3TZE - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF A TRYPTOPHANYL-TRNA SYNTHETASE FROM ENCEPHALITOZOON CUNICULI BOUND TO TRYPTOPHAN

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   27 Sep 11 (Deposition) - 12 Oct 11 (Release) - 29 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Amino Acylation, Eukaryotic Pathogen, Microsporidia, Fungi, Intracellular Parasite, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. O. Moen, T. E. Edwards, D. M. Dranow, M. C. Clifton, B. Sankaran, W. C. Van Voorhis, A. Sharma, C. Manoil, B. L. Staker, P. J. Myler, D. D. Lorimer
Ligand Co-Crystallization Of Aminoacyl-Trna Synthetases Fro Infectious Disease Organisms.
Sci Rep V. 7 223 2017
PubMed-ID: 28303005 | Reference-DOI: 10.1038/S41598-017-00367-6

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PAVA0421
	Gene	:	ECU11_0530
	Mutation	:	YES
	Organism Common	:	MICROSPORIDIAN PARASITE
	Organism Scientific	:	ENCEPHALITOZOON CUNICULI
	Organism Taxid	:	284813
	Strain	:	GB-M1
	Synonym	:	TRYPTOPHAN--TRNA LIGASE, TRPRS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	K	2	Ligand/Ion	POTASSIUM ION
2	TRP	2	Mod. Amino Acid	TRYPTOPHAN

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:84 , THR A:85 , GLY A:86 , GLN A:119 , THR A:121 , GLU A:124 , GLU A:206 , VAL A:226 , GLN A:232	BINDING SITE FOR RESIDUE TRP A 386
2	AC2	SOFTWARE	SER A:212 , PHE A:215 , ILE A:218	BINDING SITE FOR RESIDUE K A 387
3	AC3	SOFTWARE	TYR B:84 , GLY B:86 , ARG B:87 , GLY B:88 , GLN B:119 , GLU B:124 , LYS B:125 , GLU B:206 , ALA B:228 , GLN B:232 , PHE B:236	BINDING SITE FOR RESIDUE TRP B 386
4	AC4	SOFTWARE	SER B:212 , PHE B:215 , ILE B:218	BINDING SITE FOR RESIDUE K B 387

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

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

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

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_ENCCU	89-99	2	A:89-99 B:89-99

(no "Exon" information available for 3TZE)

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:361
 aligned with SYW_ENCCU | O96771 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:368
                                                                                                                                                                                                                                                                                                                                                                                                        385 
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378      | 
            SYW_ENCCU    19 VPVAIDYDKIINQFGCEKFNQALADRLEKLSGKPAHYFFRRGIVFAHRDFNLLLDEIANNRPFYLYTGRGPSSKTMHIGHTIPFLLCKYMQDAFKIRLVIQITDDEKFLWKSMRLEDAMAYGRENIKDIVALGFDPKLTYIFSNVEASHHFEENILKISKTINLNEAIKVFGFDMSSNIGQVGFPAKEIAPCFSSSFRFIGKGAMCLVPAAVDQDPFFRLARDKAKALGEKKPSSIYVSLLPDLKGVNRKMSASDPNSSIYLDDAQDTIRKKIIAYAYSGGRKTLEEHREKGGDIDVDVPFEYLKYFLDDDQELEKYRSGYIKGEITSKEMKEKCVVVIQEFVSRYQESRKRVTDDDLRAFIDINKF-   -
               SCOP domains d3tzea_ A: automated matches                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh...ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhh.eeeeehhhhh..hhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.......eeeeeee..hhhhhhhhhhhhhhhh....eeeee................hhhhh.....hhhhhhhhhhhhh.......-------..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------AA_TRNA_LIG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tze A  19 VPVAIDYDKIINQFGCEKFNQALADRLEKLSGKPAHYFFRRGIVFAHRDFNLLLDEIANNRPFYLYTGRGPSSKTMHIGHTIPFLLCKYMQDAFKIRLVIQITDDEKFLWKSMRLEDAMAYGRENIKDIVTLGFDPKLTYIFSNVEASHHFEENILKISKTINLNEAIKVFGFDMSSNIGQVGFPAKEIAPCFSSSFRFIGKGAMCLVPAAVDQDPFFRLARDKAKALGEKKPSSIYVSLLPDLKGVNRKMSASDPNSSIYLDDAQDTIRKKIIAYAYSGGRKT-------GGDIDVDVPFEYLKYFLDDDQELEKYRSGYIKGEITSKEMKEKCVVVIQEFVSRYQESRKRVTDDDLRAFIDINKFW 386
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298   |     - |     318       328       338       348       358       368       378      ||
                                                                                                                                                                                                                                                                                                                     302     310                                                                        385|
                                                                                                                                                                                                                                                                                                                                                                                                         386

Chain B from PDB  Type:PROTEIN  Length:340
 aligned with SYW_ENCCU | O96771 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:361
                                    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       303       313       323       333       343       353       363       373       383 
            SYW_ENCCU    24 DYDKIINQFGCEKFNQALADRLEKLSGKPAHYFFRRGIVFAHRDFNLLLDEIANNRPFYLYTGRGPSSKTMHIGHTIPFLLCKYMQDAFKIRLVIQITDDEKFLWKSMRLEDAMAYGRENIKDIVALGFDPKLTYIFSNVEASHHFEENILKISKTINLNEAIKVFGFDMSSNIGQVGFPAKEIAPCFSSSFRFIGKGAMCLVPAAVDQDPFFRLARDKAKALGEKKPSSIYVSLLPDLKGVNRKMSASDPNSSIYLDDAQDTIRKKIIAYAYSGGRKTLEEHREKGGDIDVDVPFEYLKYFLDDDQELEKYRSGYIKGEITSKEMKEKCVVVIQEFVSRYQESRKRVTDDDLRAFIDINK 384
               SCOP domains d3tzeb_ B: automated matches                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhh.eeeeehhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.......eeeeeee..hhhhhhhhhhhhhhhh....eeeee..........-------.........hhhhhhhhhhhhh..--------------....hhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------AA_TRNA_LIG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tze B  24 DYDKIINQFGCEKFNQALADRLEKLSGKPAHYFFRRGIVFAHRDFNLLLDEIANNRPFYLYTGRGPSSKTMHIGHTIPFLLCKYMQDAFKIRLVIQITDDEKFLWKSMRLEDAMAYGRENIKDIVTLGFDPKLTYIFSNVEASHHFEENILKISKTINLNEAIKVFGFDMSSNIGQVGFPAKEIAPCFSSSFRFIGKGAMCLVPAAVDQDPFFRLARDKAKALGEKKPSSIYVSLLPDLKGVN-------PNSSIYLDDAQDTIRKKIIAYAYS--------------DIDVDVPFEYLKYFLDDDQELEKYRSGYIKGEITSKEMKEKCVVVIQEFVSRYQESRKRVTDDDLRAFIDINW 386
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  |      -|      283       293   |     -       313       323       333       343       353       363       373       383|
                                                                                                                                                                                                                                                                            266     274                    297            312                                                                    383|
                                                                                                                                                                                                                                                                                                                                                                                                  386

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)

Encephalitozoon cuniculi [TaxId: 284813] (1)

1a	d3tzea_	A:
1b	d3tzeb_	B:

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

(no "Pfam Domain" information available for 3TZE)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SYW_ENCCU | O96771)

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
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TRP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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
	3tze
		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_ENCCU \| O96771
		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_ENCCU \| O96771
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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

2quh	HUMAN TRPRS
3foc	GIARDIA LAMBLIA TRPRS
3hv0	CRYPTOSPORIDIUM PARVUM TRPRS
3hzr	ENTAMOEBA HISTOLYTICA TRPRS RELATED ID: ENCUA.00600.A RELATED DB: TARGETDB
3i05	TRYPANOSOMA BRUCEI TRPRS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

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 (0, 0)

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