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(-) Description

Title :  CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE
 
Authors :  S. Cusack, H. Belrhali
Date :  21 Feb 94  (Deposition) - 31 Jul 94  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Synthetase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Belrhali, A. Yaremchuk, M. Tukalo, K. Larsen, C. Berthet-Colominas, R. Leberman, B. Beijer, B. Sproat, J. Als-Nielsen, G. Grubel, J. -F. Legrand, M. Lehmann, S. Cusack
Crystal Structures At 2. 5 Angstrom Resolution Of Seryl-Trna Synthetase Complexed With Two Analogs Of Seryl Adenylate.
Science V. 263 1432 1994
PubMed-ID: 8128224
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.11
    Engineered: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1AHX1Ligand/IonSERYL-HYDROXAMATE-ADENOSINE MONOPHOSPHATE
2AMP1Ligand/IonADENOSINE MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:225 , GLU A:227 , ARG A:256 , GLU A:258 , MET A:270 , ARG A:271 , VAL A:272 , PHE A:275 , LYS A:277 , GLU A:279 , GLU A:345 , THR A:346 , HIS A:347 , SER A:348 , ASN A:378 , THR A:380 , ALA A:383 , ARG A:386 , HOH A:423 , HOH A:424 , HOH A:481BINDING SITE FOR RESIDUE AHX A 422
2AC2SOFTWAREARG B:256 , GLU B:258 , MET B:270 , ARG B:271 , VAL B:272 , PHE B:275 , GLU B:345 , THR B:346 , HIS B:347 , SER B:348 , THR B:380 , ALA B:383 , ARG B:386 , HOH B:430 , HOH B:431 , HOH B:480BINDING SITE FOR RESIDUE AMP B 423

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe A:205 -Pro A:206
2Leu A:244 -Pro A:245
3Thr A:384 -Pro A:385
4Phe B:205 -Pro B:206
5Leu B:244 -Pro B:245
6Thr B:384 -Pro B:385

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1SES)

(-) 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:421
 aligned with SYS_THET2 | P34945 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:421
                                    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       390       400       410       420 
            SYS_THET2     1 MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQVPLPPWPGAPVGGEEANREIKRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPCG 421
               SCOP domains d1sesa1 A:1-110 Seryl-tRNA synthetase (SerRS)                                                                 d1sesa2 A:111-421 Seryl-tRNA synthetase (SerRS)                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sesA01 A:1-102  [code=1.10.287.40, no name defined]                                                  1sesA02 A:103-420 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhheeeeee...........hhhhhhhhhh....hhhhhhh.....eehhhhhhhhhhhhhhhhhhhhh..eeee...eeehhhhhhhh....hhhhh.......eee...hhhhhhhh....eee.hhh.eeeeeeeeee..................eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhh....eeeeeeee......eeeeeeeeeeehhhhhhhh.eee.....eee.eeeeeeeeeehhhhhhhhhhhh.....ee.hhhhhhhhh..ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ses A   1 MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQVPLPPWPGAPVGGEEANREIKRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPCG 421
                                    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       390       400       410       420 


Chain B from PDB  Type:PROTEIN  Length:421
 aligned with SYS_THET2 | P34945 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:421
                                    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       390       400       410       420 
            SYS_THET2     1 MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQVPLPPWPGAPVGGEEANREIKRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPCG 421
               SCOP domains d1sesb1 B:1-110 Seryl-tRNA synthetase (SerRS)                                                                 d1sesb2 B:111-421 Seryl-tRNA synthetase (SerRS)                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sesB01 B:1-102  [code=1.10.287.40, no name defined]                                                  1sesB02 B:103-420 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                         - CATH domains
           Pfam domains (1) Seryl_tRNA_N-1sesB01 B:1-105                                                                             --------------------------------------------------------------tRNA-synt_2b-1sesB03 B:168-340                                                                                                                                               --------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) Seryl_tRNA_N-1sesB02 B:1-105                                                                             --------------------------------------------------------------tRNA-synt_2b-1sesB04 B:168-340                                                                                                                                               --------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhheeeeee...........hhhhhhhhhh....hhhhhh......eehhhhhhhhhhhhhhhhhhhhh..eeee...eeehhhhhhh.....hhhhh.ee....eee..hhhhhhhhh....eee.hhh.eeeeeeeeee..................eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhh....eeeeeeeeehhhheeeeeeeeee....hhhhhh.eee.....eee.eeeeeeeeeehhhhhhhhhhhh.....ee.hhhhhhhhh..ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ses B   1 MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQVPLPPWPGAPVGGEEANREIKRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPCG 421
                                    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       390       400       410       420
   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: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: tRNA_bind_arm (7)
(-)
Clan: tRNA_synt_II (64)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYS_THET2 | P34945)
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:0004828    serine-tRNA ligase activity    Catalysis of the reaction: ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser).
biological process
    GO:0016260    selenocysteine biosynthetic process    The chemical reactions and pathways resulting in the formation of selenocysteine, an essential component of glutathione peroxidase and some other proteins.
    GO:0097056    selenocysteinyl-tRNA(Sec) biosynthetic process    The chemical reactions and pathways resulting in the formation of selenocysteinyl-tRNA(Sec). This process occurs through the following steps: a unique serine-tRNA with a UGA recognizing anticodon is first aminoacylated with serine; this is then phosphorylated by phosphoseryl-tRNA[Ser]Sec kinase; lastly, selenium is swapped for the phosphate on the serine.
    GO:0006434    seryl-tRNA aminoacylation    The process of coupling serine to seryl-tRNA, catalyzed by seryl-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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  1ses
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SYS_THET2 | P34945: 1ser 1set 1sry 3err 5eiu 5f7t 5iea

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1SES)