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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN S-ADENOSYLMETHIONINE SYNTHETASE 2, BETA SUBUNIT IN ORTHORHOMBIC CRYSTAL FORM
 
Authors :  W. W. Yue, N. Shafqat, J. R. C. Muniz, T. Krojer, A. C. W. Pike, A. Chaikuad C. K. Allerston, O. Gileadi, F. Von Delft, K. L. Kavanagh, C. H. Arrows A. M. Edwards, J. Weigelt, C. Bountra, U. Oppermann
Date :  25 Mar 11  (Deposition) - 20 Apr 11  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Shafqat, J. R. C. Muniz, E. S. Pilka, E. Papagrigoriou, F. Von Delft U. Oppermann, W. W. Yue
Insight Into S-Adenosylmethionine Biosynthesis From The Crystal Structures Of The Human Methionine Adenosyltransferase Catalytic And Regulatory Subunits.
Biochem. J. V. 452 27 2013
PubMed-ID: 23425511  |  Reference-DOI: 10.1042/BJ20121580

(-) Compounds

Molecule 1 - METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    Expression System VectorPNIC-CTHF
    Expression System Vector TypePLASMID
    FragmentRESIDUES 17-323
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDTDP-4-KETO-6-DEOXY-D-GLUCOSE 4-REDUCTASE, METHIONINE ADENOSYLTRANSFERASE II BETA, MAT II BETA S-ADENOSYLMETHIONINE SYNTHETASE 2,BETA SUBUNIT, MAT2B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:255 , ARG A:291 , ASN A:292BINDING SITE FOR RESIDUE SO4 A1325
2AC2SOFTWAREARG A:232 , GLN A:233BINDING SITE FOR RESIDUE SO4 A1326
3AC3SOFTWARETYR A:138 , ALA A:196 , ARG A:219 , LYS A:258BINDING SITE FOR RESIDUE SO4 A1327

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YDY)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:145 -Pro A:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_032318A293TMAT2B_HUMANPolymorphism17849948AA293T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YDY)

(-) Exons   (0, 0)

(no "Exon" information available for 2YDY)

(-) 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:260
 aligned with MAT2B_HUMAN | Q9NZL9 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:297
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       
          MAT2B_HUMAN    28 NRRVLVTGATGLLGRAVHKEFQQNNWHAVGCGFRRARPKFEQVNLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYVFDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVMFDKVQFSNKSANMDHWQQRFPTHVKDVATVCRQLAEKRMLDPSIKGTFHWSGNEQMTKYEMACAIADAFNLPSSHLRPITDSPVLGAQRPRNAQLDCSKLETLGIGQRTPFRIGIKESLWPFLI 324
               SCOP domains d2ydya_ A: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -RmlD_sub_bind-2ydyA01 A:29-323                                                                                                                                                                                                                                                                         - Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhh...eeeee.------------------hhhhhhhhh..eeee..-------------------hhhhhhhhhhhhhh..eeeeeee.hhh................hhhhhhhhhhhhhhhhhh...eeeee..ee....hhhhh.hhhhhhhhhh....eeee.......eehhhhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhh......eeee.................hhhhhhh......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ydy A  28 NRRVLVTGATGLLGRAVHKEFQQNNWHAVGCG------------------VHHIIHDFQPHVIVHCA-------------------VDASGNLAKEAAAVGAFLIYISSDYVFDGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVmFDKVQFSNKSANmDHWQQRFPTHVKDVATVCRQLAEKRmLDPSIKGTFHWSGNEQmTKYEmACAIADAFNLPSSHLRPITDSPVLGAQRPRNAQLDCSKLETLGIGQRTPFRIGIKESLWPFLI 324
                                    37        47        57 |       -         -|       87      |  -         -      |117       127       137       147       157       167       177       187       197  |    207     | 217       227       237 |     247       257   |   267       277       287       297       307       317       
                                                          59                 78              94                 114                                                                                   200-MSE      213-MSE                   239-MSE          256-MSE|                                                               
                                                                                                                                                                                                                                                                   261-MSE                                                           

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  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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YDY)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MAT2B_HUMAN | Q9NZL9)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0048270    methionine adenosyltransferase regulator activity    Modulates the activity of methionine adenosyltransferase.
    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).
biological process
    GO:0006556    S-adenosylmethionine biosynthetic process    The chemical reactions and pathways resulting in the formation of S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0048269    methionine adenosyltransferase complex    A multimeric enzyme complex composed of variable numbers of catalytic alpha subunits, and noncatalytic beta subunits. The beta subunits are believed to have a regulatory function. The enzyme complex catalyzes the synthesis of S-adenosylmethionine (AdoMet), which is the major methyl group donor, participating in the methylation of proteins, DNA, RNA, phospholipids, and other small molecules.
    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.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        MAT2B_HUMAN | Q9NZL92ydx 4ktt 4ktv 4ndn

(-) Related Entries Specified in the PDB File

2ydx CRYSTAL STRUCTURE OF HUMAN S-ADENOSYLMETHIONINE SYNTHETASE 2, BETA SUBUNIT