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Title :   CRYSTAL STRUCTURE OF CLASS I LYSYL-TRNA SYNTHETASE

Authors :   O. Nureki, T. Terada, R. Ishitani, A. Ambrogelly, M. Ibba, D. Soll, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   25 Oct 01 (Deposition) - 17 Apr 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Beta Sandwitch, Zinc-Binding Structure, Rossmann Fold, Alpha-Helix Cage, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Terada, O. Nureki, R. Ishitani, A. Ambrogelly, M. Ibba, D. Soll, S. Yokoyama
Functional Convergence Of Two Lysyl-Trna Synthetases With Unrelated Topologies.
Nat. Struct. Biol. V. 9 257 2002
PubMed-ID: 11887185 | Reference-DOI: 10.1038/NSB777
(for further references see the PDB file header)

Molecule 1 - LYSYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:95 , CYS A:99 , HIS A:100 , HIS A:106	BINDING SITE FOR RESIDUE ZN A 600
2	AC2	SOFTWARE	CYS A:177 , HIS A:180 , CYS A:199 , HIS A:203	BINDING SITE FOR RESIDUE ZN A 601
3	AC3	SOFTWARE	ASP B:95 , CYS B:99 , HIS B:100 , HIS B:106	BINDING SITE FOR RESIDUE ZN B 600
4	AC4	SOFTWARE	CYS B:177 , TYR B:197 , CYS B:199	BINDING SITE FOR RESIDUE ZN B 602

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

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

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

Asymmetric Unit (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.	SYK_PYRHO	30-39	2	A:30-39 B:30-39

Biological Unit 1 (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.	SYK_PYRHO	30-39	1	A:30-39 -

Biological Unit 2 (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.	SYK_PYRHO	30-39	1	- B:30-39

(no "Exon" information available for 1IRX)

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:507
 aligned with SYK_PYRHO | O57963 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:521
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522 
            SYK_PYRHO     3 HWADYIADKIIRERGEKEKYVVESGITPSGYVHVGNFRELFTAYIVGHALRDKGYEVRHIHMWDDYDRFRKVPRNVPQEWKDYLGMPISEVPDPWGCHESYAEHFMRKFEEEVEKLGIEVDFLYASELYKRGEYSEEIRLAFEKRDKIMEILNKYREIAKQPPLPENWWPAMVYCPEHRREAEIIEWDGGWKVKYKCPEGHEGWVDIRSGNVKLRWRVDWPMRWSHFGVDFEPAGKDHLVAGSSYDTGKEIIKEVYGKEAPLSLMYEFVGIKGQKGKMSGSKGNVILLSDLYEVLEPGLVRFIYARHRPNKEIKIDLGLGILNLYDEFDKVERIYFGVEGGKGDDEELRRTYELSMPKKPERLVAQAPFRFLAVLVQLPHLTEEDIINVLIKQGHIPRDLSKEDVERVKLRINLARNWVKKYAPEDVKFSILEKPPEVEVSEDVREAMNEVAEWLENHEEFSVEEFNNILFEVAKRRGISSREWFSTLYRLFIGKERGPRLASFLASLDRSFVIKRLRLEG 523
               SCOP domains d1irxa2 A:3-319 Class I lysyl-tRNA synthetase                                                                                                                                                                                                                                                                                d1irxa1 A:320-523 C-ter     minal domain of class I lysyl-tRNA synthetase                                                                                                                                    SCOP domains
               CATH domains 1irxA01 A:3-169,A:213-269 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                        1irxA02 A:170-212                          1irxA01 A:3-169,A:213-269                                -----------------------------------------------------------------------------------------------------------------------------------------------------------------1irxA05 A:431-523  [code=1.10.10.350, no name defined]                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....eeeeeeee......hhhhhhhhhhhhhhhhhhhh...eeeeeeee.............hhhhhhhh...............hhhhhhhhhhhhhhhh.....eeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee......ee.eeee.....eee........ee......eeehhhhhhhhhhhhh......eehhhhh..hhhhhhhhhhhhhhh.......ee..eee...---------...hhhhhhh..hhhhhhhhhhh......eee....hhhhhhhhhhhhhhhhh....-----hhhhhhhhhhh...........hhhhhhhhh.....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.hhhhh............hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------AA_TRNA_LI---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1irx A   3 HWADYIADKIIRERGEKEKYVVESGITPSGYVHVGNFRELFTAYIVGHALRDKGYEVRHIHMWDDYDRFRKVPRNVPQEWKDYLGMPISEVPDPWGCHESYAEHFMRKFEEEVEKLGIEVDLLYASELYKRGEYSEEIRLAFEKRDKIMEILNKYREIAKQPPLPENWWPAMVYCPEHRREAEIIEWDGGWKVKYKCPEGHEGWVDIRSGNVKLRWRVDWPMRWSHFGVDFEPAGKDHLVAGSSYDTGKEIIKEVYGKEAPLSLMYEFVGIKGQ---------NVILLSDLYEVLEPGLVRFIYARHRPNKEIKIDLGLGILNLYDEFEKVERIYFGVEG-----EELRRTYELSMPKKPERLVAQAPFRFLAVLVQLPHLTEEDIINVLIKQGHIPRDLSKEDVERVKLRINLARNWVKKYAPEDVKFSILEKPPEVEVSEDVREAMNEVAEWLENHEEFSVEEFNNILFEVAKRRGISSREWFSTLYRLFIGKERGPRLASFLASLDRSFVIKRLRLEG 523
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   |     -   |   292       302       312       322       332       342     | 352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522 
                                                                                                                                                                                                                                                                                                           276       286                                                     342   348

Chain B from PDB  Type:PROTEIN  Length:508
 aligned with SYK_PYRHO | O57963 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:521
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522 
            SYK_PYRHO     3 HWADYIADKIIRERGEKEKYVVESGITPSGYVHVGNFRELFTAYIVGHALRDKGYEVRHIHMWDDYDRFRKVPRNVPQEWKDYLGMPISEVPDPWGCHESYAEHFMRKFEEEVEKLGIEVDFLYASELYKRGEYSEEIRLAFEKRDKIMEILNKYREIAKQPPLPENWWPAMVYCPEHRREAEIIEWDGGWKVKYKCPEGHEGWVDIRSGNVKLRWRVDWPMRWSHFGVDFEPAGKDHLVAGSSYDTGKEIIKEVYGKEAPLSLMYEFVGIKGQKGKMSGSKGNVILLSDLYEVLEPGLVRFIYARHRPNKEIKIDLGLGILNLYDEFDKVERIYFGVEGGKGDDEELRRTYELSMPKKPERLVAQAPFRFLAVLVQLPHLTEEDIINVLIKQGHIPRDLSKEDVERVKLRINLARNWVKKYAPEDVKFSILEKPPEVEVSEDVREAMNEVAEWLENHEEFSVEEFNNILFEVAKRRGISSREWFSTLYRLFIGKERGPRLASFLASLDRSFVIKRLRLEG 523
               SCOP domains d1irxb2 B:3-319 Class I lysyl-tRNA synthetase                                                                                                                                                                                                                                                                                d1irxb1 B:320-523 C-ter    minal domain of class I lysyl-tRNA synthetase                                                                                                                                     SCOP domains
               CATH domains 1irxB01 B:3-169,B:213-269 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                        1irxB02 B:170-212                          1irxB01 B:3-169,B:213-269                                -----------------------------------------------------------------------------------------------------------------------------------------------------------------1irxB05 B:431-523  [code=1.10.10.350, no name defined]                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh...ee..eeee......hhhhhhhhhhhhhhhhhhhh...ee..eeee....................................hhhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeee...eeeeeeeee....eeeee.......eee.....eeehhhhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhh......eeee...eee...---------...hhhhhhh..hhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhhhh....----.hhhhhhhhhhh...........hhhhhhhhh.....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------AA_TRNA_LI---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1irx B   3 HWADYIADKIIRERGEKEKYVVESGITPSGYVHVGNFRELFTAYIVGHALRDKGYEVRHIHMWDDYDRFRKVPRNVPQEWKDYLGMPISEVPDPWGCHESYAEHFMRKFEEEVEKLGIEVDLLYASELYKRGEYSEEIRLAFEKRDKIMEILNKYREIAKQPPLPENWWPAMVYCPEHRREAEIIEWDGGWKVKYKCPEGHEGWVDIRSGNVKLRWRVDWPMRWSHFGVDFEPAGKDHLVAGSSYDTGKEIIKEVYGKEAPLSLMYEFVGIKGQ---------NVILLSDLYEVLEPGLVRFIYARHRPNKEIKIDLGLGILNLYDEFEKVERIYFGVEG----DEELRRTYELSMPKKPERLVAQAPFRFLAVLVQLPHLTEEDIINVLIKQGHIPRDLSKEDVERVKLRINLARNWVKKYAPEDVKFSILEKPPEVEVSEDVREAMNEVAEWLENHEEFSVEEFNNILFEVAKRRGISSREWFSTLYRLFIGKERGPRLASFLASLDRSFVIKRLRLEG 523
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   |     -   |   292       302       312       322       332       342    |  352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522 
                                                                                                                                                                                                                                                                                                           276       286                                                     342  347

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 "Pfam Domain" information available for 1IRX)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SYK_PYRHO | O57963)

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: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:0004824	lysine-tRNA ligase activity	Catalysis of the reaction: ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
biological process
	GO:0006430	lysyl-tRNA aminoacylation	The process of coupling lysine to lysyl-tRNA, catalyzed by lysyl-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.

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