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Title :   CRYSTAL STRUCTURE OF PYROCOCCUS HORIKOSHII TRYPTOPHANYL-TRNA SYNTHETASE IN COMPLEX WITH TRPAMP

Authors :   M. Zhou, X. Dong, C. Zhong, N. Shen, B. Yang, J. Ding

Date :   19 Sep 09 (Deposition) - 10 Nov 09 (Release) - 10 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Tryptophanyl-Trna Synthetase, Adenosine Triphosphate, Rossmann Fold, Crystallography, X-Ray, P. Horikoshii, Aminoacyl-Trna Synthetase, Atp-Binding, Cytoplasm, Ligase, Nucleotide-Binding, Protein Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Zhou, X. Dong, C. Zhong, N. Shen, B. Yang, J. Ding
Crystal Structure Of P. Horikoshii Tryptophanyl-Trna Synthetase And Structure-Based Phylogenetic Analysis Suggest An Archaeal Origin Of Tryptophanyl-Trna Synthetase
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PH1921, TRPS
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953
	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	SO4	2	Ligand/Ion	SULFATE ION
2	TYM	2	Ligand/Ion	TRYPTOPHANYL-5'AMP

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:77 , THR A:78 , GLY A:79 , ARG A:80 , GLY A:81 , GLY A:89 , HIS A:90 , PRO A:93 , GLN A:111 , THR A:113 , GLU A:116 , LYS A:117 , GLN A:198 , ALA A:213 , ALA A:214 , ASP A:216 , GLN A:217 , TRP A:221 , LYS A:242 , PHE A:243 , VAL A:244 , LYS A:253 , MET A:254	BINDING SITE FOR RESIDUE TYM A 400
2	AC2	SOFTWARE	HIS A:87 , HIS A:90 , LYS A:253 , SER A:255 , ALA A:256	BINDING SITE FOR RESIDUE SO4 A 393
3	AC3	SOFTWARE	TYR B:77 , GLY B:79 , ARG B:80 , GLY B:81 , GLY B:89 , HIS B:90 , PRO B:93 , GLN B:111 , THR B:113 , GLU B:116 , LYS B:117 , GLN B:198 , ALA B:213 , ALA B:214 , ASP B:216 , GLN B:217 , TRP B:221 , PHE B:243 , VAL B:244 , LYS B:253 , MET B:254	BINDING SITE FOR RESIDUE TYM B 900
4	AC4	SOFTWARE	HIS B:87 , HIS B:90 , LYS B:253 , MET B:254 , SER B:255 , ALA B:256	BINDING SITE FOR RESIDUE SO4 B 393

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

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

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

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_PYRHO	82-91	2	A:82-91 B:82-91

(no "Exon" information available for 3JXE)

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_PYRHO | O59584 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:381
                                    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 
            SYW_PYRHO     1 MVEEFKVTPWEVEGVVDYDKLIKHFGTSPLTEDLLEKTAELTKSELPIFFRRKFFFSHRDYDLILKDYEEGRGFFLYTGRGPSGPMHIGHIIPFFATKWLQEKFGVNLYIQITDDEKFLFKENLTFDDTKRWAYDNILDIIAVGFDPDKTFIFQNSEFTKIYEMAIPIAKKINFSMAKAVFGFTEQSKIGMIFFPAIQIAPTFFERKRCLIPAAIDQDPYWRLQRDFAESLGYYKTAALHSKFVPSLTSLSGKMSASKPETAIYLTDSPEDVEKKVWKFTLTGGRPTLKEQREKGGEPEKCVVFKWLEIFFEEDDKKLKERYYACKNGELTCGECKRYLISKIQEFLKEHQRRRKKAEKLVEKFKYTGKLAQEMWNEAIPE 381
               SCOP domains d3jxea_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....ee...hhhhhhhhh..ee.hhhhhhhhhhhh....hhhhhh..eeeeehhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhh....eeeee................hhhhh.....hhhhhhhhhhh..--------------------hhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------AA_TRNA_LI-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jxe A   1 MVEEFKVTPWEVEGVVDYDKLIKHFGTSPLTEDLLEKTAELTKSELPIFFRRKFFFSHRDYDLILKDYEEGRGFFLYTGRGPSGPMHIGHIIPFFATKWLQEKFGVNLYIQITDDEKFLFKENLTFDDTKRWAYDNILDIIAVGFDPDKTFIFQNSEFTKIYEMAIPIAKKINFSMAKAVFGFTEQSKIGMIFFPAIQIAPTFFERKRCLIPAAIDQDPYWRLQRDFAESLGYYKTAALHSKFVPSLTSLSGKMSASKPETAIYLTDSPEDVEKKVWKFT--------------------CVVFKWLEIFFEEDDKKLKERYYACKNGELTCGECKRYLISKIQEFLKEHQRRRKKAEKLVEKFKYTGKLAQEMWNEAIPE 381
                                    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         -         -|      310       320       330       340       350       360       370       380 
                                                                                                                                                                                                                                                                                                                 280                  301

Chain B from PDB  Type:PROTEIN  Length:363
 aligned with SYW_PYRHO | O59584 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:381
                                    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 
            SYW_PYRHO     1 MVEEFKVTPWEVEGVVDYDKLIKHFGTSPLTEDLLEKTAELTKSELPIFFRRKFFFSHRDYDLILKDYEEGRGFFLYTGRGPSGPMHIGHIIPFFATKWLQEKFGVNLYIQITDDEKFLFKENLTFDDTKRWAYDNILDIIAVGFDPDKTFIFQNSEFTKIYEMAIPIAKKINFSMAKAVFGFTEQSKIGMIFFPAIQIAPTFFERKRCLIPAAIDQDPYWRLQRDFAESLGYYKTAALHSKFVPSLTSLSGKMSASKPETAIYLTDSPEDVEKKVWKFTLTGGRPTLKEQREKGGEPEKCVVFKWLEIFFEEDDKKLKERYYACKNGELTCGECKRYLISKIQEFLKEHQRRRKKAEKLVEKFKYTGKLAQEMWNEAIPE 381
               SCOP domains d3jxeb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------tRNA-synt_1b-3jxeB01 B:69-348                                                                                                                                                                                                                                                           --------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------tRNA-synt_1b-3jxeB02 B:69-348                                                                                                                                                                                                                                                           --------------------------------- Pfam domains (2)
         Sec.struct. author .....eee..eee...hhhhhhhhhh.ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh........eeeee................hhhhh.....hhhhhhhhhhh...------------------hhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------AA_TRNA_LI-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jxe B   1 MVEEFKVTPWEVEGVVDYDKLIKHFGTSPLTEDLLEKTAELTKSELPIFFRRKFFFSHRDYDLILKDYEEGRGFFLYTGRGPSGPMHIGHIIPFFATKWLQEKFGVNLYIQITDDEKFLFKENLTFDDTKRWAYDNILDIIAVGFDPDKTFIFQNSEFTKIYEMAIPIAKKINFSMAKAVFGFTEQSKIGMIFFPAIQIAPTFFERKRCLIPAAIDQDPYWRLQRDFAESLGYYKTAALHSKFVPSLTSLSGKMSASKPETAIYLTDSPEDVEKKVWKFTL------------------KCVVFKWLEIFFEEDDKKLKERYYACKNGELTCGECKRYLISKIQEFLKEHQRRRKKAEKLVEKFKYTGKLAQEMWNEAIPE 381
                                    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|        -       300       310       320       330       340       350       360       370       380 
                                                                                                                                                                                                                                                                                                                  281                300

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)

Pyrococcus horikoshii [TaxId: 53953] (1)

1a	d3jxea_	A:
1b	d3jxeb_	B:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HUP (230)

Family: tRNA-synt_1b (51)

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (1)

1a	tRNA-synt_1b-3jxeB01	B:69-348
1b	tRNA-synt_1b-3jxeB02	B:69-348

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SYW_PYRHO | O59584)

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
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