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(-) Description

Title :  S-ADENOSYLMETHIONINE SYNTHETASE WITH ADP
 
Authors :  F. Takusagawa, S. Kamitori, G. D. Markham
Date :  10 Jan 96  (Deposition) - 11 Jul 96  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (4x)
Keywords :  Transferase, One-Carbon Metabolism, Atp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Takusagawa, S. Kamitori, G. D. Markham
Structure And Function Of S-Adenosylmethionine Synthetase: Crystal Structures Of S-Adenosylmethionine Synthetase With Adp, Bradp, And Ppi At 28 Angstroms Resolution.
Biochemistry V. 35 2586 1996
PubMed-ID: 8611562  |  Reference-DOI: 10.1021/BI952604Z

(-) Compounds

Molecule 1 - S-ADENOSYLMETHIONINE SYNTHETASE
    ChainsA
    EC Number2.5.1.6
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymMAT, ATP:L-METHIONINE S-ADENOSYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A
Biological Unit 2 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2K2Ligand/IonPOTASSIUM ION
3MG2Ligand/IonMAGNESIUM ION
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION
4PO44Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:16 , ARG A:244 , LYS A:245 , GLY A:260 , ALA A:261 , LYS A:265 , ASP A:271 , ADP A:385 , MG A:411 , MG A:412BINDING SITE FOR RESIDUE PO4 A 384
2AC2SOFTWAREASP A:271 , PO4 A:384 , ADP A:385BINDING SITE FOR RESIDUE MG A 411
3AC3SOFTWAREASP A:16 , PO4 A:384 , ADP A:385BINDING SITE FOR RESIDUE MG A 412
4AC4SOFTWAREGLU A:42 , SER A:263 , LYS A:265BINDING SITE FOR RESIDUE K A 413
5AC5SOFTWAREGLY A:243 , ILE A:246BINDING SITE FOR RESIDUE K A 414
6AC6SOFTWAREHIS A:14 , ASP A:16 , ARG A:38 , ALA A:40 , GLU A:55 , GLN A:98 , ASP A:118 , LYS A:165 , GLY A:237 , LYS A:245 , LYS A:265 , LYS A:269 , ASP A:271 , PO4 A:384 , MG A:411 , MG A:412BINDING SITE FOR RESIDUE ADP A 385

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MXB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADOMET_SYNTHASE_1PS00376 S-adenosylmethionine synthase signature 1.METK_ECOLI116-126  1A:115-125
2ADOMET_SYNTHASE_2PS00377 S-adenosylmethionine synthase signature 2.METK_ECOLI259-267  1A:258-266
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADOMET_SYNTHASE_1PS00376 S-adenosylmethionine synthase signature 1.METK_ECOLI116-126  2A:115-125
2ADOMET_SYNTHASE_2PS00377 S-adenosylmethionine synthase signature 2.METK_ECOLI259-267  2A:258-266
Biological Unit 2 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADOMET_SYNTHASE_1PS00376 S-adenosylmethionine synthase signature 1.METK_ECOLI116-126  4A:115-125
2ADOMET_SYNTHASE_2PS00377 S-adenosylmethionine synthase signature 2.METK_ECOLI259-267  4A:258-266

(-) Exons   (0, 0)

(no "Exon" information available for 1MXB)

(-) 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:378
 aligned with METK_ECOLI | P0A817 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:383
                                    11        21        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   
           METK_ECOLI     2 AKHLFTSESVSEGHPDKIADQISDAVLDAILEQDPKARVACETYVKTGMVLVGGEITTSAWVDIEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQSPDINQGVDRADPLEQGAGDQGLMFGYATNETDVLMPAPITYAHRLVQRQAEVRKNGTLPWLRPDAKSQVTFQYDDGKIVGIDAVVLSTQHSEEIDQKSLQEAVMEEIIKPILPAEWLTSATKFFINPTGRFVIGGPMGDCGLTGRKIIVDTYGGMARHGGGAFSGKDPSKVDRSAAYAARYVAKNIVAAGLADRCEIQVSYAIGVAEPTSIMVETFGTEKVPSEQLTLLVREFFDLRPYGLIQMLDLLHPIYKETAAYGHFGREHFPWEKTDKAQLLRDAAGLK 384
               SCOP domains d1mxba1 A:1-102 S-adenosylmethionine synthetase                                                       -----d1mxba2 A:108-231 S-adenosylmethionine synthetase                                                                           d1mxba3 A:232-383 S-adenosylmethionine synthetase                                                                                                        SCOP domains
               CATH domains 1mxbA03  1mxbA02 A:10-101,A:233-269  [code=3.30.300.10, no name defined]                             ------1mxbA01 A:108-135,A:270-382 1mxbA03 A:1-9,A:136-232  [code=3.30.300.10, no name defined]                                     1mxbA02 A:10-101,A:233-269           1mxbA01 A:108-135,A:270-382  [code=3.30.300.10, no name defined]                                                 - CATH domains
               Pfam domains S-AdoMet_synt_N-1mxbA03 A:1-100                                                                     -----------S-AdoMet_synt_M-1mxbA02 A:112-230                                                                                      -S-AdoMet_synt_C-1mxbA01 A:232-369                                                                                                         -------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee......hhhhhhhhhhhh....hhh.......eeeeeeeee....-----...hhh......eeeeeeee........hhhhhhhhhhhhhhhhhh..........eeeeeeeeee..eeeee.eeeeee.......hhhhhhhhhhh.......hhh.....eeee.....................hhhhh...................hhhhhhhhhhhhhhhhhh.....eeeeeeee........eeeeee.......hhhhhhhhhhh....hhhhhhh........hhhh..........hhh....hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ADOMET_SYNT------------------------------------------------------------------------------------------------------------------------------------ADOMET_SY--------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mxb A   1 AKHLFTSESVSEGHPDKIADQISDAVLDAILEQDPKARVACETYVKTGMVLVGGEITTSAWVDIEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQSPDI-----RADPLEQGAGDQGLMFGYATNETDVLMPAPITYAHRLVQRQAEVRKNGTLPWLRPDAKSQVTFQYDDGKIVGIDAVVLSTQHSEEIDQKSLQEAVMEEIIKPILPAEWLTSATKFFINPTGRFVIGGPMGDCGLTGRKIIVDTYGGMARHGGGAFSGKDPSKVDRSAAYAARYVAKNIVAAGLADRCEIQVSYAIGVAEPTSIMVETFGTEKVPSEQLTLLVREFFDLRPYGLIQMLDLLHPIYKETAAYGHFGREHFPWEKTDKAQLLRDAAGLK 383
                                    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   
                                                                                                                               102   108                                                                                                                                                                                                                                                                                   

   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (3, 3)

Asymmetric Unit

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (METK_ECOLI | P0A817)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004478    methionine adenosyltransferase activity    Catalysis of the reaction: ATP + L-methionine + H2O = phosphate + diphosphate + S-adenosyl-L-methionine.
    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:0030955    potassium ion binding    Interacting selectively and non-covalently with potassium (K+) ions.
    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: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.
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:0033353    S-adenosylmethionine cycle    A cyclic series of interconversions involving S-adenosylmethionine, S-adenosyl-L-homocysteine, L-cysteine, and L-methionine. Couples utilization of the methyl group of SAM with recycling of the homocysteinyl group and regeneration of methionine.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        METK_ECOLI | P0A8171fug 1mxa 1mxc 1p7l 1rg9 1xra 1xrb 1xrc

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