1L0W - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   ASPARTYL-TRNA SYNTHETASE-1 FROM SPACE-GROWN CRYSTALS

Authors :   J. D. Ng, C. Sauter, B. Lorber, N. Kirkland, J. Arnez, R. Giege

Date :   14 Feb 02 (Deposition) - 20 Mar 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

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

Keywords :   Space-Grown Crystal, Dimeric Enzyme, Flexible Domains, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. Ng, C. Sauter, B. Lorber, N. Kirkland, J. Arnez, R. Giege
Comparative Analysis Of Space-Grown And Earth-Grown Crystals Of An Aminoacyl-Trna Synthetase: Space-Grown Crystals Are More Useful For Structural Determination.
Acta Crystallogr. , Sect. D V. 58 645 2002
PubMed-ID: 11914489 | Reference-DOI: 10.1107/S0907444902003177
(for further references see the PDB file header)

Molecule 1 - ASPARTYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Synonym	:	ASPARTYL-TRNA SYNTHETASE-1, ASPRS-1, ASPRS, ASPARTATE--TRNA LIGASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1L0W)

(no "Site" information available for 1L0W)

(no "SS Bond" information available for 1L0W)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:272	-	Pro A:273
2	Ala A:561	-	Pro A:562
3	Leu B:1272	-	Pro B:1273

(no "SAP(SNP)/Variant" information available for 1L0W)

(no "PROSITE Motif" information available for 1L0W)

(no "Exon" information available for 1L0W)

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:580
 aligned with SYD_THETH | P36419 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:580
                                    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       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580
           SYD_THETH      1 MRRTHYAGSLRETHVGEEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASPAYATAERVRPEWVVRAKGLVRLRPEPNPRLATGRVEVELSALEVLAEAKTPPFPVDAGWRGEEEKEASEELRLKYRYLDLRRRRMQENLRLRHRVIKAIWDFLDREGFVQVETPFLTKSTPEGARDFLVPYRHEPGLFYALPQSPQLFKQMLMVAGLDRYFQIARCFRDEDLRADRQPDFTQLDLEMSFVEVEDVLELNERLMAHVFREALGVELPLPFPRLSYEEAMERYGSDKPDLRFGLELKEVGPLFRQSGFRVFQEAESVKALALPKALSRKEVAELEEVAKRHKAQGLAWARVEEGGFSGGVAKFLEPVREALLQATEARPGDTLLFVAGPRKVAATALGAVRLRAADLLGLKREGFRFLWVVDFPLLEWDEEEEAWTYMHHPFTSPHPEDLPLLEKDPGRVRALAYDLVLNGVEVGGGSIRIHDPRLQARVFRLLGIGEEEQREKFGFFLEALEYGAPPHGGIAWGLDRLLALMTGSPSIREVIAFPKNKEGKDPLTGAPSPVPEEQLRELGLMVVRP  580
               SCOP domains d1l0wa1 A:1-104 Aspartyl-tRNA synthetase (AspRS)                                                        d1l0wa3 A:105-294,A:415-580 Aspartyl-tRNA synthetase (AspRS)                                                                                                                                  d1l0wa2 A:295-414 Prokaryotic AspRS, insert domain                                                                      d1l0wa3 A:105-294,A:415-580 Aspartyl-tRNA synthetase (AspRS)                                                                                                           SCOP domains
               CATH domains 1l0wA01 A:1-106 Nucleic acid-binding proteins                                                             ------------------------------1l0wA02 A:137-277,A:416-580 Bira Bifunctional Protein; Domain 2                                                                              1l0wA03 A:278-415  [code=3.30.1360.30, no name defined]                                                                                   1l0wA02 A:137-277,A:416-580 Bira Bifunctional Protein; Domain 2                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh..eeeeeeeeeeeee....eeeeeee..eeeeeee.....hhhhhh......eeeeeeeeee............eeeeeeeeeeee..........hhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee.................eee......eeee....hhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh.........eeehhhhhhhhh............ee.hhhhh....hhhhhh.eeeeeee....hhhhhhhhhhhhhhh.....eeeeee..eee..hhhhhh.hhhhhhhhhh.....eeeeeeehhhhhhhhhhhhhhhhhhhh........eeeee.............................hhhhhhhhhh...eeeeee..eeeeeeee...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhh..hhhhhh................ee.hhhhhhhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1l0w A    1 MRRTHYAGSLRETHVGEEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASPAYATAERVRPEWVVRAKGLVRLRPEPNPRLATGRVEVELSALEVLAEAKTPPFPVDAGWRGEEEKEASEELRLKYRYLDLRRRRMQENLRLRHRVIKAIWDFLDREGFVQVETPFLTKSTPEGARDFLVPYRHEPGLFYALPQSPQLFKQMLMVAGLDRYFQIARCFRDEDLRADRQPDFTQLDLEMSFVEVEDVLELNERLMAHVFREALGVELPLPFPRLSYEEAMERYGSDKPDLRFGLELKEVGPLFRQSGFRVFQEAESVKALALPKALSRKEVAELEEVAKRHKAQGLAWARVEEGGFSGGVAKFLEPVREALLQATEARPGDTLLFVAGPRKVAATALGAVRLRAADLLGLKREGFRFLWVVDFPLLEWDEEEEAWTYMHHPFTSPHPEDLPLLEKDPGRVRALAYDLVLNGVEVGGGSIRIHDPRLQARVFRLLGIGEEEQREKFGFFLEALEYGAPPHGGIAWGLDRLLALMTGSPSIREVIAFPKNKEGKDPLTGAPSPVPEEQLRELGLMVVRP  580
                                    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       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580

Chain B from PDB  Type:PROTEIN  Length:580
 aligned with SYD_THETH | P36419 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:580
                                    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       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580
           SYD_THETH      1 MRRTHYAGSLRETHVGEEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASPAYATAERVRPEWVVRAKGLVRLRPEPNPRLATGRVEVELSALEVLAEAKTPPFPVDAGWRGEEEKEASEELRLKYRYLDLRRRRMQENLRLRHRVIKAIWDFLDREGFVQVETPFLTKSTPEGARDFLVPYRHEPGLFYALPQSPQLFKQMLMVAGLDRYFQIARCFRDEDLRADRQPDFTQLDLEMSFVEVEDVLELNERLMAHVFREALGVELPLPFPRLSYEEAMERYGSDKPDLRFGLELKEVGPLFRQSGFRVFQEAESVKALALPKALSRKEVAELEEVAKRHKAQGLAWARVEEGGFSGGVAKFLEPVREALLQATEARPGDTLLFVAGPRKVAATALGAVRLRAADLLGLKREGFRFLWVVDFPLLEWDEEEEAWTYMHHPFTSPHPEDLPLLEKDPGRVRALAYDLVLNGVEVGGGSIRIHDPRLQARVFRLLGIGEEEQREKFGFFLEALEYGAPPHGGIAWGLDRLLALMTGSPSIREVIAFPKNKEGKDPLTGAPSPVPEEQLRELGLMVVRP  580
               SCOP domains d1l0wb1 B:1001-1104 Aspartyl-tRNA synthetase (AspRS)                                                    d1l0wb3 B:1105-1294,B:1415-1580 Aspartyl-tRNA synthetase (AspRS)                                                                                                                              d1l0wb2 B:1295-1414 Prokaryotic AspRS, insert domain                                                                    d1l0wb3 B:1105-1294,B:1415-1580 Aspartyl-tRNA synthetase (AspRS)                                                                                                       SCOP domains
               CATH domains 1l0wB01 B:1001-1106 Nucleic acid-binding proteins                                                         ------------------------------1l0wB02 B:1137-1277,B:1416-1580 Bira Bifunctional Protein; Domain 2                                                                          1l0wB03 B:1278-1415  [code=3.30.1360.30, no name defined]                                                                                 1l0wB02 B:1137-1277,B:1416-1580 Bira Bifunctional Protein; Domain 2                                                                                                   CATH domains
           Pfam domains (1) ------------------tRNA_anti-1l0wB03 B:1019-1100                                                     -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAD-1l0wB01 B:1312-1400                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------------tRNA_anti-1l0wB04 B:1019-1100                                                     -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAD-1l0wB02 B:1312-1400                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------tRNA-synt_2-1l0wB05 B:1123-1553                                                                                                                                                                                                                                                                                                                                                                                                                --------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------tRNA-synt_2-1l0wB06 B:1123-1553                                                                                                                                                                                                                                                                                                                                                                                                                --------------------------- Pfam domains (4)
         Sec.struct. author .....hhhhhhhhhh..eeeeeeeeeeeee....eeeeeee..eeeeeee.....hhhhhh......eeeeeeeeee............eeeeeeeeeeee..........hhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee.................eee......eeee....hhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh.........eeehhhhhhhhh............ee.hhhhh....hhhhhh.eeeeeee....hhhhhhhhhhhhhhh.....eeeeee..eee..hhhhhh.hhhhhhhhhh.....eeeeeeehhhhhhhhhhhhhhhhhhhh........eeeee........................hhhhhhhhhhhhhhh...eeeeee..eeeeeeee...hhhhhhhhhhhhh....hhhhhhhhhhhhhh.....eeeeeeehhhhhhhhhh..hhhhhh................ee.hhhhhhhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1l0w B 1001 MRRTHYAGSLRETHVGEEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASPAYATAERVRPEWVVRAKGLVRLRPEPNPRLATGRVEVELSALEVLAEAKTPPFPVDAGWRGEEEKEASEELRLKYRYLDLRRRRMQENLRLRHRVIKAIWDFLDREGFVQVETPFLTKSTPEGARDFLVPYRHEPGLFYALPQSPQLFKQMLMVAGLDRYFQIARCFRDEDLRADRQPDFTQLDLEMSFVEVEDVLELNERLMAHVFREALGVELPLPFPRLSYEEAMERYGSDKPDLRFGLELKEVGPLFRQSGFRVFQEAESVKALALPKALSRKEVAELEEVAKRHKAQGLAWARVEEGGFSGGVAKFLEPVREALLQATEARPGDTLLFVAGPRKVAATALGAVRLRAADLLGLKREGFRFLWVVDFPLLEWDEEEEAWTYMHHPFTSPHPEDLPLLEKDPGRVRALAYDLVLNGVEVGGGSIRIHDPRLQARVFRLLGIGEEEQREKFGFFLEALEYGAPPHGGIAWGLDRLLALMTGSPSIREVIAFPKNKEGKDPLTGAPSPVPEEQLRELGLMVVRP 1580
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370      1380      1390      1400      1410      1420      1430      1440      1450      1460      1470      1480      1490      1500      1510      1520      1530      1540      1550      1560      1570      1580

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)

Thermus thermophilus. Organism_taxid: 274. (3)

1a	1l0wA02	A:137-277,A:416-580
1b	1l0wB02	B:1137-1277,B:1416-1580

Topology: Gyrase A; domain 2 (166)

Homologous Superfamily: [code=3.30.1360.30, no name defined] (7)

Thermus thermophilus. Organism_taxid: 274. (2)

2a	1l0wA03	A:278-415
2b	1l0wB03	B:1278-1415

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

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

Homologous Superfamily: Nucleic acid-binding proteins (483)

Thermus thermophilus. Organism_taxid: 274. (5)

3a	1l0wA01	A:1-106
3b	1l0wB01	B:1001-1106

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GAD (2)

Family: GAD (2)

Thermus thermophilus (1)

1a	GAD-1l0wB01	B:1312-1400
1b	GAD-1l0wB02	B:1312-1400

Clan: OB (224)

Family: tRNA_anti (18)

Thermus thermophilus (1)

2a	tRNA_anti-1l0wB03	B:1019-1100
2b	tRNA_anti-1l0wB04	B:1019-1100

Clan: tRNA_synt_II (64)

Family: tRNA-synt_2 (8)

Thermus thermophilus (1)

3a	tRNA-synt_2-1l0wB05	B:1123-1553
3b	tRNA-synt_2-1l0wB06	B:1123-1553

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SYD_THETH | P36419)

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: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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:561 - Pro A:562	[ RasMol ]
		Leu A:272 - Pro A:273	[ RasMol ]
		Leu B:1272 - Pro B:1273	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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