1ASY | PTR005 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

Title :   CLASS II AMINOACYL TRANSFER RNA SYNTHETASES: CRYSTAL STRUCTURE OF YEAST ASPARTYL-TRNA SYNTHETASE COMPLEXED WITH TRNA ASP

Authors :   M. Ruff, J. Cavarelli, B. Rees, S. Krishnaswamy, J. C. Thierry, D. Moras

Date :   19 Jan 95 (Deposition) - 08 May 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Complex (Aminoacyl-Trna Synthase/Trna) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Ruff, S. Krishnaswamy, M. Boeglin, A. Poterszman, A. Mitschler, A. Podjarny, B. Rees, J. C. Thierry, D. Moras
Class Ii Aminoacyl Transfer Rna Synthetases: Crystal Structure Of Yeast Aspartyl-Trna Synthetase Complexed With Trna(Asp).
Science V. 252 1682 1991
PubMed-ID: 2047877
(for further references see the PDB file header)

Molecule 1 - T-RNA (75-MER)
	Chains	:	R, S
	EC Number	:	6.1.1.12
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - ASPARTYL-TRNA SYNTHETASE
	Chains	:	A, B
	Engineered	:	YES
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	R	S

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 16)

No.	Name	Count	Type	Full Name
1	1MG	2	Mod. Nucleotide	1N-METHYLGUANOSINE-5'-MONOPHOSPHATE
2	5MC	2	Mod. Nucleotide	5-METHYLCYTIDINE-5'-MONOPHOSPHATE
3	5MU	2	Mod. Nucleotide	5-METHYLURIDINE 5'-MONOPHOSPHATE
4	H2U	4	Mod. Nucleotide	5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
5	PSU	6	Mod. Nucleotide	PSEUDOURIDINE-5'-MONOPHOSPHATE

(no "Site" information available for 1ASY)

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

Asymmetric/Biological Unit

No.	Residues
1	Arg A:556	-	Pro A:557
2	Arg B:556	-	Pro B:557

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

(no "PROSITE Motif" information available for 1ASY)

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YLL018C	1	YLL018C.1	XII:111574-109901	1674	SYDC_YEAST	1-557	557	2	A:68-557 B:68-557	490 490

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:490
 aligned with SYDC_YEAST | P04802 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:490
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       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       517       527       537       547       557
           SYDC_YEAST    68 EDTAKDNYGKLPLIQSRDSDRTGQKRVKFVDLDEAKDSDKEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTISKNMVKWAGSLNLESIVLVRGIVKKVDEPIKSATVQNLEIHITKIYTISETPEALPILLEDASRSEAEAEAAGLPVVNLDTRLDYRVIDLRTVTNQAIFRIQAGVCELFREYLATKKFTEVHTPKLLGAPSEGGSSVFEVTYFKGKAYLAQSPQFNKQQLIVADFERVYEIGPVFRAENSNTHRHMTEFTGLDMEMAFEEHYHEVLDTLSELFVFIFSELPKRFAHEIELVRKQYPVEEFKLPKDGKMVRLTYKEGIEMLRAAGKEIGDFEDLSTENEKFLGKLVRDKYDTDFYILDKFPLEIRPFYTMPDPANPKYSNSYDFFMRGEEILSGAQRIHDHALLQERMKAHGLSPEDPGLKDYCDGFSYGCPPHAGGGIGLERVVMFYLDLKNIRRASLFPRDPKRLRP 557
               SCOP domains d1asya1 A:68-204 Aspartyl-tRNA synthetase (AspRS)                                                                                        d1asya2 A:205-557 Aspartyl-tRNA synthetase (AspRS)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1asyA01 A:68-204 Nucleic acid-binding proteins                                                                                           1asyA02 A:205-557 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..................hhh...........eeeeeeeeeee....eeeeeee....eeeeeee........hhhhhhhhh.....eeeeeeeeee............eeeee.eeeeee.........hhhhh..hhhhh........hhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhh......................................hhhhhhhhh....eeeeeeee..............eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh................eeeehhhhhhhhhh............hhhhhhhhhhhhhhh...eeeee.......................eeeee..eeeeeeeee...hhhhhhhhhh.......hhhhhhhhhh......eeeeeeehhhhhhhhh....hhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:68-557 UniProt: 1-557 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                        Transcript 1
                 1asy A  68 EDTAKDNYGKLPLIQSRDSDRTGQKRVKFVDLDEAKDSDKEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTISKNMVKWAGSLNLESIVLVRGIVKKVDEPIKSATVQNLEIHITKIYTISETPEALPILLEDASRSEAEAEAAGLPVVNLDTRLDYRVIDLRTVTNQAIFRIQAGVCELFREYLATKKFTEVHTPKLLGAPSEGGSSVFEVTYFKGKAYLAQSPQFNKQQLIVADFERVYEIGPVFRAENSNTHRHMTEFTGLDMEMAFEEHYHEVLDTLSELFVFIFSELPKRFAHEIELVRKQYPVEEFKLPKDGKMVRLTYKEGIEMLRAAGKEIGDFEDLSTENEKFLGKLVRDKYDTDFYILDKFPLEIRPFYTMPDPANPKYSNSYDFFMRGEEILSGAQRIHDHALLQERMKAHGLSPEDPGLKDYCDGFSYGCPPHAGGGIGLERVVMFYLDLKNIRRASLFPRDPKRLRP 557
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       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       517       527       537       547       557

Chain B from PDB  Type:PROTEIN  Length:490
 aligned with SYDC_YEAST | P04802 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:490
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       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       517       527       537       547       557
           SYDC_YEAST    68 EDTAKDNYGKLPLIQSRDSDRTGQKRVKFVDLDEAKDSDKEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTISKNMVKWAGSLNLESIVLVRGIVKKVDEPIKSATVQNLEIHITKIYTISETPEALPILLEDASRSEAEAEAAGLPVVNLDTRLDYRVIDLRTVTNQAIFRIQAGVCELFREYLATKKFTEVHTPKLLGAPSEGGSSVFEVTYFKGKAYLAQSPQFNKQQLIVADFERVYEIGPVFRAENSNTHRHMTEFTGLDMEMAFEEHYHEVLDTLSELFVFIFSELPKRFAHEIELVRKQYPVEEFKLPKDGKMVRLTYKEGIEMLRAAGKEIGDFEDLSTENEKFLGKLVRDKYDTDFYILDKFPLEIRPFYTMPDPANPKYSNSYDFFMRGEEILSGAQRIHDHALLQERMKAHGLSPEDPGLKDYCDGFSYGCPPHAGGGIGLERVVMFYLDLKNIRRASLFPRDPKRLRP 557
               SCOP domains d1asyb1 B:68-204 Aspartyl-tRNA synthetase (AspRS)                                                                                        d1asyb2 B:205-557 Aspartyl-tRNA synthetase (AspRS)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1asyB01 B:68-204 Nucleic acid-binding proteins                                                                                           1asyB02 B:205-557 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..................hhh..hhhh...eeeeeeeeeeee.......eeeee....eeeee..........hhhhhhhh......eeeeeeeeee............eeeee.eeeeee.........hhhhh..hhhhhh.......hhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhh......................eeee..eeee.....hhhhhhhhh.......eeeeee............eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................eee.hhhhhhhhhhh...........hhhhhhhhhhhhhhh...eeee.......................eeeeee..eeeeeee.....hhhhhhhhhh.......hhhhhhhhhhh............hhhhhhhhh....hhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:68-557 UniProt: 1-557 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                        Transcript 1
                 1asy B  68 EDTAKDNYGKLPLIQSRDSDRTGQKRVKFVDLDEAKDSDKEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTISKNMVKWAGSLNLESIVLVRGIVKKVDEPIKSATVQNLEIHITKIYTISETPEALPILLEDASRSEAEAEAAGLPVVNLDTRLDYRVIDLRTVTNQAIFRIQAGVCELFREYLATKKFTEVHTPKLLGAPSEGGSSVFEVTYFKGKAYLAQSPQFNKQQLIVADFERVYEIGPVFRAENSNTHRHMTEFTGLDMEMAFEEHYHEVLDTLSELFVFIFSELPKRFAHEIELVRKQYPVEEFKLPKDGKMVRLTYKEGIEMLRAAGKEIGDFEDLSTENEKFLGKLVRDKYDTDFYILDKFPLEIRPFYTMPDPANPKYSNSYDFFMRGEEILSGAQRIHDHALLQERMKAHGLSPEDPGLKDYCDGFSYGCPPHAGGGIGLERVVMFYLDLKNIRRASLFPRDPKRLRP 557
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       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       517       527       537       547       557

Chain R from PDB  Type:RNA  Length:75
                                                                                                           
                 1asy R 601 UCCGUGAUAGUUuAAuGGuCAGAAUGGGCGCuUGUCgCGUGCCAGAUcGGGGuuCAAUUCCCCGUCGCGGAGCCA 676
                                   610  |  | 620       630 |    |640     ||651  ||   661       671     
                                      613-PSU |          632-PSU|      646||    ||                     
                                         616-H2U              637-1MG   648|    ||                     
                                            619-H2U                      649-5MC||                     
                                                                              654-5MU                  
                                                                               655-PSU

Chain S from PDB  Type:RNA  Length:75
                                                                                                           
                 1asy S 601 UCCGUGAUAGUUuAAuGGuCAGAAUGGGCGCuUGUCgCGUGCCAGAUcGGGGuuCAAUUCCCCGUCGCGGAGCCA 676
                                   610  |  | 620       630 |    |640     ||651  ||   661       671     
                                      613-PSU |          632-PSU|      646||    ||                     
                                         616-H2U              637-1MG   648|    ||                     
                                            619-H2U                      649-5MC||                     
                                                                              654-5MU                  
                                                                               655-PSU

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: BirA Bifunctional Protein; domain 2 (111)

Homologous Superfamily: Bira Bifunctional Protein; Domain 2 (111)

[unclassified] (3)

1a	1asyA02	A:205-557
1b	1asyB02	B:205-557

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: Nucleic acid-binding proteins (483)

[unclassified] (49)

2a	1asyA01	A:68-204
2b	1asyB01	B:68-204

(no "Pfam Domain" information available for 1ASY)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SYDC_YEAST | P04802)

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:0004815	aspartate-tRNA ligase activity	Catalysis of the reaction: ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp).
	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:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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.
biological process
	GO:0006422	aspartyl-tRNA aminoacylation	The process of coupling aspartate to aspartyl-tRNA, catalyzed by aspartyl-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: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: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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	Ligands, Modified Residues, Ions
		1MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		5MC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		5MU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		H2U	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PSU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 1asy)

	Cis Peptide Bonds
		Arg A:556 - Pro A:557	[ RasMol ]
		Arg B:556 - Pro B:557	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
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	RNA: ribbon; protein: ribbon, secondary structure [ mono GIF format \| stereo GIF format ]
Midas
	RNA: ribbon, plates; protein: ribbon, secondary structure [ mono GIF format \| stereo GIF format ]
	spacefill [ mono GIF format \| stereo GIF format ]
Setor
	RNA: ribbon, sticks; protein: ribbon [ mono GIF format \| stereo GIF format ]
	spacefill [ mono GIF format \| stereo GIF format ]
	RNA: ribbon, sticks; protein: spacefill [ mono GIF format \| stereo GIF format ]
Distance Plot
	representative atom CA, O3* [ mono GIF format \| mono PDF format ]

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(no "Related Entries Specified in the PDB File" available for 1ASY)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 16)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (1, 2)

Sequences/Alignments

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SCOP Domains (2, 4)

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