2ZTG - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ARCHAEOGLOBUS FULGIDUS ALANYL-TRNA SYNTHETASE LACKING THE C-TERMINAL DIMERIZATION DOMAIN IN COMPLEX WITH ALA-SA

Authors :   M. Naganuma, S. Sekine, R. Fukunaga, S. Yokoyama

Date :   01 Oct 08 (Deposition) - 30 Jun 09 (Release) - 30 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A

Keywords :   Class-Ii Aminoacyl-Trna Synthetase, Aminoacyl-Trna Synthetase, Atp-Binding, Cytoplasm, Ligase, Nucleotide- Binding, Protein Biosynthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Naganuma, S. Sekine, R. Fukunaga, S. Yokoyama
Unique Protein Architecture Of Alanyl-Trna Synthetase For Aminoacylation, Editing, And Dimerization.
Proc. Natl. Acad. Sci. Usa V. 106 8489 2009
PubMed-ID: 19423669 | Reference-DOI: 10.1073/PNAS.0901572106
(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	:	PET26B
	Expression System Strain	:	ROSETTA2(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ALARS-DELTAC
	Gene	:	AF_2255, ALAS
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234
	Synonym	:	ALANINE-TRNA LIGASE, ALARS

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 18)

No.	Name	Count	Type	Full Name
1	A5A	1	Ligand/Ion	'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE
2	MSE	15	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:128 , ASP A:131 , ARG A:140 , HIS A:141 , LEU A:142 , PHE A:145 , MSE A:147 , TRP A:191 , GLU A:209 , VAL A:210 , ALA A:211 , THR A:212 , VAL A:214 , ASP A:242 , THR A:243 , GLY A:244 , GLY A:246 , ARG A:249 , HOH A:1025 , HOH A:1152	BINDING SITE FOR RESIDUE A5A A 801
2	AC2	SOFTWARE	HIS A:452 , HOH A:1054 , HOH A:1055 , HOH A:1129 , HOH A:1144 , HOH A:1146	BINDING SITE FOR RESIDUE ZN A 901
3	AC3	SOFTWARE	HIS A:600 , HIS A:604 , CYS A:703 , HIS A:707 , HOH A:1114	BINDING SITE FOR RESIDUE ZN A 902

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

Asymmetric/Biological Unit

No.	Residues
1	Cys A:23	-	Pro A:24
2	Gln A:105	-	Pro A:106
3	Asn A:118	-	Pro A:119

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

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_ARCFU	60-746	1	A:60-739

(no "Exon" information available for 2ZTG)

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:739
 aligned with SYA_ARCFU | O28029 from UniProtKB/Swiss-Prot  Length:906

    Alignment length:739
                                    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       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730         
            SYA_ARCFU     1 MTLDEEYLDITFLTENGFVRKRCPKCGKHFWTADPEREICGDPPCESYSFIGNPVFKKPFELDEMREYYLNFFERRGHGRIERYPVVARWRTDIYLTIASIADFQPFVTSGVAPPPANPLTISQPCIRLDDLDSVGRTGRHLTLFEMMAHHAFNYPGKEIYWKNETVAYCTELLNELGVKKEDIVYKEEPWAGGGNAGPCLEAIVGGLEVATLVFMNLEEHPEGDIEIKGARYRKMDNYIVDTGYGLERFVWASKGTPTVYDAIFPEVVDTIIDNSNVSFNREDERVRRIVAESSKLAGIMGELRGERLNQLRKSVADTVGVSVEELEGIVVPLEKVYSLADHTRCILFMLGDGLVPSNAGAGYLARLMIRRSLRLAEELELGLDLYDLVEMHKKILGFEFDVPLSTVQEILELEKERYRTTVSKGTRLVERLVERKKKLEKDDLIELYDSHGIPVELAVGIAAEKGAEVEMPKDIYAELAKRHSKAEKVQEKKITLQNEYPATEKLYYDDPTLLEFEAEVIGVEGDFVILNRSAFYPESGGQDNDVGYLIANGGKFEVVDVLEADGVVLHVVKGAKPEVGTKVKGVIDSDVRWRHMRHHSATHVLLYSLQKVLGNHVWQAGARKEFSKARLDVTHFRRPSEEEIKEIEMLANREILANKPIKWEWMDRIEAERKFGFRLYQGGVPPGRKIRVVQVGDDVQACGGTHCRSTGEIGMLKILKVESIQDGVIRFEFAAGEA 739
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------tRNA-synt_2c-2ztgA02 A:64-592                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    --------------------------------------------------------------------------------------------------tRNA_SAD-2ztgA01 A:691-733                 ------ Pfam domains
         Sec.struct. author .hhhhhhh.hhhhhh...eee........eee............................hhhhhhhhhhhhhhh...ee..................hhhhhhh..............eeeeeeee.hhhhhhh........eeeeeeeeeee.......hhhhhhhhhhhhhhhh..hhhhheeeeeeeee..eeeeeeeeee..eeeeeeeeeeeee.....eee..eeeeeeeeeeeeeeeehhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhh........hhhhhhhhh.....................ee.........eeeeeeeeee..eeee.ee.............eeeee..eeeee.eeeee..eeeee..........eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........eeeee.....hhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhh.......eeeeeee..eeee.......hhhhhh.eeeeeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------AA_TRNA_LIGASE_II_ALA  PDB: A:60-739 UniProt: 60-746                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztg A   1 mTLDEEYLDITFLTENGFVRKRCPKCGKHFWTADPEREICGDPPCESYSFIGNPVFKKPFELDEmREYYLNFFERRGHGRIERYPVVARWRTDIYLTIASIADFQPFVTSGVAPPPANPLTISQPCIRLDDLDSVGRTGRHLTLFEmmAHHAFNYPGKEIYWKNETVAYCTELLNELGVKKEDIVYKEEPWAGGGNAGPCLEAIVGGLEVATLVFmNLEEHPEGDIEIKGARYRKmDNYIVDTGYGLERFVWASKGTPTVYDAIFPEVVDTIIDNSNVSFNREDERVRRIVAESSKLAGImGELRGERLNQLRKSVADTVGVSVEELEGIVVPLEKVYSLADHTRCILFmLGDGLVPSNAGAGYLARLmIRRSLRLAEELELGLDLYDLVEmHKKILGFEFDVPLSTVQEILELEKERYRTTVSKGTRLVERLVERKKKLEKDDLIELYDSHGIPVELAVGIAAEKGAEVEmPKDIYAELAKRHSKAEKVQEKKITLQNEYPATEKLYYDDPTLLEFEAEVIGVEGDFVILNRSAFYPESGGQDNDVGYLIANGGKFEVVDVLEADGVVLHVVKGAKPEVGTKVKGVIDSDVRWRHmRHHSATHVLLYSLQKVLGNHVWQAGARKEFSKARLDVTHFRRPSEEEIKEIEmLANREILANKPIKWEWmDRIEAERKFGFRLYQGGVPPGRKIRVVQVGDDVQACGGTHCRSTGEIGmLKILKVESIQDGVIRFEFAAGEA 739
                            |       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       430       440       450       460       470 |     480       490       500       510       520       530       540       550       560       570       580       590      |600       610       620       630       640       650       660      |670       680       690       700       710     | 720       730         
                            |                                                              65-MSE                                                                           147-MSE                                                              216-MSE             236-MSE                                                          301-MSE                                          350-MSE            369-MSE                392-MSE                                                                         472-MSE                                                                                                                      597-MSE                                              650-MSE          667-MSE                                          716-MSE                   
                            1-MSE                                                                                                                                            148-MSE

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 2ZTG)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SYA_ARCFU | O28029)

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 ]
		Cys A:23 - Pro A:24	[ RasMol ]
		Gln A:105 - Pro A:106	[ RasMol ]

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	2ztg
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	SYA_ARCFU \| O28029	:	2zvf 3wqy 3wqz

(no "Related Entries Specified in the PDB File" available for 2ZTG)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (3, 3)

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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Pfam Domains (2, 2)

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