQRIQKKFKLKLRLPQFVQNKDTNRIMDLFDPTKKMSKSSKNQNGVIYLDDPKEVVVKKIRQATTDSFNKIRFAPKTQPGVTNMLTILKALLKEPVNQSLTNQLGNDLEAYFSTKSYLDLKNALTEATVNLLVNIQRKREQISREQVFNCLQAGKNQAQATARTTLALFYDGFGLGSQNIK 346
               SCOP domains d2yy5b_ B: automated matches                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2yy5B01 B:1-190,B:310-346 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                               2yy5B02 B:191-309 Tyrosyl-Transfer RNA Synthetase                                                                      2yy5B01 B:1-190,B:310-346             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......hhhhhhhh..hhhhhhhhheeeeeehhhhhh....hhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhh......eee.......................hhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yy5 B   1 MMKRALTGIQASGKQHLGNYLGVMQSLIELQEQCQLFVFVADLHSITVDFQPQALKQNNFDLVRTLLAVGLDPQKACLFLQSDLLEHSMMGYLMMVQSNLGELQRMTQFKAKKAEQTRNPNGTLNIPTGLLTYPALMAGDILLYQPDIVPVGNDQKQHLELTRDLAQRIQKKFKLKLRLPQFVQNKDTNRIMDLFDPTKKMSKSSKNQNGVIYLDDPKEVVVKKIRQATTDSFNKIRFASKTQPGVTNMLTILKALLKEPVNQSLTNQLGNDLEAYFSTKSYLDLKNALTEATVNLLVNIQRKREQISREQVFNCLQAGKNQAQATARTTLALFYDGFGLGSQNIK 346
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340

Chain C from PDB  Type:PROTEIN  Length:336
 aligned with SYW_MYCPN | P75510 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:345
                                    11        21        31        41        51        61        71        81        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     
            SYW_MYCPN     2 MKRALTGIQASGKQHLGNYLGVMQSLIELQEQCQLFVFVADLHSITVDFQPQALKQNNFDLVRTLLAVGLDPQKACLFLQSDLLEHSMMGYLMMVQSNLGELQRMTQFKAKKAEQTRNPNGTLNIPTGLLTYPALMAGDILLYQPDIVPVGNDQKQHLELTRDLAQRIQKKFKLKLRLPQFVQNKDTNRIMDLFDPTKKMSKSSKNQNGVIYLDDPKEVVVKKIRQATTDSFNKIRFAPKTQPGVTNMLTILKALLKEPVNQSLTNQLGNDLEAYFSTKSYLDLKNALTEATVNLLVNIQRKREQISREQVFNCLQAGKNQAQATARTTLALFYDGFGLGSQNIK 346
               SCOP domains d2yy5c_ C: automated matches                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2yy5C01 C:2-190,C:310-346 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                              2yy5C02 C:191-309 Tyrosyl-Transfer RNA Synthetase                                                                      2yy5C01 C:2-190,C:310-346             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhh..hhhhhhhhheeeeeehhhhhh....hhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh---------....hhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhh......eee.......................hhhhh.....hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yy5 C   2 MKRALTGIQASGKQHLGNYLGVMQSLIELQEQCQLFVFVADLHSITVDFQPQALKQNNFDLVRTLLAVGLDPQKACLFLQSDLLEHSMMGYLMMVQSNLGELQRMTQFKAKKA---------LNIPTGLLTYPALMAGDILLYQPDIVPVGNDQKQHLELTRDLAQRIQKKFKLKLRLPQFVQNKDTNRIMDLFDPTKKMSKSSKNQNGVIYLDDPKEVVVKKIRQATTDSFNKIRFASKTQPGVTNMLTILKALLKEPVNQSLTNQLGNDLEAYFSTKSYLDLKNALTEATVNLLVNIQRKREQISREQVFNCLQAGKNQAQATARTTLALFYDGFGLGSQNIK 346
                                    11        21        31        41        51        61        71        81        91       101       111  |      -  |    131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341     
                                                                                                                                          114       124

Chain D from PDB  Type:PROTEIN  Length:346
 aligned with SYW_MYCPN | P75510 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:346
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340      
            SYW_MYCPN     1 MMKRALTGIQASGKQHLGNYLGVMQSLIELQEQCQLFVFVADLHSITVDFQPQALKQNNFDLVRTLLAVGLDPQKACLFLQSDLLEHSMMGYLMMVQSNLGELQRMTQFKAKKAEQTRNPNGTLNIPTGLLTYPALMAGDILLYQPDIVPVGNDQKQHLELTRDLAQRIQKKFKLKLRLPQFVQNKDTNRIMDLFDPTKKMSKSSKNQNGVIYLDDPKEVVVKKIRQATTDSFNKIRFAPKTQPGVTNMLTILKALLKEPVNQSLTNQLGNDLEAYFSTKSYLDLKNALTEATVNLLVNIQRKREQISREQVFNCLQAGKNQAQATARTTLALFYDGFGLGSQNIK 346
               SCOP domains d2yy5d_ D: automated matches                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2yy5D01 D:1-190,D:310-346 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                               2yy5D02 D:191-309 Tyrosyl-Transfer RNA Synthetase                                                                      2yy5D01 D:1-190,D:310-346             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......hhhhhhhh..hhhhhhhhheeeeeehhhhhh....hhhhhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhh......eee.......................hhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhh....hhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yy5 D   1 MMKRALTGIQASGKQHLGNYLGVMQSLIELQEQCQLFVFVADLHSITVDFQPQALKQNNFDLVRTLLAVGLDPQKACLFLQSDLLEHSMMGYLMMVQSNLGELQRMTQFKAKKAEQTRNPNGTLNIPTGLLTYPALMAGDILLYQPDIVPVGNDQKQHLELTRDLAQRIQKKFKLKLRLPQFVQNKDTNRIMDLFDPTKKMSKSSKNQNGVIYLDDPKEVVVKKIRQATTDSFNKIRFASKTQPGVTNMLTILKALLKEPVNQSLTNQLGNDLEAYFSTKSYLDLKNALTEATVNLLVNIQRKREQISREQVFNCLQAGKNQAQATARTTLALFYDGFGLGSQNIK 346
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340

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 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)

Mycoplasma pneumoniae [TaxId: 272634] (1)

1a	d2yy5a_	A:
1b	d2yy5b_	B:
1c	d2yy5c_	C:
1d	d2yy5d_	D:

Asymmetric 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)

Mycoplasma pneumoniae m129. Organism_taxid: 272634. Strain: m129. (1)

1a	2yy5A01	A:2-190,A:310-346
1b	2yy5C01	C:2-190,C:310-346
1c	2yy5B01	B:1-190,B:310-346
1d	2yy5D01	D:1-190,D:310-346

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Tyrosyl-Transfer RNA Synthetase (70)

Homologous Superfamily: Tyrosyl-Transfer RNA Synthetase (70)

Mycoplasma pneumoniae m129. Organism_taxid: 272634. Strain: m129. (1)

2a	2yy5A02	A:191-309
2b	2yy5B02	B:191-309
2c	2yy5C02	C:191-309
2d	2yy5D02	D:191-309

(no "Pfam Domain" information available for 2YY5)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SYW_MYCPN | P75510)

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:0004830	tryptophan-tRNA ligase activity	Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp).
biological process
	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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2yy5)

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Access by PDB/NDB ID
	2yy5
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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Access by UniProt ID/Accession number
	SYW_MYCPN \| P75510
		Comparative Protein Structure Models	:	ModBase
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Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

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Cis Peptide Bonds (0, 0)

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