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Title :   THE CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF ALANYL-TRNA SYNTHETASE IN COMPLEX WTIH GLYCINE

Authors :   M. A. Swairjo, P. R. Schimmel

Date :   03 Jan 05 (Deposition) - 25 Jan 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.23

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

Keywords :   Alpha-Beta Fold, Amino Acid Binding, Helix-Loop Helix Motif, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Swairjo, P. R. Schimmel
Breaking Sieve For Steric Exclusion Of A Noncognate Amino Acid From Active Site Of A Trna Synthetase.
Proc. Natl. Acad. Sci. Usa V. 102 988 2005
PubMed-ID: 15657145 | Reference-DOI: 10.1073/PNAS.0409024102
(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	:	PET20B+
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ALAS
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	ALANINE-TRNA LIGASE, ALARS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GLY	1	Mod. Amino Acid	GLYCINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GLY	1	Mod. Amino Acid	GLYCINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	GLY	2	Mod. Amino Acid	GLYCINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:92 , ASN A:194 , ASP A:217 , HOH A:501 , HOH A:681	BINDING SITE FOR RESIDUE GLY A 500

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

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

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

Asymmetric 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_AQUAE	3-704	1	A:2-500

Biological Unit 1 (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_AQUAE	3-704	1	A:2-500

Biological Unit 2 (1, 2)

	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_AQUAE	3-704	2	A:2-500

(no "Exon" information available for 1YFT)

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:449
 aligned with SYA_AQUAE | O67323 from UniProtKB/Swiss-Prot  Length:867

    Alignment length:465
                                    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     
            SYA_AQUAE     2 SLSAHEIRELFLSFFEKKGHTRVKSAPLVPENDPTLLFVNAGMVPFKNVFLGLEKRPYKRATSCQKCLRVSGKHNDLEQVGYTSRHHTFFEMLGNFSFGDYFKKEAIEYAWEFVTEVLKLPKEKLYVSVYKDDEEAYRIWNEHIGIPSERIWRLGEEDNFWQMGDVGPCGPSSEIYVDRGEEYEGDERYLEIWNLVFMQYNRDENGVLTPLPHPNIDTGMGLERIASVLQGKNSNFEIDIIFPLIQFGEEVSGKKYGEKFETDVALRVIADHLRAITFAISDGVIPSNEGRGYVIRRILRRAMRFGYKLGIENPFLYKGVDLVVDIMKEPYPELELSREFVKGIVKGEEKRFIKTLKAGMEYIQEVIQKALEEGRKTLSGKEVFTAYDTYGFPVDLIDEIAREKGLGIDLEGFQCELEEQRERARKHFKVEAKKVKPVYSHLKELGKTSAFVGYEHMEWESQVVG 466
               SCOP domains d1yfta2 A:1-236 Alanyl-tRNA synthetase (AlaRS)                                                                                                                                                                                              d1yfta1 A:237-457 Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)                                                                                                                                               - SCOP domains
               CATH domains 1yftA01 A:1-233 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                      ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...ee....................hhhhhhhhh........eeeeeeeee.ee..ee.............eeeeeeeee....hhhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhh....hhh.eeeehhhhheee....eeeeeeeeeeee.....hhhhheeeeeeeeeeeeee.....eeeeeeeeeeeeeehhhhhhhhh...hhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhh...hhhhhhhhhhh...eehhhhhhhhhhhhhhhhh..---------.......hhhhhh....------....-. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -AA_TRNA_LIGASE_II_ALA  PDB: A:2-500 UniProt: 3-704                                                                                                                                                                                                                                                                                                                                                                                                                               PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yft A   1 SLSAHEIRELFLSFFEKKGHTRVKSAPLVPENDPTLLFVNAGMVPFKNVFLGLEKRPYKRATSCQKCLRVSGKHNDLEQVGYTSRHHTFFEMLGNFSFGDYFKKEAIEYAWEFVTEVLKLPKEKLYVSVYKDDEEAYRIWNEHIGIPSERIWRLGEEDNFWQMGDVGPCGPSSEIYVDRGEEYEGDERYLEIWNLVFMQYNRDENGVLTPLPHPNIDTGMGLERIASVLQGKNSNFEIDIIFPLIQFGEEVSGKKYGEKFETDVALRVIADHLRAITFAISDGVIPSNEGRGYVIRRILRRAMRFGYKLGIENPFLYKGVDLVVDIMKEPYPELELSREFVKGIVKGEEKRFIKTLKAGMEYIQEVIQKALEEGRKTLSGKEVFTAYDTYGFPVDLIDEIAREKGLGIDLEGFQCELEEQRERARKH---------PVYSHLKELGKTSAFVG------AAAL-G 500
                                    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      |  -      |440       450  |    454  | |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    427       437             453    454  | |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        457 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          500

Legend:		→ Mismatch	(orange background)
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	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 Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: BirA Bifunctional Protein; domain 2 (111)

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

Aquifex aeolicus. Organism_taxid: 63363. (6)

1yftA01

A:1-233

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

Asymmetric Unit(hide GO term definitions)

Chain A (SYA_AQUAE | O67323)

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:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
	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: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:0006400	tRNA modification	The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
	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.

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	6.1.1.7
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	SYA_AQUAE \| O67323	:	1riq 1yfr 1yfs 1ygb 3g98 3htz

1riq	CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF AQUIFEX AEOLICUS ALANYL-TRNA SYNTHETASE, APO ENZYME.
1yfr	CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF A. AEOLICUS ALANLY-TRNA SYNTHETASE IN COMPLEX WITH ATP AND MAGNESIUM.
1yfs	CRYSTAL SRTUCTURE OF THE CATALYTIC FRAGMENT OF A. AEOLICUS ALANYL-TRNA SYNTHETASE IN COMPLEX WITH L-ALANINE
1ygb	CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF ALANYL-TRNA SYNTHETASE IN COMPLEX WITH L-SERINE

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