2HSM - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURAL BASIS OF YEAST AMINOACYL-TRNA SYNTHETASE COMPLEX FORMATION REVEALED BY CRYSTAL STRUCTURES OF TWO BINARY SUB-COMPLEXES

Authors :   H. Simader, D. Suck

Date :   22 Jul 06 (Deposition) - 05 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Protein Complex Protein Interaction Gst-Fold, Ligase/Rna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Simader, M. Hothorn, C. Kohler, J. Basquin, G. Simos, D. Suck
Structural Basis Of Yeast Aminoacyl-Trna Synthetase Complex Formation Revealed By Crystal Structures Of Two Binary Sub-Complexes.
Nucleic Acids Res. V. 34 3968 2006
PubMed-ID: 16914447 | Reference-DOI: 10.1093/NAR/GKL560
(for further references see the PDB file header)

Molecule 1 - GLUTAMYL-TRNA SYNTHETASE, CYTOPLASMIC
	Chains	:	A
	EC Number	:	6.1.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM-DERIVATIVE
	Expression System Strain	:	BL21 DE3 STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-207
	Gene	:	GUS1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	GLUTAMATE-TRNA LIGASE, GLURS, P85

Molecule 2 - GU4 NUCLEIC-BINDING PROTEIN 1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM DERIVATIVE
	Expression System Strain	:	BL21 DE3 STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-122
	Gene	:	ARC1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	G4P1 PROTEIN, P42, ARC1 PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2HSM)

(no "Site" information available for 2HSM)

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

Asymmetric/Biological Unit

No.	Residues
1	Tyr B:18	-	Pro B:19
2	Val B:20	-	Ser B:21

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

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

Asymmetric/Biological Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YGL105W	1	YGL105W.1	VII:307440-308570	1131	ARC1_YEAST	1-376	376	1	B:3-123	121

2.1	YGL245W	1	YGL245W.1	VII:39023-41149	2127	SYEC_YEAST	1-708	708	1	A:19-196	178

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:178
 aligned with SYEC_YEAST | P46655 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
           SYEC_YEAST     1 MPSTLTINGKAPIVAYAELIAARIVNALAPNSIAIKLVDDKKAPAAKLDDATEDVFNKITSKFAAIFDNGDKEQVAKWVNLAQKELVIKNFAKLSQSLETLDSQLNLRTFILGGLKYSAADVACWGALRSNGMCGSIIKNKVDVNVSRWYTLLEMDPIFGEAHDFLSKSLLELKKSAN 178
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhh...eeeeee.......eee.....hhhhhhhhhh.......hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:19-196 UniProt: 1-708 [INCOMPLETE]                                                                                                                                Transcript 2
                 2hsm A  19 MPSTLTINGKAPIVAYAELIAARIVNALAPNSIAIKLVDDKKAPAAKLDDATEDVFNKITSKFAAIFDNGDKEQVAKWVNLAQKELVIKNFAKLSQSLETLDSQLNLRTFILGGLKYSAADVACWGALRSNGMCGSIIKNKVDVNVSRWYTLLEMDPIFGEAHDFLSKSLLELKKSAN 196
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with ARC1_YEAST | P46672 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
           ARC1_YEAST     1 MSDLVTKFESLIISKYPVSFTKEQSAQAAQWESVLKSGQIQPHLDQLNLVLRDNTFIVSTLYPTSTDVHVFEVALPLIKDLVASSKDVKSTYTTYRHILRWIDYMQNLLEVSSTDKLEINH 121
               SCOP domains d2hsmb_ B: GU4 nucleic-binding protein 1, Arc1p                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-123 UniProt: 1-376 [INCOMPLETE]                                                                        Transcript 1
                 2hsm B   3 MSDLVTKFESLIISKYPVSFTKEQSAQAAQWESVLKSGQIQPHLDQLNLVLRDNTFIVSTLYPTSTDVHVFEVALPLIKDLVASSKDVKSTYTTYRHILRWIDYMQNLLEVSSTDKLEINH 123
                                    12        22        32        42        52        62        72        82        92       102       112       122

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: All alpha proteins (14657)

Fold: GST C-terminal domain-like (353)

Superfamily: GST C-terminal domain-like (353)

Family: Arc1p N-terminal domain-like (4)

Protein domain: GU4 nucleic-binding protein 1, Arc1p (4)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (4)

d2hsmb_

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SYEC_YEAST | P46655)

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:0004818	glutamate-tRNA ligase activity	Catalysis of the reaction: ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu).
	GO:0004819	glutamine-tRNA ligase activity	Catalysis of the reaction: ATP + L-glutamine + tRNA(Gln) = AMP + diphosphate + L-glutaminyl-tRNA(Gln).
	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:0016876	ligase activity, forming aminoacyl-tRNA and related compounds	Catalysis of the joining of an amino acid and a nucleic acid (usually tRNA) or poly(ribitol phosphate), with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. The reaction forms an aminoacyl-tRNA or a related compound.
	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:0006425	glutaminyl-tRNA aminoacylation	The process of coupling glutamine to glutaminyl-tRNA, catalyzed by glutaminyl-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:0006424	glutamyl-tRNA aminoacylation	The process of coupling glutamate to glutamyl-tRNA, catalyzed by glutamyl-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.
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:0017102	methionyl glutamyl tRNA synthetase complex	A complex consisting of methionyl- and glutamyl-tRNA synthetases. The tRNA synthetases present in the complex bind to their cognate tRNAs more efficiently than they do as monomers.
	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.

Chain B (ARC1_YEAST | P46672)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0008047	enzyme activator activity	Binds to and increases the activity of an enzyme.
	GO:0080025	phosphatidylinositol-3,5-bisphosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-3,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 5' positions.
	GO:0032266	phosphatidylinositol-3-phosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position.
	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:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
biological process
	GO:0051351	positive regulation of ligase activity	Any process that activates or increases the frequency, rate or extent of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0017102	methionyl glutamyl tRNA synthetase complex	A complex consisting of methionyl- and glutamyl-tRNA synthetases. The tRNA synthetases present in the complex bind to their cognate tRNAs more efficiently than they do as monomers.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2hsm)

	Sites
(no "Sites" information available for 2hsm)

	Cis Peptide Bonds
		Tyr B:18 - Pro B:19	[ RasMol ]
		Val B:20 - Ser B:21	[ RasMol ]

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	2hsm
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		Orientation in Membranes	:	OPM
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	ARC1_YEAST \| P46672
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	SYEC_YEAST \| P46655
		Comparative Protein Structure Models	:	ModBase
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	6.1.1.17
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		Pathway	:	KEGG \| MetaCyc

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	ARC1_YEAST \| P46672
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		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ARC1_YEAST \| P46672	:	2hqt 2hrk 2hsn 4r1j
	SYEC_YEAST \| P46655	:	2hra 2hrk

2hqt	ISOLATED ARC1P N-TERMINUS
2hra	ISOLATED GLURS N-TERMINUS
2hrk	SAME COMPLEX UNDER CRYO CONDITIONS, SLIGHT LATTICE TRANSITION RESULTING IN 14 % LESS SOLVENT.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (2, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (23, 27)

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