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(-) Description

Title :  CRYSTAL STRUCTURE OF MAMMALIAN MITOCHONDRIAL SERYL-TRNA SYNTHETASE COMPLEXED WITH SERYL-ADENYLATE
 
Authors :  S. Chimnaronk, M. G. Jeppesen, T. Suzuki, J. Nyborg, K. Watanabe
Date :  25 Jun 04  (Deposition) - 06 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chimnaronk, M. G. Jeppesen, T. Suzuki, J. Nyborg, K. Watanabe
Dual-Mode Recognition Of Noncanonical Trnas(Ser) By Seryl-Trna Synthetase In Mammalian Mitochondria
Embo J. V. 24 3369 2005
PubMed-ID: 16163389  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600811
(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
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-19B
    Expression System Strain: BL21(DE3) ROSETTA (NOVAGEN)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SERRSMT
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: MITOCHONDRIAL SERYL-TRNA SYNTHETASE, SERINE--TRNA LIGASE, SERRSMT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SRP2Ligand/IonSERYL ADENYLATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:282 , GLU A:284 , ARG A:313 , GLU A:315 , TYR A:326 , ARG A:327 , VAL A:328 , PHE A:331 , GLU A:335 , GLU A:401 , VAL A:402 , THR A:403 , SER A:404 , ASN A:434 , THR A:436 , ALA A:439 , HOH A:902 , HOH A:954 , HOH A:1040 , HOH A:1134BINDING SITE FOR RESIDUE SRP A 900
2AC2SOFTWARETHR B:282 , GLU B:284 , ARG B:313 , GLU B:315 , TYR B:326 , ARG B:327 , VAL B:328 , PHE B:331 , GLU B:335 , GLU B:401 , VAL B:402 , THR B:403 , SER B:404 , ASN B:434 , THR B:436 , ALA B:439 , HOH B:905 , HOH B:1014BINDING SITE FOR RESIDUE SRP B 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:301 -Pro A:302
2Leu B:301 -Pro B:302

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WLE)

(-) 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:465
 aligned with SYSM_BOVIN | Q9N0F3 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:467
                                    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       430       440       450       460       470       480       490       500       
           SYSM_BOVIN    41 RNLLYEHAREGYSALPLLDMESLCAYPEDAARALDLRKGELRSKDLPGIISTWQELRQLREQIRSLEEEKEAVTEAVRALVVNQDNSQVQQDPQYQSLRARGREIRKQLTLLYPKEAQLEEQFYLRALRLPNQTHPDVPVGDESQARVLHVVGDKPAFSFQPRGHLEIAEKLDIIRQKRLSHVSGHRSYYLRGAGALLQHGLVNFTLNKLIHRGFTPMTVPDLLRGVVFEGCGMTPNAKPSQIYNIDPSRFEDLNLAGTAEVGLAGYFMDHSVAFRDLPIRMVCSSTCYRAETDTGKEPWGLYRVHHFTKVEMFGVTGPGLEQSSELLEEFLSLQMEILTELGLHFRVLDMPTQELGLPAYRKFDIEAWMPGRGRFGEVTSASNCTDFQSRRLHIMFQTEAGELQFAHTVNATGCAVPRLLIALLESYQQKDGSVLVPPALQPYLGTDRITTPTHVPLQYIGPNQPQ 507
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------1wleA02 A:155-473 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                          ----------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhheeeeee...........hhhhhhhhh..ee.............eeehhhhhhhhhhhhhhhhhhhhh..eeee...eehhhhhhhhh.....................ee..hhhhhhhhhhh.eeee.hhh.eeeeeeeeee.......--........eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....eeeeeeeee....eeeeeeeeee..hhhhhhhh.eee.....eee.eeeeeeeeehhhhhhhhhhhhh.....ee.hhhhhhhhh..ee........ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wle A  24 RNLLYEHAREGYSALPLLDMESLCAYPEDAARALDLRKGELRSKDLPGIISTWQELRQLREQIRSLEEEKEAVTEAVRALVVNQDNSQVQQDPQYQSLRARGREIRKQLTLLYPKEAQLEEQFYLRALRLPNQTHPDVPVGDESQARVLHVVGDKPAFSFQPRGHLEIAEKLDIIRQKRLSHVSGHRSYYLRGAGALLQHGLVNFTLNKLIHRGFTPMTVPDLLRGVVFEGCGMTPNAKPSQIYNIDPSRFEDLNLAGTAEVGLAGYFMDHSVAFRDLPIRMVCSSTCYRAETDTG--PWGLYRVHHFTKVEMFGVTGPGLEQSSELLEEFLSLQMEILTELGLHFRVLDMPTQELGLPAYRKFDIEAWMPGRGRFGEVTSASNCTDFQSRRLHIMFQTEAGELQFAHTVNATGCAVPRLLIALLESYQQKDGSVLVPPALQPYLGTDRITTPTHVPLQYIGPNQPQ 490
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313     | 323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       
                                                                                                                                                                                                                                                                                                                                 319  |                                                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                    322                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:469
 aligned with SYSM_BOVIN | Q9N0F3 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:469
                                    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       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498         
           SYSM_BOVIN    39 QDRNLLYEHAREGYSALPLLDMESLCAYPEDAARALDLRKGELRSKDLPGIISTWQELRQLREQIRSLEEEKEAVTEAVRALVVNQDNSQVQQDPQYQSLRARGREIRKQLTLLYPKEAQLEEQFYLRALRLPNQTHPDVPVGDESQARVLHVVGDKPAFSFQPRGHLEIAEKLDIIRQKRLSHVSGHRSYYLRGAGALLQHGLVNFTLNKLIHRGFTPMTVPDLLRGVVFEGCGMTPNAKPSQIYNIDPSRFEDLNLAGTAEVGLAGYFMDHSVAFRDLPIRMVCSSTCYRAETDTGKEPWGLYRVHHFTKVEMFGVTGPGLEQSSELLEEFLSLQMEILTELGLHFRVLDMPTQELGLPAYRKFDIEAWMPGRGRFGEVTSASNCTDFQSRRLHIMFQTEAGELQFAHTVNATGCAVPRLLIALLESYQQKDGSVLVPPALQPYLGTDRITTPTHVPLQYIGPNQPQ 507
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------1wleB02 B:155-473 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                          ----------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_2b-1wleB01 B:221-396                                                                                                                                                  ---------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_2b-1wleB02 B:221-396                                                                                                                                                  ---------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhheeeeee...........hhhhhhhhh..ee.............eeehhhhhhhhhhhhhhhhhhhhh..eeee...eehhhhhhhhh.....................ee..hhhhhhhhhhh.eeee.hhh.eeeeeeeeee.................eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....eeeeeeeee....eeeeeeeeee..hhhhhhhh.eee.....eee.eeeeeeeeehhhhhhhhhhhhh.....ee.hhhhhhhhh..ee........ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wle B  22 QDRNLLYEHAREGYSALPLLDMESLCAYPEDAARALDLRKGELRSKDLPGIISTWQELRQLREQIRSLEEEKEAVTEAVRALVVNQDNSQVQQDPQYQSLRARGREIRKQLTLLYPKEAQLEEQFYLRALRLPNQTHPDVPVGDESQARVLHVVGDKPAFSFQPRGHLEIAEKLDIIRQKRLSHVSGHRSYYLRGAGALLQHGLVNFTLNKLIHRGFTPMTVPDLLRGVVFEGCGMTPNAKPSQIYNIDPSRFEDLNLAGTAEVGLAGYFMDHSVAFRDLPIRMVCSSTCYRAETDTGKEPWGLYRVHHFTKVEMFGVTGPGLEQSSELLEEFLSLQMEILTELGLHFRVLDMPTQELGLPAYRKFDIEAWMPGRGRFGEVTSASNCTDFQSRRLHIMFQTEAGELQFAHTVNATGCAVPRLLIALLESYQQKDGSVLVPPALQPYLGTDRITTPTHVPLQYIGPNQPQ 490
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481
   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 1WLE)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYSM_BOVIN | Q9N0F3)
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: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.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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