1NZJ - JenaLib

Title :   CRYSTAL STRUCTURE AND ACTIVITY STUDIES OF ESCHERICHIA COLI YADB ORF

Authors :   V. Campanacci, D. Y. Kern, H. D. Becker, S. Spinelli, C. Valencia, R. Vincentelli, F. Pagot, C. Bignon, R. Giege, C. Cambillau

Date :   18 Feb 03 (Deposition) - 13 Apr 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Zn Cluster, Glutamyl T-Rna Synthetase, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Campanacci, D. Y. Dubois, H. D. Becker, D. Kern, S. Spinelli, C. Valencia, F. Pagot, A. Salomoni, S. Grisel, R. Vincentelli, C. Bignon, J. Lapointe, R. Giege, C. Cambillau
The Escherichia Coli Yadb Gene Product Reveals A Novel Aminoacyl-Trna Synthetase Like Activity.
J. Mol. Biol. V. 337 273 2004
PubMed-ID: 15003446 | Reference-DOI: 10.1016/J.JMB.2004.01.027
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:273
 aligned with GLUQ_ECOLI | P27305 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:286
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293      
           GLUQ_ECOLI    14 TQYIGRFAPSPSGELHFGSLIAALGSYLQARARQGRWLVRIEDIDPPREVPGAAETILRQLEHYGLHWDGDVLWQSQRHDAYREALAWLHEQGLSYYCTCTRARIQSIGGIYDGHCRVLHHGPDNAAVRIRQQHPVTQFTDQLRGIIHADEKLAREDFIIHRRDGLFAYNLAVVVDDHFQGVTEIVRGADLIEPTVRQISLYQLFGWKVPDYIHLPLALNPQGAKLSKQNHAPALPKGDPRPVLIAALQFLGQQAEAHWQDFSVEQILQSAVKNWRLTAVPESAIV 299
               SCOP domains d1nzja_ A: Glutamyl-Q tRNA-Asp synthetase YadB                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---tRNA-synt_1c-1nzjA01 A:7-288                                                                                                                                                                                                                                                              - Pfam domains
         Sec.struct. author ...eeee........hhhhhhhhhhhhhhhhhh..eeeeee...hhhhh..hhhhhhhhhhhhh........ee...hhhhhhhhhhhhhhh..eeee..hhhhhhhh..................eeee.......eeee...eeee.hhhhhhh..eee......hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhh....eeeee.ee..-------------......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.hhhhh....ee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzj A   4 TQYIGRFAPSPSGELHFGSLIAALGSYLQARARQGRWLVRIEDIDPPREVPGAAETILRQLEHYGLHWDGDVLWQSQRHDAYREALAWLHEQGLSYYCTCTRARIQSIGGIYDGHCRVLHHGPDNAAVRIRQQHPVTQFTDQLRGIIHADEKLAREDFIIHRRDGLFAYNLAVVVDDHFQGVTEIVRGADLIEPTVRQISLYQLFGWKVPDYIHLPLALN-------------ALPKGDPRPVLIAALQFLGQQAEAHWQDFSVEQILQSAVKNWRLTAVPESAIV 289
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223         -   |   243       253       263       273       283      
                                                                                                                                                                                                                                                     223           237

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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (GLUQ_ECOLI | P27305)

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: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:0004818	glutamate-tRNA ligase activity	Catalysis of the reaction: ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu).
	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: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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006424	glutamyl-tRNA aminoacylation	The process of coupling glutamate to glutamyl-tRNA, catalyzed by glutamyl-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:0002097	tRNA wobble base modification	The process in which the nucleotide at position 34 in the anticodon of a tRNA is post-transcriptionally modified.
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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