2ZUE - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PYROCOCCUS HORIKOSHII ARGINYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(ARG) AND AN ATP ANALOG (ANP)

Authors :   M. Konno, T. Sumida, E. Uchikawa, Y. Mori, T. Yanagisawa, S. Sekine, S. Yokoyama

Date :   16 Oct 08 (Deposition) - 18 Aug 09 (Release) - 18 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Rrs/Trna(Arg)/Atp, Aminoacyl-Trna Synthetase, Atp-Binding, Cytoplasm, Ligase, Nucleotide-Binding, Protein Biosynthesis, Ligase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Konno, T. Sumida, E. Uchikawa, Y. Mori, T. Yanagisawa, S. Sekine, S. Yokoyama
Modeling Of Trna-Assisted Mechanism Of Arg Activation Based On A Structure Of Arg-Trna Synthetase, Trna, And An Atp Analog (Anp)
Febs J. V. 276 4763 2009
PubMed-ID: 19656186 | Reference-DOI: 10.1111/J.1742-4658.2009.07178.X
(for further references see the PDB file header)

Molecule 1 - ARGINYL-TRNA SYNTHETASE
	Chains	:	A
	EC Number	:	6.1.1.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28C
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ARGS, PH1478
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953
	Synonym	:	ARGININE--TRNA LIGASE, ARGRS

Molecule 2 - TRNA-ARG
	Chains	:	B
	Engineered	:	YES
	Other Details	:	THIS TRNA OCCURS FROM PYROCOCCUS HORIKOSHII, IN VITRO TRANSCRIPTION
	Synthetic	:	YES

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ANP	-1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:128 , ASN A:129 , LYS A:132 , HIS A:135 , GLY A:137 , HIS A:138 , ASN A:141 , GLN A:171 , ILE A:383 , GLY A:384 , GLU A:386 , TYR A:415 , HIS A:417 , VAL A:418 , MG A:800 , HOH A:1022 , HOH A:1073 , HOH A:1290 , HOH A:1305 , HOH A:1339	BINDING SITE FOR RESIDUE ANP A 700
2	AC2	SOFTWARE	ASN A:129 , ANP A:700	BINDING SITE FOR RESIDUE MG A 800

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

(no "Cis Peptide Bond" information available for 2ZUE)

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

Asymmetric Unit (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.	SYR_PYRHO	130-139	1	A:130-139

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.	SYR_PYRHO	130-139	1	A:130-139

Biological Unit 2 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_I	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.	SYR_PYRHO	130-139	0	-

Biological Unit 3 (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.	SYR_PYRHO	130-139	1	A:130-139

(no "Exon" information available for 2ZUE)

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
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Chain A from PDB  Type:PROTEIN  Length:628
 aligned with SYR_PYRHO | O59147 from UniProtKB/Swiss-Prot  Length:629

    Alignment length:628
                                    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        
           SYR_PYRHO      2 LMEIRESVKERIEEIIKEIAPQWEGEIELKETPDPKLGDFGTPIAFKLAKLLKRPPIEIAEKIVEKLKLNLPEGIKDVKAVNGYINVFIDYPHFARILINDILAKGDRFGSSEIGKGKKVIVEHTSVNPTKPLHMGHARNAILGDVMARILRFLGYEVEVQNYIDDLGIQFAQVYWGYLRLKEEFERIMNELRERGLKDNPIDHALGLLYVEVNRRLEDNPELENEIRDIMKKLESGELYGRKLAEEVVRAQMVTTYKLGVKYDLLVWESDIVRRKLFEIALELLSKNENFYIPSDGKYRGAFVMDLRKLFPDMKNPILVLRRSDGTATYTGKDIAYHLWKFGKIDVDLLYKEWDSTTWTTAPDGKSMPNKFGNANIVINVIGAEQKHPQLAIKYALQLLGFEDAAANLYHLAYEHVERPEGKFSGRKGTWVGFTVDEVIQEAVKRARELIEEKNPALSDEEKAEVAEKVGIGAIRYNLIKYSPDKKIIFRWEDVLNFEGESAPYIQYAHARCSSILRKAEEEGIKVDPETLFKNADFTKLSERERELVIMLSKFPRIVEQAGKDVKPHLIAWFANELASLFNKFYMDHPVLKAEEGVREARLLLVMAVEQVLKNALYLMGIEAPERM  629
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------2zueA02 A:117-510 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                                                                                                                                   2zueA03 A:511-629 Isoleucyl-tRNA Synthetase; Domain 1                                                                   CATH domains
           Pfam domains (1) --Arg_tRNA_synt_N-2zueA04 A:4-90                                                         -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_1d-2zueA02 A:368-493                                                                                                -------------DALR_1-2zueA01 A:507-629                                                                                                    Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_1d-2zueA03 A:368-493                                                                                                ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhh.........ee..hhhhh.eeehhhhhhhhhhh.hhhhhhhhhhhhhh......eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh.........eeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhh...ee..........eeee...........eeeee......hhhhhhhhhhhhhh.......eeee.....eee....ee.........eeeeeee..hhhhhhhhhhhhhhh.hhhhhhheeeeee..ee................hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh......ee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------AA_TRNA_LI---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2zue A    2 LMEIRESVKERIEEIIKEIAPQWEGEIELKETPDPKLGDFGTPIAFKLAKLLKRPPIEIAEKIVEKLKLNLPEGIKDVKAVNGYINVFIDYPHFARILINDILAKGDRFGSSEIGKGKKVIVEHTSVNPTKPLHMGHARNAILGDVMARILRFLGYEVEVQNYIDDLGIQFAQVYWGYLRLKEEFERIMNELRERGLKDNPIDHALGLLYVEVNRRLEDNPELENEIRDIMKKLESGELYGRKLAEEVVRAQMVTTYKLGVKYDLLVWESDIVRRKLFEIALELLSKNENFYIPSDGKYRGAFVMDLRKLFPDMKNPILVLRRSDGTATYTGKDIAYHLWKFGKIDVDLLYKEWDSTTWTTAPDGKSMPNKFGNANIVINVIGAEQKHPQLAIKYALQLLGFEDAAANLYHLAYEHVERPEGKFSGRKGTWVGFTVDEVIQEAVKRARELIEEKNPALSDEEKAEVAEKVGIGAIRYNLIKYSPDKKIIFRWEDVLNFEGESAPYIQYAHARCSSILRKAEEEGIKVDPETLFKNADFTKLSERERELVIMLSKFPRIVEQAGKDVKPHLIAWFANELASLFNKFYMDHPVLKAEEGVREARLLLVMAVEQVLKNALYLMGIEAPERM  629
                                    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

Chain B from PDB  Type:RNA  Length:76
                                                                                                             
                2zue B  901 GGACCGGUAGCCUAGCCAGGACAGGGCGGCGGCCUCCUAAGCCGCAGGUCCGGGGUUCAAAUCCCCGCCGGUCCGC  974
                                   910       919 |     928       938       948       958       968      
                                          917A   |                                                      
                                              920A

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 2ZUE)

Asymmetric Unit(hide GO term definitions)

Chain A (SYR_PYRHO | O59147)

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:0004814	arginine-tRNA ligase activity	Catalysis of the reaction: ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg).
	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: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:0006420	arginyl-tRNA aminoacylation	The process of coupling arginine to arginyl-tRNA, catalyzed by arginyl-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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	Cis Peptide Bonds
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Biological Units
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	2zue
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	6.1.1.19
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	SYR_PYRHO \| O59147	:	2zuf

2zuf	THE SAME PROTEIN COMPLEXED WITH TRNA(ARG)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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