1YFR - JenaLib

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Title :   CRYSTAL STRUCTURE OF ALANYL-TRNA SYNTHETASE IN COMPLEX WITH ATP AND MAGNESIUM

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 :   2.15

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

Keywords :   Alpha-Beta Fold, Bent Atp Conformation, Magnesium Bridge, 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, B
	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	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	6	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:174 , GLU A:191 , ASN A:194 , ATP A:1500 , MG A:1504 , HOH A:1510	BINDING SITE FOR RESIDUE MG A 1502
2	AC2	SOFTWARE	ATP A:1500 , HOH A:1505 , HOH A:1506	BINDING SITE FOR RESIDUE MG A 1503
3	AC3	SOFTWARE	GLU A:174 , ATP A:1500 , MG A:1502 , HOH A:1509 , HOH A:1531	BINDING SITE FOR RESIDUE MG A 1504
4	AC4	SOFTWARE	GLU B:174 , GLU B:191 , ASN B:194 , ATP B:2500 , MG B:2504 , HOH B:2506	BINDING SITE FOR RESIDUE MG B 2502
5	AC5	SOFTWARE	ARG B:69 , ATP B:2500 , HOH B:2505	BINDING SITE FOR RESIDUE MG B 2503
6	AC6	SOFTWARE	GLU B:174 , GLU B:191 , LYS B:354 , ATP B:2500 , MG B:2502	BINDING SITE FOR RESIDUE MG B 2504
7	AC7	SOFTWARE	ARG A:85 , HIS A:86 , HIS A:87 , GLU A:191 , ASN A:194 , GLY A:219 , GLY A:221 , ARG A:224 , ASN A:235 , MG A:1502 , MG A:1503 , MG A:1504 , HOH A:1505 , HOH A:1507 , HOH A:1531 , HOH A:1569 , HOH A:1590	BINDING SITE FOR RESIDUE ATP A 1500
8	AC8	SOFTWARE	ARG B:69 , ARG B:85 , HIS B:86 , HIS B:87 , MET B:92 , GLU B:191 , ILE B:192 , ASN B:194 , GLY B:219 , GLY B:221 , ARG B:224 , MG B:2502 , MG B:2503 , MG B:2504 , HOH B:2572 , HOH B:2600	BINDING SITE FOR RESIDUE ATP B 2500

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

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

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

Asymmetric Unit (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:2-453 B:2-453

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:2-453 -

Biological Unit 2 (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	- B:2-453

(no "Exon" information available for 1YFR)

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:448
 aligned with SYA_AQUAE | O67323 from UniProtKB/Swiss-Prot  Length:867

    Alignment length:457
                                    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       
            SYA_AQUAE     2 SLSAHEIRELFLSFFEKKGHTRVKSAPLVPENDPTLLFVNAGMVPFKNVFLGLEKRPYKRATSCQKCLRVSGKHNDLEQVGYTSRHHTFFEMLGNFSFGDYFKKEAIEYAWEFVTEVLKLPKEKLYVSVYKDDEEAYRIWNEHIGIPSERIWRLGEEDNFWQMGDVGPCGPSSEIYVDRGEEYEGDERYLEIWNLVFMQYNRDENGVLTPLPHPNIDTGMGLERIASVLQGKNSNFEIDIIFPLIQFGEEVSGKKYGEKFETDVALRVIADHLRAITFAISDGVIPSNEGRGYVIRRILRRAMRFGYKLGIENPFLYKGVDLVVDIMKEPYPELELSREFVKGIVKGEEKRFIKTLKAGMEYIQEVIQKALEEGRKTLSGKEVFTAYDTYGFPVDLIDEIAREKGLGIDLEGFQCELEEQRERARKHFKVEAKKVKPVYSHLKELGKTSAFVGYEHM 458
               SCOP domains d1yfra2 A:1-236 Alanyl-tRNA synthetase (AlaRS)                                                                                                                                                                                              d1yfra1 A:237-457 Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)                                                                                                                                         SCOP domains
               CATH domains 1yfrA01 A:1-233 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..eee......................hhhhhh........eeeeeeeee.ee..ee.............eeeeeeeeee...hhhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhh....hhh.eeeehhhhheee....eeeeeeeeeeee..........eeeeeeeeeeeeee.....eeeeeeeeeee.eehhhhhhhhh...hhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh....hhhhhhhhhhh...eehhhhhhhhhhhhhh.....---------.......hhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -AA_TRNA_LIGASE_II_ALA  PDB: A:2-453 UniProt: 3-704                                                                                                                                                                                                                                                                                                                                                                                                                       PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yfr A   1 SLSAHEIRELFLSFFEKKGHTRVKSAPLVPENDPTLLFVNAGMVPFKNVFLGLEKRPYKRATSCQKCLRVSGKHNDLEQVGYTSRHHTFFEMLGNFSFGDYFKKEAIEYAWEFVTEVLKLPKEKLYVSVYKDDEEAYRIWNEHIGIPSERIWRLGEEDNFWQMGDVGPCGPSSEIYVDRGEEYEGDERYLEIWNLVFMQYNRDENGVLTPLPHPNIDTGMGLERIASVLQGKNSNFEIDIIFPLIQFGEEVSGKKYGEKFETDVALRVIADHLRAITFAISDGVIPSNEGRGYVIRRILRRAMRFGYKLGIENPFLYKGVDLVVDIMKEPYPELELSREFVKGIVKGEEKRFIKTLKAGMEYIQEVIQKALEEGRKTLSGKEVFTAYDTYGFPVDLIDEIAREKGLGIDLEGFQCELEEQRERARKH---------PVYSHLKELGKTSAFVGAAAL 457
                                    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       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    427       437

Chain B from PDB  Type:PROTEIN  Length:448
 aligned with SYA_AQUAE | O67323 from UniProtKB/Swiss-Prot  Length:867

    Alignment length:457
                                    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       
            SYA_AQUAE     2 SLSAHEIRELFLSFFEKKGHTRVKSAPLVPENDPTLLFVNAGMVPFKNVFLGLEKRPYKRATSCQKCLRVSGKHNDLEQVGYTSRHHTFFEMLGNFSFGDYFKKEAIEYAWEFVTEVLKLPKEKLYVSVYKDDEEAYRIWNEHIGIPSERIWRLGEEDNFWQMGDVGPCGPSSEIYVDRGEEYEGDERYLEIWNLVFMQYNRDENGVLTPLPHPNIDTGMGLERIASVLQGKNSNFEIDIIFPLIQFGEEVSGKKYGEKFETDVALRVIADHLRAITFAISDGVIPSNEGRGYVIRRILRRAMRFGYKLGIENPFLYKGVDLVVDIMKEPYPELELSREFVKGIVKGEEKRFIKTLKAGMEYIQEVIQKALEEGRKTLSGKEVFTAYDTYGFPVDLIDEIAREKGLGIDLEGFQCELEEQRERARKHFKVEAKKVKPVYSHLKELGKTSAFVGYEHM 458
               SCOP domains d1yfrb2 B:1-236 Alanyl-tRNA synthetase (AlaRS)                                                                                                                                                                                              d1yfrb1 B:237-457 Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)                                                                                                                                         SCOP domains
               CATH domains 1yfrB01 B:1-233 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----tRNA-synt_2c-1yfrB01 B:6-453                                                                                                                                                                                                                                                                                                                                                                                                                                    ---- Pfam domains (1)
           Pfam domains (2) -----tRNA-synt_2c-1yfrB02 B:6-453                                                                                                                                                                                                                                                                                                                                                                                                                                    ---- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhh.............................hhhhhhhhhh.......eeeeeeeee..hhhhhhhhhh........eeeeeeeee....hhhhhhhhhhhhhhh....hhh.ee......hhhhhhhhhh............hhhhhee.....eeeeeeeeeeee.....hhhh.eeeeeeeeeeeeee.....eeeeeeeeeeeeeehhhhhhhhh..........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhh...hhhhhhhhhh....ee....hhhhhhhhhh.....---------.......hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -AA_TRNA_LIGASE_II_ALA  PDB: B:2-453 UniProt: 3-704                                                                                                                                                                                                                                                                                                                                                                                                                       PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yfr B   1 SLSAHEIRELFLSFFEKKGHTRVKSAPLVPENDPTLLFVNAGMVPFKNVFLGLEKRPYKRATSCQKCLRVSGKHNDLEQVGYTSRHHTFFEMLGNFSFGDYFKKEAIEYAWEFVTEVLKLPKEKLYVSVYKDDEEAYRIWNEHIGIPSERIWRLGEEDNFWQMGDVGPCGPSSEIYVDRGEEYEGDERYLEIWNLVFMQYNRDENGVLTPLPHPNIDTGMGLERIASVLQGKNSNFEIDIIFPLIQFGEEVSGKKYGEKFETDVALRVIADHLRAITFAISDGVIPSNEGRGYVIRRILRRAMRFGYKLGIENPFLYKGVDLVVDIMKEPYPELELSREFVKGIVKGEEKRFIKTLKAGMEYIQEVIQKALEEGRKTLSGKEVFTAYDTYGFPVDLIDEIAREKGLGIDLEGFQCELEEQRERARKH---------PVYSHLKELGKTSAFVGAAAL 457
                                    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       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    427       437

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 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)

Aquifex aeolicus. Organism_taxid: 63363. (6)

1a	1yfrA01	A:1-233
1b	1yfrB01	B:1-233

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: tRNA_synt_II (64)

Family: tRNA-synt_2c (8)

Aquifex aeolicus (4)

1a	tRNA-synt_2c-1yfrB01	B:6-453
1b	tRNA-synt_2c-1yfrB02	B:6-453

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric Unit
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	Cis Peptide Bonds
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	1yfr
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	SYA_AQUAE \| O67323	:	1riq 1yfs 1yft 1ygb 3g98 3htz

1riq	CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF AQUIFEX AEOLICUS ALANYL TRNA SYNTHETASE.
1yfs	CRYSTAL STRUCTURE OF CATALYTIC FRAGMENT OF A. AEOLICUS ALANYL-TRNA SYNTHETASE IN COMPLEX WITH L-ALANINE
1yft	CRYSTAL STRUCTURE OF CATALYTIC FRAGMENT OF A. AEOLICUS ALANYL-TRNA SYNTHETASE IN COMPLEX WITH GLYCINE
1ygb	CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF ALANYL-TRNA SYNTHETASE IN COMPLEX WITH L-SERINE

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