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Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF THE HUMAN CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN

Authors :   E. Seiradake, W. Mao, V. Hernandez, S. J. Baker, J. J. Plattner, M. R. K. Alley, S. Cusack

Date :   03 Apr 09 (Deposition) - 19 May 09 (Release) - 23 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.25

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

Keywords :   Aminoacyl-Trna Synthetase, Phosphoprotein, Editing Domain, Nucleotide-Binding, Hydrolysis Of Mis-Charged Trnas, Protein Biosynthesis, Leucyl-Trna Synthetase, Human, Ligase, Cytoplasm, Atp-Binding, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Seiradake, W. Mao, V. Hernandez, S. J. Baker, J. J. Plattner, M. R. K. Alley, S. Cusack
Crystal Structures Of The Human And Fungal Cytosolic Leucyl-Trna Synthetase Editing Domains: A Structural Basis For The Rational Design Of Antifungal Benzoxaboroles.
J. Mol. Biol. V. 390 196 2009
PubMed-ID: 19426743 | Reference-DOI: 10.1016/J.JMB.2009.04.073

Molecule 1 - LEUCYL-TRNA SYNTHETASE, CYTOPLASMIC
	Chains	:	A, B
	EC Number	:	6.1.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPROEX HTB
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	EDITING OR CP1 DOMAIN, RESIDUES 260-509
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	LEUCINE--TRNA LIGASE, LEURS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 20)

No.	Name	Count	Type	Full Name
1	MSE	20	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2WFD)

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:260	-	Pro A:261
2	Glu A:273	-	Pro A:274
3	Gly B:260	-	Pro B:261
4	Glu B:273	-	Pro B:274

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_070438	Y	373	C	SYLC_HUMAN	Disease (ILFS1)	201861847	A/B	Y	373	C

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

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

(no "Exon" information available for 2WFD)

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:252
 aligned with SYLC_HUMAN | Q9P2J5 from UniProtKB/Swiss-Prot  Length:1176

    Alignment length:252
                                   267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507  
           SYLC_HUMAN   258 GVGPQEYTLLKLKVLEPYPSKLSGLKGKNIFLVAATLRPETMFGQTNCWVRPDMKYIGFETVNGDIFICTQKAARNMSYQGFTKDNGVVPVVKELMGEEILGASLSAPLTSYKVIYVLPMLTIKEDKGTGVVTSVPSDSPDDIAALRDLKKKQALRAKYGIRDDMVLPFEPVPVIEIPGFGNLSAVTICDELKIQSQNDREKLAEAKEKIYLKGFYEGIMLVDGFKGQKVQDVKKTIQKKMIDAGDALIYME 509
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeee...hhhhhhhh...eeeeeee.hhhhh....eeee......eeee.....eeeehhhhhhhh.............eeee.........eee........eeeee............eee....hhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------C---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wfd A 258 AmGPQEYTLLKLKVLEPYPSKLSGLKGKNIFLVAATLRPETmFGQTNCWVRPDmKYIGFETVNGDIFICTQKAARNmSYQGFTKDNGVVPVVKELmGEEILGASLSAPLTSYKVIYVLPmLTIKEDKGTGVVTSVPSDSPDDIAALRDLKKKQALRAKYGIRDDmVLPFEPVPVIEIPGFGNLSAVTICDELKIQSQNDREKLAEAKEKIYLKGFYEGImLVDGFKGQKVQDVKKTIQKKmIDAGDALIYmE 509
                             |     267       277       287       297 |     307   |   317       327      |337       347     | 357       367       377       387       397       407       417    |  427       437       447       457       467       477       487       497|      507| 
                             |                                     299-MSE     311-MSE                334-MSE            353-MSE                 377-MSE                                      422-MSE                                                477-MSE              498-MSE   508-MSE
                           259-MSE

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with SYLC_HUMAN | Q9P2J5 from UniProtKB/Swiss-Prot  Length:1176

    Alignment length:252
                                   267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507  
           SYLC_HUMAN   258 GVGPQEYTLLKLKVLEPYPSKLSGLKGKNIFLVAATLRPETMFGQTNCWVRPDMKYIGFETVNGDIFICTQKAARNMSYQGFTKDNGVVPVVKELMGEEILGASLSAPLTSYKVIYVLPMLTIKEDKGTGVVTSVPSDSPDDIAALRDLKKKQALRAKYGIRDDMVLPFEPVPVIEIPGFGNLSAVTICDELKIQSQNDREKLAEAKEKIYLKGFYEGIMLVDGFKGQKVQDVKKTIQKKMIDAGDALIYME 509
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --tRNA-synt_1-2wfdB01 B:260-509                                                                                                                                                                                                                              Pfam domains (1)
           Pfam domains (2) --tRNA-synt_1-2wfdB02 B:260-509                                                                                                                                                                                                                              Pfam domains (2)
         Sec.struct. author ......eeeeeeeee...hhhhhhhh...eeeeeee.hhhhh....eeee......eeee.....eeeehhhhhhhh.............eeee.........eee........eeeee............eee....hhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------C---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wfd B 258 AmGPQEYTLLKLKVLEPYPSKLSGLKGKNIFLVAATLRPETmFGQTNCWVRPDmKYIGFETVNGDIFICTQKAARNmSYQGFTKDNGVVPVVKELmGEEILGASLSAPLTSYKVIYVLPmLTIKEDKGTGVVTSVPSDSPDDIAALRDLKKKQALRAKYGIRDDmVLPFEPVPVIEIPGFGNLSAVTICDELKIQSQNDREKLAEAKEKIYLKGFYEGImLVDGFKGQKVQDVKKTIQKKmIDAGDALIYmE 509
                             |     267       277       287       297 |     307   |   317       327      |337       347     | 357       367       377       387       397       407       417    |  427       437       447       457       467       477       487       497|      507| 
                             |                                     299-MSE     311-MSE                334-MSE            353-MSE                 377-MSE                                      422-MSE                                                477-MSE              498-MSE   508-MSE
                           259-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 '\|'

(no "SCOP Domain" information available for 2WFD)

(no "CATH Domain" information available for 2WFD)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HUP (230)

Family: tRNA-synt_1 (17)

Homo sapiens (Human) (1)

1a	tRNA-synt_1-2wfdB01	B:260-509
1b	tRNA-synt_1-2wfdB02	B:260-509

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SYLC_HUMAN | Q9P2J5)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0002161	aminoacyl-tRNA editing activity	The hydrolysis of an incorrectly aminoacylated tRNA.
	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:0004823	leucine-tRNA ligase activity	Catalysis of the reaction: L-leucine + ATP + tRNA(Leu) = AMP + diphosphate + 2 H(+) + Leu-tRNA(Leu).
	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).
biological process
	GO:0006429	leucyl-tRNA aminoacylation	The process of coupling leucine to leucyl-tRNA, catalyzed by leucyl-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:0006450	regulation of translational fidelity	Any process that modulates the ability of the translational apparatus to interpret the genetic code.
	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.
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: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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	Cis Peptide Bonds
		Glu A:273 - Pro A:274	[ RasMol ]
		Glu B:273 - Pro B:274	[ RasMol ]
		Gly A:260 - Pro A:261	[ RasMol ]
		Gly B:260 - Pro B:261	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 20)

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Cis Peptide Bonds (4, 4)

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