1JII - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF S. AUREUS TYRRS IN COMPLEX WITH SB-219383

Authors :   X. Qiu, C. A. Janson, W. W. Smith, R. L. Jarvest

Date :   02 Jul 01 (Deposition) - 26 Oct 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)
Biol. Unit 2: A  (2x)

Keywords :   Tyrosyl-Trna Synthetase, Staphylococcus Aureus, Truncation, Structure Based Inhibitor Design, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Qiu, C. A. Janson, W. W. Smith, S. M. Green, P. Mcdevitt, K. Johanson, P. Carter, M. Hibbs, C. Lewis, A. Chalker, A. Fosberry, J. Lalonde, J. Berge, P. Brown, C. S. Houge-Frydrych, R. L. Jarvest
Crystal Structure Of Staphylococcus Aureus Tyrosyl-Trna Synthetase In Complex With A Class Of Potent And Specific Inhibitors.
Protein Sci. V. 10 2008 2001
PubMed-ID: 11567092 | Reference-DOI: 10.1110/PS.18001

Molecule 1 - TYROSYL-TRNA SYNTHETASE
	Chains	:	A
	EC Number	:	6.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Synonym	:	TYROSINE--TRNA LIGASE
	Variant	:	AUREUS N315

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	383	1	Ligand/Ion	[2-AMINO-3-(4-HYDROXY-PHENYL)-PROPIONYLAMINO]- (2,4,5,8-TETRAHYDROXY-7-OXA-2-AZA-BICYCLO[3.2.1]OCT-3-YL)-ACETIC ACID

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	383	2	Ligand/Ion	[2-AMINO-3-(4-HYDROXY-PHENYL)-PROPIONYLAMINO]- (2,4,5,8-TETRAHYDROXY-7-OXA-2-AZA-BICYCLO[3.2.1]OCT-3-YL)-ACETIC ACID

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	383	2	Ligand/Ion	[2-AMINO-3-(4-HYDROXY-PHENYL)-PROPIONYLAMINO]- (2,4,5,8-TETRAHYDROXY-7-OXA-2-AZA-BICYCLO[3.2.1]OCT-3-YL)-ACETIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:36 , GLY A:38 , ALA A:39 , ASP A:40 , GLY A:49 , HIS A:50 , PRO A:53 , LEU A:70 , ASP A:80 , ASN A:124 , TYR A:170 , GLN A:174 , ASP A:177 , ASP A:195 , GLN A:196	BINDING SITE FOR RESIDUE 383 A 421

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

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

(no "SAP(SNP)/Variant" information available for 1JII)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_I	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.	SYY_STAAE	41-51	1	A:41-51

Biological Unit 1 (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.	SYY_STAAE	41-51	2	A:41-51

Biological Unit 2 (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.	SYY_STAAE	41-51	2	A:41-51

(no "Exon" information available for 1JII)

Asymmetric 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:319
 aligned with SYY_STAAE | A6QHR2 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:319
                                    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         
            SYY_STAAE     2 TNVLIEDLKWRGLIYQQTDEQGIEDLLNKEQVTLYCGADPTADSLHIGHLLPFLTLRRFQEHGHRPIVLIGGGTGMIGDPSGKSEERVLQTEEQVDKNIEGISKQMHNIFEFGTDHGAVLVNNRDWLGQISLISFLRDYGKHVGVNYMLGKDSIQSRLEHGISYTEFTYTILQAIDFGHLNRELNCKIQVGGSDQWGNITSGIELMRRMYGQTDAYGLTIPLVTKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWINQSDEDVIKFLKYFTFLGKEEIDRLEQSKNEAPHLREAQKTLAEEVTKFIHGEDALNDAIRIS 320
               SCOP domains d1jiia_ A: Tyrosyl-tRNA synthetase (TyrRS)                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -1jiiA01 A:3-223 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                        1jiiA02 A:224-319 Tyrosyl-Transfer RNA Synthetase                                               - CATH domains
               Pfam domains --------------------------tRNA-synt_1b-1jiiA01 A:28-320                                                                                                                                                                                                                                                                         Pfam domains
         Sec.struct. author .hhhhhhhhhhh...ee.hhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhh....eeeeee...hhhhh............hhhhhhhhhhhhhhhhhhhh........eeeehhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh.....eeeee..........................hhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------AA_TRNA_LIG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jii A   2 TNVLIEDLKWRGLIYQQTDEQGIEDLLNKEQVTLYCGADPTADSLHIGHLLPFLTLRRFQEHGHRPIVLIGGGTGMIGDPSGKSEERVLQTEEQVDKNIEGISKQMHNIFEFGTDHGAVLVNNRDWLGQISLISFLRDYGKHVGVNYMLGKDSIQSRLEHGISYTEFTYTILQAIDFGHLNRELNCKIQVGGSDQWGNITSGIELMRRMYGQTDAYGLTIPLVTKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWINQSDEDVIKFLKYFTFLGKEEIDRLEQSKNEAPHLREAQKTLAEEVTKFIHGEDALNDAIRIS 320
                                    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

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

Protein domain: Tyrosyl-tRNA synthetase (TyrRS) (25)

Staphylococcus aureus [TaxId: 1280] (4)

d1jiia_

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HUP (230)

Family: tRNA-synt_1b (51)

Staphylococcus aureus (strain Newman) (4)

tRNA-synt_1b-1jiiA01

A:28-320

Asymmetric Unit(hide GO term definitions)

Chain A (SYY_STAAE | A6QHR2)

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: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: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.

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Biological Units
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	SYY_STAAE \| A6QHR2	:	1jij 1jik 1jil

1jij	SAME PROTEIN, DIFFERENT INHIBITOR
1jik	SAME PROTEIN, DIFFERENT INHIBITOR
1jil	SAME PROTEIN, DIFFERENT INHIBITOR

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