3QTC - JenaLib

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMOMERS, AN O-METHYL TYROSYL-TRNA SYNTHETASE EVOLVED FROM METHANOSARCINA MAZEI PYLRS, COMPLEXED WITH O-METHYL TYROSINE AND AMP-PNP

Authors :   N. Dellas, J. K. Takimoto, J. P. Noel, L. Wang

Date :   22 Feb 11 (Deposition) - 25 May 11 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Pyrrolysyl-Trna Synthetase, Aminoacyl-Trna Synthetase, Atp Binding, O-Methyl Tyrosine Binding, Magnesium Binding, Aminoacylation, Esterification, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. K. Takimoto, N. Dellas, J. P. Noel, L. Wang
Stereochemical Basis For Engineered Pyrrolysyl-Trna Synthetase And The Efficient In Vivo Incorporation Of Structurally Divergent Non-Native Amino Acids.
Acs Chem. Biol. V. 6 733 2011
PubMed-ID: 21545173 | Reference-DOI: 10.1021/CB200057A

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:487 , HOH A:490 , HOH A:492 , HOH A:494 , ANP A:810	BINDING SITE FOR RESIDUE MG A 800
2	AC2	SOFTWARE	GLU A:396 , SER A:399 , HOH A:498 , HOH A:521 , ANP A:810	BINDING SITE FOR RESIDUE MG A 801
3	AC3	SOFTWARE	HOH A:70 , MET A:300 , THR A:302 , TRP A:348 , SER A:399 , LEU A:401 , GLY A:419 , ALA A:420 , HOH A:545 , EDO A:812	BINDING SITE FOR RESIDUE 0A1 A 811
4	AC4	SOFTWARE	THR A:302 , TYR A:306 , LEU A:401 , TRP A:417 , HOH A:512 , 0A1 A:811	BINDING SITE FOR RESIDUE EDO A 812
5	AC5	SOFTWARE	LYS A:429 , ASP A:433 , PHE A:434	BINDING SITE FOR RESIDUE EDO A 813
6	AC6	SOFTWARE	TYR A:242 , LEU A:246 , GLU A:249 , LYS A:431 , HIS A:432	BINDING SITE FOR RESIDUE EDO A 814
7	AC7	SOFTWARE	HOH A:23 , ASN A:241 , ARG A:439 , ALA A:440 , ASN A:448 , GLY A:449	BINDING SITE FOR RESIDUE EDO A 815
8	AC8	SOFTWARE	TYR A:272 , ASN A:307 , ARG A:310 , LYS A:311 , GLU A:357 , GLU A:444	BINDING SITE FOR RESIDUE EDO A 817
9	AC9	SOFTWARE	HOH A:1 , HOH A:6 , HOH A:79 , HOH A:130 , HOH A:138 , ARG A:330 , GLU A:332 , HIS A:338 , LEU A:339 , PHE A:342 , MET A:344 , GLU A:396 , LEU A:397 , SER A:398 , SER A:399 , GLY A:421 , GLY A:423 , ARG A:426 , HOH A:487 , HOH A:490 , HOH A:492 , HOH A:494 , HOH A:498 , MG A:800 , MG A:801	BINDING SITE FOR RESIDUE ANP A 810

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:257
 aligned with PYLS_METMA | Q8PWY1 from UniProtKB/Swiss-Prot  Length:454

    Alignment length:267
                                   197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       
           PYLS_METMA   188 PALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSESYYNGISTNL 454
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------tRNA-synt_2b-3qtcA01 A:242-378                                                                                                           ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.....----...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eee....eeehhhhhhh......hhhhhh.ee...eee...hhhhhhhhhhhhh......eeeeeeeeee...........eeeeeeeeee....hhhhhhhhhhhhhhhhh...eee.------.eeeeeee..eeeeeeee..hhhhhhhh....eeeeeeehhhhhhhhhh..hhhhhh....ee..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qtc A 188 PALTKSQTDRLEVLLNPKDE----SGKPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLTPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTMLVFWQMGSGCTRENLESIITDFLNHLGIDFKIVG------GDTLDVMHGDLELSSALVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSESYYNGISTNL 454
                                   197       207    |  217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377|      387       397       407       417       427       437       447       
                                             207  212                                                                                                                                                                   378    385

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (PYLS_METMA | Q8PWY1)

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: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: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.
biological process
	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: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.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		0A1	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ANP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp A:318 - Pro A:319	[ RasMol ]
		Gly A:403 - Pro A:404	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3qtc
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PYLS_METMA \| Q8PWY1
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	6.1.1.26
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description