3PRH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   TRYPTOPHANYL-TRNA SYNTHETASE VAL144PRO MUTANT FROM B. SUBTILIS

Authors :   A. K. Antonczak, Z. Simova, I. Yonemoto, M. Bochtler, A. Piasecka, H. Cz A. Brancale, E. M. Tippmann

Date :   29 Nov 10 (Deposition) - 19 Jan 11 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Trprs, Protein Biosynthesis, Translation, Class I Trna Synthetase, Rossmann Fold, High Motif, Kmsks Motif, Aminoacyl-Trna Synthetase, Ligase, Atp-Binding, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Antonczak, Z. Simova, I. T. Yonemoto, M. Bochtler, A. Piasecka, H. Czapinska, A. Brancale, E. M. Tippmann
Importance Of Single Molecular Determinants In The Fidelity Of Expanded Genetic Codes.
Proc. Natl. Acad. Sci. Usa V. 108 1320 2011
PubMed-ID: 21224416 | Reference-DOI: 10.1073/PNAS.1012276108

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET151/D-TOPO
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	939361, BSU11420, SYNTHETIC GENE CODON OPTIMIZED FOR ESCHERICHIA COLI, TRPS
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	168
	Synonym	:	TRYPTOPHAN-TRNA LIGASE, TRPRS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3PRH)

(no "Site" information available for 3PRH)

(no "SS Bond" information available for 3PRH)

(no "Cis Peptide Bond" information available for 3PRH)

(no "SAP(SNP)/Variant" information available for 3PRH)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_I	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.	SYW_BACSU	11-20	2	A:11-20 B:11-20

(no "Exon" information available for 3PRH)

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:316
 aligned with SYW_BACSU | P21656 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:326
                                    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      
            SYW_BACSU     2 KQTIFSGIQPSGSVTLGNYIGAMKQFVELQHDYNSYFCIVDQHAITVPQDRLELRKNIRNLAALYLAVGLDPEKATLFIQSEVPAHAQAGWMMQCVAYIGELERMTQFKDKSKGNEAVVSGLLTYPPLMAADILLYGTDLVPVGEDQKQHLELTRNLAERFNKKYNDIFTIPEVKIPKVGARIMSLNDPLKKMSKSDPNQKAYITLLDEPKQLEKKIKSAVTDSEGIVKFDKENKPGVSNLLTIYSILGNTTIEELEAKYEGKGYGEFKGDLAEVVVNALKPIQDRYYELIESEELDRILDEGAERANRTANKMLKKMENAMGLGR 327
               SCOP domains d3prha_ A: automated matches                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhh....eeeeeehhhhhh....hhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh..hhhhhhh..----------..hhhhhhhhhhhhhhhhh....ee.....hhhhhhhhhhhhhhhhhhh.......ee..................................hhhhhhhhhhh...............hhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3prh A   2 KQTIFSGIQPSGSVTLGNYIGAMKQFVELQHDYNSYFCIVDQHAITVPQDRLELRKNIRNLAALYLAVGLDPEKATLFIQSEVPAHAQAGWMMQCVAYIGELERMT----------AVVSGLLTYPPLMAADILLYGTDLVPPGEDQKQHLELTRNLAERFNKKYNDIFTIPEVKIPKVGARIMSLNDPLKKMSKSDPNQKAYITLLDEPKQLEKKIKSAVTDSEGIVKFDKENKPGVSNLLTIYSILGNTTIEELEAKYEGKGYGEFKGDLAEVVVNALKPIQDRYYELIESEELDRILDEGAERANRTANKMLKKMENAMGLGR 327
                                    11        21        31        41        51        61        71        81        91       101     |   -      |121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      
                                                                                                                                   107        118

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with SYW_BACSU | P21656 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:326
                                    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      
            SYW_BACSU     2 KQTIFSGIQPSGSVTLGNYIGAMKQFVELQHDYNSYFCIVDQHAITVPQDRLELRKNIRNLAALYLAVGLDPEKATLFIQSEVPAHAQAGWMMQCVAYIGELERMTQFKDKSKGNEAVVSGLLTYPPLMAADILLYGTDLVPVGEDQKQHLELTRNLAERFNKKYNDIFTIPEVKIPKVGARIMSLNDPLKKMSKSDPNQKAYITLLDEPKQLEKKIKSAVTDSEGIVKFDKENKPGVSNLLTIYSILGNTTIEELEAKYEGKGYGEFKGDLAEVVVNALKPIQDRYYELIESEELDRILDEGAERANRTANKMLKKMENAMGLGR 327
               SCOP domains d3prhb_ B: automated matches                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) tRNA-synt_1b-3prhB01 B:2-282                                                                                                                                                                                                                                                             --------------------------------------------- Pfam domains (1)
           Pfam domains (2) tRNA-synt_1b-3prhB02 B:2-282                                                                                                                                                                                                                                                             --------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhh....eeeeeehhhhhh....hhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh..hhhhhhh.-------------hhhhhhhhhhhhhhhhh....ee.....hhhhhhhhhhhhhhhhhhh.......ee..----............................hhhhhhhhhhh...............hhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3prh B   2 KQTIFSGIQPSGSVTLGNYIGAMKQFVELQHDYNSYFCIVDQHAITVPQDRLELRKNIRNLAALYLAVGLDPEKATLFIQSEVPAHAQAGWMMQCVAYIGELERM-------------VSGLLTYPPLMAADILLYGTDLVPPGEDQKQHLELTRNLAERFNKKYNDIFTIPEVKI----ARIMSLNDPLKKMSKSDPNQKAYITLLDEPKQLEKKIKSAVTDSEGIVKFDKENKPGVSNLLTIYSILGNTTIEELEAKYEGKGYGEFKGDLAEVVVNALKPIQDRYYELIESEELDRILDEGAERANRTANKMLKKMENAMGLGR 327
                                    11        21        31        41        51        61        71        81        91       101    |    -       121       131       141       151       161       171     |   -|      191       201       211       221       231       241       251       261       271       281       291       301       311       321      
                                                                                                                                  106           120                                                      177  182

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Adenine nucleotide alpha hydrolase-like (440)

Superfamily: Nucleotidylyl transferase (325)

Family: automated matches (67)

Protein domain: automated matches (67)

Bacillus subtilis [TaxId: 1423] (1)

1a	d3prha_	A:
1b	d3prhb_	B:

(no "CATH Domain" information available for 3PRH)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HUP (230)

Family: tRNA-synt_1b (51)

Bacillus subtilis (1)

1a	tRNA-synt_1b-3prhB01	B:2-282
1b	tRNA-synt_1b-3prhB02	B:2-282

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SYW_BACSU | P21656)

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: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:0004830	tryptophan-tRNA ligase activity	Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp).
biological process
	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.
	GO:0006436	tryptophanyl-tRNA aminoacylation	The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-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.
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
	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
(no "Ligands, Modified Residues, Ions" information available for 3prh)

	Sites
(no "Sites" information available for 3prh)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3prh)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3prh
		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
	SYW_BACSU \| P21656
		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)
	6.1.1.2
		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

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SYW_BACSU \| P21656
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 3PRH)

1d2r	2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE
1m83	CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH ATP IN A CLOSED, PRE-TRANSITION STATE CONFORMATION
1mau	CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH ATP AND TRYPTOPHANAMIDE IN A PRE-TRANSITION STATE CONFORMATION
1maw	CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHAN IN AN OPEN CONFORMATION
1mb2	CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHAN IN AN OPEN CONFORMATION
2ov4	CRYSTAL STRUCTURE OF B. STEAROTHERMOPHILUS TRYPTOPHANYL TRNA SYNTHETASE IN COMPLEX WITH ADENOSINE TETRAPHOSPHATE
3fi0	CRYSTAL STRUCTURE ANALYSIS OF B. STEAROTHERMOPHILUS TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHAN, AMP, AND INORGANIC PHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File