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(-) Description

Title :  CRYSTAL STRUCTURE OF HISTIDYL-TRNA SYNTHETASE FROM THERMOPLASMA ACIDOPHILUM
 
Authors :  Y. Tanaka, N. Sakai, M. Yao, N. Watanabe, T. Tamura, I. Tanaka
Date :  01 Dec 04  (Deposition) - 06 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Structural Genomics, Dimer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Tanaka, N. Sakai, M. Yao, N. Watanabe, T. Tamura, I. Tanaka
Crystal Structure Of Histidyl-Trna Synthetase From Thermoplasma Acidophilum
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISTIDYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HISS
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303
    Synonym: HISTIDINE--TRNA LIGASE, HISRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 26)

Asymmetric/Biological Unit (1, 26)
No.NameCountTypeFull Name
1MSE26Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1WU7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WU7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:98 -Pro A:99
2Arg B:98 -Pro B:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WU7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WU7)

(-) Exons   (0, 0)

(no "Exon" information available for 1WU7)

(-) 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:424
 aligned with SYH_THEAC | Q9HLX5 from UniProtKB/Swiss-Prot  Length:426

    Alignment length:424
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422    
            SYH_THEAC     3 RLQIEKIRGFRDFYPEDMDVEKFIFKTAEEAAEAFGFRRIDFPSLEYLDLYRIKSGEELLQQTYSFVDKGGREVTLIPEATPSTVRMVTSRKDLQRPLRWYSFPKVWRYEEPQAGRYREHYQFNADIFGSDSPEADAEVIALASSILDRLGLQDIYEIRINSRKIMEEIIGGMTSSDPFSVFSIIDRYHKISREEFVDQLRSAGIGEDGVSMIADLCSGTRGIDEMARITGKSSEEIARMAAVEDLLASYGVKNVRYDFSIVRGLSYYTGIVFEAYDRSGQFRAILGGGRYDNLASLMSGESVPAVGFGMGDAVISLLLKRENVQIPREKKSVYICRVGKINSSIMNEYSRKLRERGMNVTVEIMERGLSAQLKYASAIGADFAVIFGERDLERGVVTIRNMYTGSQENVGLDSVVEHLISQAT 426
               SCOP domains d1wu7a2 A:3-329 Histidyl-tRNA synthetase (HisRS)                                                                                                                                                                                                                                                                                       d1wu7a1 A:330-426 Histidyl-tRNA synthetase (HisRS), C-terminal domain                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhhh....hhhhhh.eee.....eeee...hhhhhhhhhh........eeeee..eee...........eeeeeeeeee...hhhhhhhhhhhhhhhhhhh.....eeeeeeehhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhh.....ee.............eeeeeee.........eeee..hhhhhhhh....eeeeeeehhhhhhhhhhh.........eeeeeee...hhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...eeeeeehhhhhh.eeeeee.....eeeee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wu7 A   3 RLQIEKIRGFRDFYPEDmDVEKFIFKTAEEAAEAFGFRRIDFPSLEYLDLYRIKSGEELLQQTYSFVDKGGREVTLIPEATPSTVRmVTSRKDLQRPLRWYSFPKVWRYEEPQAGRYREHYQFNADIFGSDSPEADAEVIALASSILDRLGLQDIYEIRINSRKImEEIIGGmTSSDPFSVFSIIDRYHKISREEFVDQLRSAGIGEDGVSmIADLCSGTRGIDEmARITGKSSEEIARmAAVEDLLASYGVKNVRYDFSIVRGLSYYTGIVFEAYDRSGQFRAILGGGRYDNLASLmSGESVPAVGFGmGDAVISLLLKRENVQIPREKKSVYICRVGKINSSImNEYSRKLRERGmNVTVEImERGLSAQLKYASAIGADFAVIFGERDLERGVVTIRNmYTGSQENVGLDSVVEHLISQAT 426
                                    12       |22        32        42        52        62        72        82      | 92       102       112       122       132       142       152       162     | 172  |    182       192       202       212 |     222     | 232       242       252       262       272       282       292       302       312       322       332       342     | 352       362    |  372       382       392       402 |     412       422    
                                            20-MSE                                                               89-MSE                                                                        168-MSE  |                                    214-MSE       228-MSE       242-MSE                                                   300-MSE     312-MSE                             348-MSE     360-MSE  |                                  404-MSE                  
                                                                                                                                                                                                      175-MSE                                                                                                                                                                                         367-MSE                                                       


Chain B from PDB  Type:PROTEIN  Length:420
 aligned with SYH_THEAC | Q9HLX5 from UniProtKB/Swiss-Prot  Length:426

    Alignment length:420
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424
            SYH_THEAC     5 QIEKIRGFRDFYPEDMDVEKFIFKTAEEAAEAFGFRRIDFPSLEYLDLYRIKSGEELLQQTYSFVDKGGREVTLIPEATPSTVRMVTSRKDLQRPLRWYSFPKVWRYEEPQAGRYREHYQFNADIFGSDSPEADAEVIALASSILDRLGLQDIYEIRINSRKIMEEIIGGMTSSDPFSVFSIIDRYHKISREEFVDQLRSAGIGEDGVSMIADLCSGTRGIDEMARITGKSSEEIARMAAVEDLLASYGVKNVRYDFSIVRGLSYYTGIVFEAYDRSGQFRAILGGGRYDNLASLMSGESVPAVGFGMGDAVISLLLKRENVQIPREKKSVYICRVGKINSSIMNEYSRKLRERGMNVTVEIMERGLSAQLKYASAIGADFAVIFGERDLERGVVTIRNMYTGSQENVGLDSVVEHLISQ 424
               SCOP domains d1wu7b2 B:5-329 Histidyl-tRNA synthetase (HisRS)                                                                                                                                                                                                                                                                                     d1wu7b1 B:330-424 Histidyl-tRNA synthetase (HisRS), C-terminal domain                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------tRNA-synt_His-1wu7B03 B:11-313                                                                                                                                                                                                                                                                                 --------------------HGTP_anticodon-1wu7B01 B:334-424                                                            Pfam domains (1)
           Pfam domains (2) ------tRNA-synt_His-1wu7B04 B:11-313                                                                                                                                                                                                                                                                                 --------------------HGTP_anticodon-1wu7B02 B:334-424                                                            Pfam domains (2)
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh..ee.....eee.hhhh.....hhhhhh.eee.....eeee...hhhhhhhhhh........eeeee..eee...........eeeeeeeeee...hhhhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhhh..........hhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhhh.....ee.............eeeeeee.........eeee..hhhhhhhh....eeeeeeehhhhhhhhhhh.........eeeeeee...hhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...eeeeeehhhhhh.eeeeee.....eeeee..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wu7 B   5 QIEKIRGFRDFYPEDmDVEKFIFKTAEEAAEAFGFRRIDFPSLEYLDLYRIKSGEELLQQTYSFVDKGGREVTLIPEATPSTVRmVTSRKDLQRPLRWYSFPKVWRYEEPQAGRYREHYQFNADIFGSDSPEADAEVIALASSILDRLGLQDIYEIRINSRKImEEIIGGmTSSDPFSVFSIIDRYHKISREEFVDQLRSAGIGEDGVSmIADLCSGTRGIDEmARITGKSSEEIARmAAVEDLLASYGVKNVRYDFSIVRGLSYYTGIVFEAYDRSGQFRAILGGGRYDNLASLmSGESVPAVGFGmGDAVISLLLKRENVQIPREKKSVYICRVGKINSSImNEYSRKLRERGmNVTVEImERGLSAQLKYASAIGADFAVIFGERDLERGVVTIRNmYTGSQENVGLDSVVEHLISQ 424
                                    14     |  24        34        44        54        64        74        84    |   94       104       114       124       134       144       154       164   |   174|      184       194       204       214       224   |   234       244       254       264       274       284       294     | 304       314       324       334       344   |   354     | 364  |    374       384       394       404       414       424
                                          20-MSE                                                               89-MSE                                                                        168-MSE  |                                    214-MSE       228-MSE       242-MSE                                                   300-MSE     312-MSE                             348-MSE     360-MSE  |                                  404-MSE                
                                                                                                                                                                                                    175-MSE                                                                                                                                                                                         367-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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WU7)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: IIaaRS-ABD (13)
(-)
Clan: tRNA_synt_II (64)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYH_THEAC | Q9HLX5)
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:0004821    histidine-tRNA ligase activity    Catalysis of the reaction: ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His).
    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.
biological process
    GO:0006427    histidyl-tRNA aminoacylation    The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-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.
    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.
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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