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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE FROM CAMPYLOBACTER JEJUNI
 
Authors :  Y. Kim, M. Zhou, J. Hasseman, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  14 Mar 10  (Deposition) - 31 Mar 10  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Structure, Csgid, Aminoacyl-Trna Synthetase, Atp-Binding, Ligase, Nucleotide-Binding, Protein Biosynthesis, Structural Genomics, Structural Genomics Of Infectious Diseases, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, M. Zhou, J. Hasseman, W. F. Anderson, A. Joachimiak
Crystal Structure Of Tryptophanyl-Trna Synthetase From Campylobacter Jejuni
To Be Published 2010
PubMed: search

(-) Compounds

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: 511693
    Expression System Vector Type: PLASMID
    Gene: CJ0388, TRPS
    Organism Scientific: CAMPYLOBACTER JEJUNI
    Organism Taxid: 192222
    Strain: NCTC 11168
    Synonym: TRYPTOPHAN--TRNA LIGASE, TRPRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 28)

Asymmetric/Biological Unit (3, 28)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE20Mod. Amino AcidSELENOMETHIONINE
3SO45Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:14 , ASN A:17 , SER A:191 , LYS A:192 , HOH A:431BINDING SITE FOR RESIDUE SO4 A 321
2AC2SOFTWAREGLY A:258 , TYR A:259 , GLY A:260 , HOH A:389 , HOH A:390BINDING SITE FOR RESIDUE SO4 A 322
3AC3SOFTWARESER A:203 , GLU A:204 , LYS A:205BINDING SITE FOR RESIDUE GOL A 323
4AC4SOFTWARELYS A:287 , PRO A:288 , SER A:289BINDING SITE FOR RESIDUE SO4 A 324
5AC5SOFTWAREHIS B:14 , ASN B:17 , SER B:191 , LYS B:192BINDING SITE FOR RESIDUE SO4 B 321
6AC6SOFTWARELYS B:287 , PRO B:288 , SER B:289BINDING SITE FOR RESIDUE SO4 B 323
7AC7SOFTWAREHIS B:42 , THR B:45BINDING SITE FOR RESIDUE GOL B 324
8AC8SOFTWARELEU B:4 , GLY B:6 , MSE B:128 , ASP B:131 , ILE B:132 , VAL B:140 , HIS B:149 , HOH B:403BINDING SITE FOR RESIDUE GOL B 325

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M5W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M5W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M5W)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYW_CAMJE9-18
 		  2A:9-18
B:9-18

(-) Exons   (0, 0)

(no "Exon" information available for 3M5W)

(-) Sequences/Alignments

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:309
 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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......hhhhhhhhhhhhhhh......eeee...hhhhhh.hhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh-------.hhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhh......eee.----...........hhhhh.......hhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m5w A   0 AmRVLTGLQPSGDLHIGNYFGAIKQmVDAQEKSQmFmFIANYHAmTSSQDGEKLKQNSLKAAAAFLSLGIDPQKSVFWLQSDVKEVmELYWILSQFTPmGLLERAHSYKD-------ASHGLFSYPVLmAADILLFDTRIVPVGKDQIQHVEIARDIALKVNNEWGEIFTLPEARV----AVVVGTDGAKmSKSYQNTIDIFSSEKTLKKQISSIVTDSTALEDPKDHENCNIFKIAKLFLDESGQKELQIRYEKGGEGYGHFKIYLNELVNAYFKEAREKYNELLEKPSHLKEILDFGATKARKIAQEKmQKIYEKIGL 319
                             |       9        19     |  29    | | 39    |   49        59        69        79      | 89        99       109       119       129       139       149       159       169     |   -|      189|      199       209       219       229       239       249       259       269       279       289       299       309|      319
                             |                      25-MSE   34-MSE    44-MSE                                    86-MSE      98-MSE    109     117        128-MSE                                        175  180       190-MSE                                                                                                                 310-MSE     
                             1-MSE                             36-MSE                                                                                                                                                                                                                                                                                       


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

    Alignment length:321
                              1                                                                                                                                                                                                                                                                                                                              
                              |      8        18        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 
            SYW_CAMJE     - --MRVLTGLQPSGDLHIGNYFGAIKQMVDAQEKSQMFMFIANYHAMTSSQDGEKLKQNSLKAAAAFLSLGIDPQKSVFWLQSDVKEVMELYWILSQFTPMGLLERAHSYKDKVAKGLSASHGLFSYPVLMAADILLFDTRIVPVGKDQIQHVEIARDIALKVNNEWGEIFTLPEARVNEEVAVVVGTDGAKMSKSYQNTIDIFSSEKTLKKQISSIVTDSTALEDPKDHENCNIFKIAKLFLDESGQKELQIRYEKGGEGYGHFKIYLNELVNAYFKEAREKYNELLEKPSHLKEILDFGATKARKIAQEKMQKIYEKIGL 319
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --tRNA-synt_1b-3m5wB01 B:1-275                                                                                                                                                                                                                                                       -------------------------------------------- Pfam domains (1)
           Pfam domains (2) --tRNA-synt_1b-3m5wB02 B:1-275                                                                                                                                                                                                                                                       -------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhh......eeee..--.......................hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------AA_TRNA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m5w B  -1 NAmRVLTGLQPSGDLHIGNYFGAIKQmVDAQEKSQmFmFIANYHAmTSSQDGEKLKQNSLKAAAAFLSLGIDPQKSVFWLQSDVKEVmELYWILSQFTPmGLLERAHSYKDKVAKGLSASHGLFSYPVLmAADILLFDTRIVPVGKDQIQHVEIARDIALKVNNEWGEIFTLPEARVNE--AVVVGTDGAKmSKSYQNTIDIFSSEKTLKKQISSIVTDSTALEDPKDHENCNIFKIAKLFLDESGQKELQIRYEKGGEGYGHFKIYLNELVNAYFKEAREKYNELLEKPSHLKEILDFGATKARKIAQEKmQKIYEKIGL 319
                              |      8        18      | 28     | |38     |  48        58        68        78       |88        98       108       118       128       138       148       158       168        |- |     188 |     198       208       218       228       238       248       258       268       278       288       298       308 |     318 
                              1-MSE                  25-MSE   34-MSE    44-MSE                                    86-MSE      98-MSE                       128-MSE                                          177  |       190-MSE                                                                                                                 310-MSE     
                                                                36-MSE                                                                                                                                         180
   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)

(no "SCOP Domain" information available for 3M5W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M5W)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (9, 9)

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.

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        SYW_CAMJE | Q9PIB4: 3tzl

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