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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF ALANYL-TRNA SYNTHETASE WITHOUT OLIGOMERIZATION DOMAIN

Authors :   M. Sokabe, T. Ose, K. Tokunaga, A. Nakamura, O. Nureki, M. Yao, I. Tanaka

Date :   10 Feb 09 (Deposition) - 21 Jul 09 (Release) - 21 Jul 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A

Keywords :   Ligase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sokabe, T. Ose, A. Nakamura, K. Tokunaga, O. Nureki, M. Yao, I. Tanaka
The Structure Of Alanyl-Trna Synthetase With Editing Domain.
Proc. Natl. Acad. Sci. Usa V. 106 11028 2009
PubMed-ID: 19549823 | Reference-DOI: 10.1073/PNAS.0904645106
(for further references see the PDB file header)

Molecule 1 - ALANYL-TRNA SYNTHETASE
	Chains	:	A
	EC Number	:	6.1.1.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET26
	Expression System Strain	:	BL21(DE3)-CODONPLUS-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ALAS, PH0297, PH0297
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953
	Strain	:	OT3
	Synonym	:	ALANINE-TRNA LIGASE, ALARS

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:613 , HIS A:617 , GLN A:715 , CYS A:717 , HOH A:759	BINDING SITE FOR RESIDUE ZN A 753
2	AC2	SOFTWARE	CYS A:20 , CYS A:23 , CYS A:37 , CYS A:42	BINDING SITE FOR RESIDUE ZN A 754

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

Asymmetric/Biological Unit

No.	Residues
1	Pro A:40	-	Pro A:41
2	Gln A:105	-	Pro A:106
3	Asn A:118	-	Pro A:119

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_II_ALA	PS50860	Alanyl-transfer RNA synthetases family profile.	SYA_PYRHO	57-760	1	A:57-752

(no "Exon" information available for 2ZZF)

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:728
 aligned with SYA_PYRHO | O58035 from UniProtKB/Swiss-Prot  Length:915

    Alignment length:751
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751 
            SYA_PYRHO     2 EFIMKTRMFEEEGWIRKKCKVCGKPFWTLDPDRETCGDPPCDEYQFIGKPGIPRKYTLDEMREKFLRFFEKHEIYPHGRVKRYPVLPRWRDDVLLVGASIMDFQPWVISGEADPPANPLVISQPSIRFTDIDNVGITGRHFTIFEMMAHHAFNYPGKPIYWMDETVELAFEFFTKELKMKPEDITFKENPWAGGGNAGPAFEVLYRGLEVATLVFMQYKKAPENAPQDQVVVIKGEKYIPMETKVVDTGYGLERLVWMSQGTPTAYDAVLGYVVEPLKKMAGIEKIDEKILMENSRLAGMFDIEDLGDLRYLREQVAKRVGITVEELEKAIRPYELIYAIADHTKALTFMLADGVVPSNVKAGYLARLLIRKSIRHLRELGLEVPLSEIVALHIKELHKTFPEFKEMEDIILEMIELEEKKYAETLRRGSDLVRREIAKLKKKGIKEIPVEKLVTFYESHGLTPEIVKEIAEKEGVKVNIPDNFYSMVAKEAERTKEEKGEELVDFELLKDLPDTRRLYYEDPFMKEFDAKVLRVIKDWVILDATAFYPEGGGQPYDTGVLIVNGREVKVTNVQKVGKVIIHKVEDPGAFKEGMIVHGKIDWKRRIQHMRHHTGTHVLMGALVRVLGRHVWQAGSQLTTDWARLDISHYKRISEEELKEIEMLANRIVMEDRKVTWEWLPRTTAEQKYGFRLYQGGVVPGREIRVVKIEDWDVQACGGTHLPSTGLVGPIKILRTERIQDGVERIIFACGE 752
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------tRNA-synt_2c-2zzfA02 A:61-605                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    --------------------------------------------------------------------------------------------------tRNA_SAD-2zzfA01 A:704-747                  ----- Pfam domains
         Sec.struct. author .....hhhhhhh..eeee......eeee............................hhhhhhhhhhhhhhh......ee..................hhhhhhh..............eeeeeeee...hhhhh........eeeeeeeeeee.......hhhhhhhhhhhhhhhh...hhh.eeeee..ee...eee.eeeeee..eeeeeeeeeeee.----------------...eeeeeeeeeeeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhh..........hhhhhhhhh....-------.............eehhhhh....eeeeeeeeee..eeee.ee.............eeee....eeeeeeeeee..eeeeee.hhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhh........eeeeeee...eeee........hhhhh.eeeeeeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------AA_TRNA_LIGASE_II_ALA  PDB: A:57-752 UniProt: 57-760                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zzf A   2 EFIMKTRMFEEEGWIRKKCKVCGKPFWTLDPDRETCGDPPCDEYQFIGKPGIPRKYTLDEMREKFLRFFEKHEIYPHGRVKRYPVLPRWRDDVLLVGASIMDFQPWVISGEADPPANPLVISQPSIRFTDIDNVGITGRHFTIFEMMAHHAFNYPGKPIYWMDETVELAFEFFTKELKMKPEDITFKENPWAGGGNAGPAFEVLYRGLEVATLVFMQYKK----------------KYIPMETKVVDTGYGLERLVWMSQGTPTAYDAVLGYVVEPLKKMAGIEKIDEKILMENSRLAGMFDIEDLGDLRYLREQVAKRVGITVEELEKAIRPYELIYAIADHTKALTFMLADGVVPSNVKAGYLARLLIRKSIRHLRELGLEVPLSEIVALHIKELHKTFPEFKEMEDIILEMIELEEKKYAETLRRGSDLVRREIAKLKKKGIKEIPVEKLVTFYESHGLTPEIVKEIAEKEGVKVNIPDNFYSMVAKEAERT-------LVDFELLKDLPDTRRLYYEDPFMKEFDAKVLRVIKDWVILDATAFYPEGGGQPYDTGVLIVNGREVKVTNVQKVGKVIIHKVEDPGAFKEGMIVHGKIDWKRRIQHMRHHTGTHVLMGALVRVLGRHVWQAGSQLTTDWARLDISHYKRISEEELKEIEMLANRIVMEDRKVTWEWLPRTTAEQKYGFRLYQGGVVPGREIRVVKIEDWDVQACGGTHLPSTGLVGPIKILRTERIQDGVERIIFACGE 752
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221         -      |241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491    |    -  |    511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751 
                                                                                                                                                                                                                                                     221              238                                                                                                                                                                                                                                                               496     504

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 2ZZF)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SYA_PYRHO | O58035)

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:0004813	alanine-tRNA ligase activity	Catalysis of the reaction: ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala).
	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: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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006419	alanyl-tRNA aminoacylation	The process of coupling alanine to alanyl-tRNA, catalyzed by alanyl-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: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: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
		Asn A:118 - Pro A:119	[ RasMol ]
		Gln A:105 - Pro A:106	[ RasMol ]
		Pro A:40 - Pro A:41	[ RasMol ]

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	2zzf
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	SYA_PYRHO \| O58035
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	6.1.1.7
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	SYA_PYRHO \| O58035	:	2zze 2zzg

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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