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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE SELENOCYSTEINE SYNTHASE, SODIUM IODIDE SOAK
 
Authors :  O. M. Ganichkin, M. C. Wahl
Date :  12 Nov 07  (Deposition) - 18 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Disorder-Order Transition, Phosphate-Loop, Pyridoxal Phosphate, Selenocysteine Synthase (Secs, Sepsecs), Soluble Liver Antigen/Liver And Pancreas Antigen (Sla/Lp), Protein Biosynthesis, Selenium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. M. Ganichkin, X. M. Xu, B. A. Carlson, H. Mix, D. L. Hatfield, V. N. Gladyshev, M. C. Wahl
Structure And Catalytic Mechanism Of Eukaryotic Selenocysteine Synthase.
J. Biol. Chem. V. 283 5849 2008
PubMed-ID: 18093968  |  Reference-DOI: 10.1074/JBC.M709342200

(-) Compounds

Molecule 1 - O-PHOSPHOSERYL-TRNA(SEC) SELENIUM TRANSFERASE
    Chains: A
    EC Number: 2.9.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM-13-SECS
    Expression System Strain: BL21 ROSETTA2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ELASTASE-RESISTANT FRAGMENT: RESIDUES 19-468
    Gene: SEPSECS, D5ERTD135E
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 63)

Asymmetric Unit (2, 63)
No.NameCountTypeFull Name
1IOD62Ligand/IonIODIDE ION
2LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
Biological Unit 1 (2, 252)
No.NameCountTypeFull Name
1IOD248Ligand/IonIODIDE ION
2LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(-) Sites  (45, 45)

Asymmetric Unit (45, 45)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:75 , HOH A:797BINDING SITE FOR RESIDUE IOD A 501
02AC2SOFTWARELYS A:173 , HOH A:624BINDING SITE FOR RESIDUE IOD A 502
03AC3SOFTWAREGLY A:312BINDING SITE FOR RESIDUE IOD A 503
04AC4SOFTWARELYS A:158BINDING SITE FOR RESIDUE IOD A 505
05AC5SOFTWAREGLY A:68 , GLN A:399BINDING SITE FOR RESIDUE IOD A 507
06AC6SOFTWARELEU A:202 , ARG A:234 , THR A:379BINDING SITE FOR RESIDUE IOD A 508
07AC7SOFTWAREALA A:80BINDING SITE FOR RESIDUE IOD A 509
08AC8SOFTWAREASN A:428BINDING SITE FOR RESIDUE IOD A 511
09AC9SOFTWARELYS A:177BINDING SITE FOR RESIDUE IOD A 512
10BC1SOFTWARELYS A:177BINDING SITE FOR RESIDUE IOD A 513
11BC2SOFTWAREGLY A:213 , GLU A:215BINDING SITE FOR RESIDUE IOD A 514
12BC3SOFTWAREHOH A:688BINDING SITE FOR RESIDUE IOD A 515
13BC4SOFTWARESER A:259 , ARG A:341 , LYS A:342BINDING SITE FOR RESIDUE IOD A 516
14BC5SOFTWAREARG A:271BINDING SITE FOR RESIDUE IOD A 518
15BC6SOFTWARELYS A:456BINDING SITE FOR RESIDUE IOD A 519
16BC7SOFTWARECYS A:41 , ASN A:124 , CYS A:331BINDING SITE FOR RESIDUE IOD A 520
17BC8SOFTWARELYS A:127BINDING SITE FOR RESIDUE IOD A 521
18BC9SOFTWARELYS A:339 , HOH A:731BINDING SITE FOR RESIDUE IOD A 522
19CC1SOFTWARETHR A:350 , GLN A:351BINDING SITE FOR RESIDUE IOD A 523
20CC2SOFTWARECYS A:431BINDING SITE FOR RESIDUE IOD A 524
21CC3SOFTWARETHR A:389 , PRO A:407BINDING SITE FOR RESIDUE IOD A 525
22CC4SOFTWAREHOH A:657BINDING SITE FOR RESIDUE IOD A 526
23CC5SOFTWAREASP A:455BINDING SITE FOR RESIDUE IOD A 527
24CC6SOFTWARESER A:393 , THR A:397 , ARG A:398 , HOH A:666BINDING SITE FOR RESIDUE IOD A 528
25CC7SOFTWAREASN A:119 , HOH A:654BINDING SITE FOR RESIDUE IOD A 533
26CC8SOFTWAREMET A:444 , GLN A:445BINDING SITE FOR RESIDUE IOD A 535
27CC9SOFTWAREHOH A:580 , HOH A:620BINDING SITE FOR RESIDUE IOD A 536
28DC1SOFTWAREGLU A:43 , SER A:332 , ARG A:335BINDING SITE FOR RESIDUE IOD A 537
29DC2SOFTWAREARG A:453BINDING SITE FOR RESIDUE IOD A 538
30DC3SOFTWAREVAL A:79BINDING SITE FOR RESIDUE IOD A 539
31DC4SOFTWAREGLY A:96 , SER A:112BINDING SITE FOR RESIDUE IOD A 540
32DC5SOFTWARESER A:112BINDING SITE FOR RESIDUE IOD A 541
33DC6SOFTWAREHOH A:640BINDING SITE FOR RESIDUE IOD A 543
34DC7SOFTWARELYS A:163 , HIS A:216BINDING SITE FOR RESIDUE IOD A 546
35DC8SOFTWARELYS A:261 , CYS A:262BINDING SITE FOR RESIDUE IOD A 547
36DC9SOFTWAREGLU A:48 , SER A:49BINDING SITE FOR RESIDUE IOD A 549
37EC1SOFTWAREGLU A:29BINDING SITE FOR RESIDUE IOD A 551
38EC2SOFTWARESER A:133 , GLN A:267BINDING SITE FOR RESIDUE IOD A 552
39EC3SOFTWARESER A:260 , HOH A:683BINDING SITE FOR RESIDUE IOD A 555
40EC4SOFTWARELYS A:208BINDING SITE FOR RESIDUE IOD A 556
41EC5SOFTWARELYS A:116 , ILE A:117BINDING SITE FOR RESIDUE IOD A 557
42EC6SOFTWARELYS A:386BINDING SITE FOR RESIDUE IOD A 559
43EC7SOFTWARESER A:393BINDING SITE FOR RESIDUE IOD A 560
44EC8SOFTWARECYS A:137BINDING SITE FOR RESIDUE IOD A 561
45EC9SOFTWAREGLN A:304BINDING SITE FOR RESIDUE IOD A 562

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:105 -Pro A:106
2Ala A:228 -Pro A:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BCA)

(-) Exons   (0, 0)

(no "Exon" information available for 3BCA)

(-) Sequences/Alignments

Asymmetric 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:436
 aligned with SPCS_MOUSE | Q6P6M7 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:444
                                    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       432       442       452       462    
           SPCS_MOUSE    23 EARRAHEHLIRLLLEQGKCPEDGWDESTLELFLHELAVMDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNSLVLNVIKLAGVHSVASCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRIDQKSCFKSMVTAGFEPVVIENVLEGDELRTDLKAVEAKIQELGPEHILCLHSTTACFAPRVPDRLEELAVICANYDIPHVVNNAYGLQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNEPFIQDISKMYPGRASASPSLDVLITLLSLGCSGYRKLLKERKEMFVYLSTQLKKLAEAHNERLLQTPHNPISLAMTLKTIDGHHDKAVTQLGSMLFTRQVSGARAVPLGNVQTVSGHTFRGFMSHADNYPCAYLNAAAAIGMKMQDVDLFIKRLDKCLNIVRKEQT 466
               SCOP domains d3bcaa_ A: Selenocysteinyl-tRNA synthase (SepSecS)                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..............hhhhhhhh........--------...hhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh..eeeee..eee..eee.hhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eeeeehhhhhh.....eeeee.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.........hhhhhhhhhhhhh.....eee....eeee..eeee............eeeee.....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bca A  23 EARRAHEHLIRLLLEQGKCPEDGWDESTLELFLHELAVMDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIG--------QPKAAGSSLLNKITNSLVLNVIKLAGVHSVASCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRIDQKSCFKSMVTAGFEPVVIENVLEGDELRTDLKAVEAKIQELGPEHILCLHSTTACFAPRVPDRLEELAVICANYDIPHVVNNAYGLQSSKCMHLIQQGARVGRIDAFVQSLDkNFMVPVGGAIIAGFNEPFIQDISKMYPGRASASPSLDVLITLLSLGCSGYRKLLKERKEMFVYLSTQLKKLAEAHNERLLQTPHNPISLAMTLKTIDGHHDKAVTQLGSMLFTRQVSGARAVPLGNVQTVSGHTFRGFMSHADNYPCAYLNAAAAIGMKMQDVDLFIKRLDKCLNIVRKEQT 466
                                    32        42        52        62        72        82        92   |     -  |    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       432       442       452       462    
                                                                                                    96      105                                                                                                                                                                                284-LLP
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (SPCS_MOUSE | Q6P6M7)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016785    transferase activity, transferring selenium-containing groups    Catalysis of the transfer of a selenium-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0001514    selenocysteine incorporation    The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine.
    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: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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        SPCS_MOUSE | Q6P6M7: 3bc8 3bcb

(-) Related Entries Specified in the PDB File

3bc8 CRYSTAL STRUCTURE OF MOUSE SELENOCYSTEINE SYNTHASE
3bcb CRYSTAL STRUCTURE OF MOUSE SELENOCYSTEINE SYNTHASE, SODIUM PHOSPHATE SOAK