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Title :   CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE FROM CAMPYLOBACTER JEJUNI COMPLEXED WITH ADP AND TRYPTOPHANE

Authors :   Y. Kim, M. Zhou, S. Grimshaw, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)

Date :   27 Sep 11 (Deposition) - 05 Oct 11 (Release) - 05 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha-Beta Structure, Cytosol, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, M. Zhou, S. Grimshaw, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Tryptophanyl-Trna Synthetase From Campylobacter Jejuni Complexed With Adp And Tryptophane
To Be Published
PubMed: search

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21 MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CJ0388, TRPS
	Organism Scientific	:	CAMPYLOBACTER JEJUNI SUBSP. JEJUNI
	Organism Taxid	:	192222
	Strain	:	NCTC 11168
	Synonym	:	TRYPTOPHAN--TRNA LIGASE, TRPRS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 30)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
3	NA	2	Ligand/Ion	SODIUM ION
4	PO4	4	Ligand/Ion	PHOSPHATE ION
5	TRP	2	Mod. Amino Acid	TRYPTOPHAN

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:8 , HIS A:14 , GLY A:16 , ASN A:17 , GLY A:20 , ALA A:21 , VAL A:182 , LYS A:189 , MSE A:190 , SER A:191 , LYS A:192 , NA A:336 , HOH A:444	BINDING SITE FOR RESIDUE ADP A 330
02	AC2	SOFTWARE	GLY A:6 , GLN A:8 , PHE A:37 , HIS A:42 , TYR A:124 , MSE A:128 , ASP A:131 , VAL A:140 , GLN A:146	BINDING SITE FOR RESIDUE TRP A 331
03	AC3	SOFTWARE	LEU A:221 , GLY A:258 , TYR A:259 , GLY A:260 , HIS A:261	BINDING SITE FOR RESIDUE PO4 A 332
04	AC4	SOFTWARE	SER A:203 , GLU A:204	BINDING SITE FOR RESIDUE PO4 A 333
05	AC5	SOFTWARE	ARG A:103 , GLN A:148 , LYS B:275	BINDING SITE FOR RESIDUE PO4 A 335
06	AC6	SOFTWARE	SER A:193 , ADP A:330	BINDING SITE FOR RESIDUE NA A 336
07	AC7	SOFTWARE	HIS B:14 , GLY B:16 , ASN B:17 , GLY B:20 , VAL B:182 , LYS B:189 , MSE B:190 , SER B:191 , LYS B:192 , NA B:333	BINDING SITE FOR RESIDUE ADP B 330
08	AC8	SOFTWARE	GLY B:6 , PHE B:37 , HIS B:42 , MSE B:128 , ASP B:131 , VAL B:140 , GLN B:146 , HOH B:392	BINDING SITE FOR RESIDUE TRP B 331
09	AC9	SOFTWARE	GLY B:11 , LYS B:52 , ASN B:56	BINDING SITE FOR RESIDUE PO4 B 332
10	BC1	SOFTWARE	SER B:193 , ADP B:330	BINDING SITE FOR RESIDUE NA B 333

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

Asymmetric/Biological Unit

No.	Residues
1	Glu B:177	-	Glu B:178

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

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_CAMJE	9-18	2	A:9-18 B:9-18

(no "Exon" information available for 3TZL)

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:319
 aligned with SYW_CAMJE | Q9PIB4 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    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         
            SYW_CAMJE     1 MRVLTGLQPSGDLHIGNYFGAIKQMVDAQEKSQMFMFIANYHAMTSSQDGEKLKQNSLKAAAAFLSLGIDPQKSVFWLQSDVKEVMELYWILSQFTPMGLLERAHSYKDKVAKGLSASHGLFSYPVLMAADILLFDTRIVPVGKDQIQHVEIARDIALKVNNEWGEIFTLPEARVNEEVAVVVGTDGAKMSKSYQNTIDIFSSEKTLKKQISSIVTDSTALEDPKDHENCNIFKIAKLFLDESGQKELQIRYEKGGEGYGHFKIYLNELVNAYFKEAREKYNELLEKPSHLKEILDFGATKARKIAQEKMQKIYEKIGL 319
               SCOP domains d3tzla_ A: automated matches                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......hhhhhhhhhhhhhhh......eeeehhhhhh....hhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhh......eee................hhhhh.......hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------AA_TRNA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tzl A   1 mRVLTGLQPSGDLHIGNYFGAIKQmVDAQEKSQmFmFIANYHAmTSSQDGEKLKQNSLKAAAAFLSLGIDPQKSVFWLQSDVKEVmELYWILSQFTPmGLLERAHSYKDKVAKGLSASHGLFSYPVLmAADILLFDTRIVPVGKDQIQHVEIARDIALKVNNEWGEIFTLPEARVNEEVAVVVGTDGAKmSKSYQNTIDIFSSEKTLKKQISSIVTDSTALEDPKDHENCNIFKIAKLFLDESGQKELQIRYEKGGEGYGHFKIYLNELVNAYFKEAREKYNELLEKPSHLKEILDFGATKARKIAQEKmQKIYEKIGL 319
                            |       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         
                            |                      25-MSE   34-MSE    44-MSE                                    86-MSE      98-MSE                       128-MSE                                                       190-MSE                                                                                                                 310-MSE     
                            1-MSE                             36-MSE

Chain B from PDB  Type:PROTEIN  Length:320
 aligned with SYW_CAMJE | Q9PIB4 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:320
                             1                                                                                                                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319
            SYW_CAMJE     - -MRVLTGLQPSGDLHIGNYFGAIKQMVDAQEKSQMFMFIANYHAMTSSQDGEKLKQNSLKAAAAFLSLGIDPQKSVFWLQSDVKEVMELYWILSQFTPMGLLERAHSYKDKVAKGLSASHGLFSYPVLMAADILLFDTRIVPVGKDQIQHVEIARDIALKVNNEWGEIFTLPEARVNEEVAVVVGTDGAKMSKSYQNTIDIFSSEKTLKKQISSIVTDSTALEDPKDHENCNIFKIAKLFLDESGQKELQIRYEKGGEGYGHFKIYLNELVNAYFKEAREKYNELLEKPSHLKEILDFGATKARKIAQEKMQKIYEKIGL 319
               SCOP domains d3tzlb_ B: automated matches                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhh....eeeeeehhhhhh....hhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhh......eee............................hhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tzl B   0 AmRVLTGLQPSGDLHIGNYFGAIKQmVDAQEKSQmFmFIANYHAmTSSQDGEKLKQNSLKAAAAFLSLGIDPQKSVFWLQSDVKEVmELYWILSQFTPmGLLERAHSYKDKVAKGLSASHGLFSYPVLmAADILLFDTRIVPVGKDQIQHVEIARDIALKVNNEWGEIFTLPEARVNEEVAVVVGTDGAKmSKSYQNTIDIFSSEKTLKKQISSIVTDSTALEDPKDHENCNIFKIAKLFLDESGQKELQIRYEKGGEGYGHFKIYLNELVNAYFKEAREKYNELLEKPSHLKEILDFGATKARKIAQEKmQKIYEKIGL 319
                             |       9        19     |  29    | | 39    |   49        59        69        79      | 89        99       109       119       129       139       149       159       169       179       189|      199       209       219       229       239       249       259       269       279       289       299       309|      319
                             1-MSE                  25-MSE   34-MSE    44-MSE                                    86-MSE      98-MSE                       128-MSE                                                       190-MSE                                                                                                                 310-MSE     
                                                               36-MSE

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)

Campylobacter jejuni [TaxId: 192222] (3)

1a	d3tzla_	A:
1b	d3tzlb_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SYW_CAMJE | Q9PIB4)

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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	Cis Peptide Bonds
		Glu B:177 - Glu B:178	[ RasMol ]

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	SYW_CAMJE \| Q9PIB4	:	3m5w

3m5w	THE SAME PROTEIN, APO-FORM RELATED ID: IDP90555 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 30)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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