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(-) Description

Title :  A. THALIANA COBALAMINE INDEPENDENT METHIONINE SYNTHASE
 
Authors :  J. -L. Ferrer, S. Ravanel, M. Robert, R. Dumas
Date :  15 Jul 04  (Deposition) - 14 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Methionine, Synthase, Homocysteine, Methyltetrahydrofolate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. -L. Ferrer, S. Ravanel, M. Robert, R. Dumas
Crystal Structures Of Cobalamin-Independent Methionine Synthase Complexed With Zinc, Homocysteine, And Methyltetrahydrofolate
J. Biol. Chem. V. 279 44235 2004
PubMed-ID: 15326182  |  Reference-DOI: 10.1074/JBC.C400325200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE-- HOMOCYSTEINE METHYLTRANSFERASE
    ChainsA
    EC Number2.1.1.14
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-MS1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCIMS
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymVITAMIN-B12-INDEPENDENT METHIONINE SYNTHASE ISOZYME, COBALAMIN-INDEPENDENT METHIONINE SYNTHASE ISOZYME

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 26)

Asymmetric/Biological Unit (5, 26)
No.NameCountTypeFull Name
1C2F1Ligand/Ion5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
2MET1Ligand/IonMETHIONINE
3MSE18Mod. Amino AcidSELENOMETHIONINE
4SO44Ligand/IonSULFATE ION
5ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:647 , CYS A:649 , CYS A:733 , HOH A:774BINDING SITE FOR RESIDUE ZN A 766
2AC2SOFTWARETYR A:132 , HIS A:135 , GLU A:194 , HIS A:658 , ASP A:662BINDING SITE FOR RESIDUE ZN A 767
3AC3SOFTWAREPRO A:79 , PRO A:80 , ARG A:81 , GLU A:123 , LYS A:169 , HOH A:798BINDING SITE FOR RESIDUE SO4 A 768
4AC4SOFTWAREARG A:610 , TYR A:650 , SER A:651 , HIS A:652BINDING SITE FOR RESIDUE SO4 A 769
5AC5SOFTWARELYS A:55 , ASP A:150 , THR A:201 , TRP A:202BINDING SITE FOR RESIDUE SO4 A 770
6AC6SOFTWAREPRO A:575 , ARG A:576 , HIS A:577BINDING SITE FOR RESIDUE SO4 A 771
7AC7SOFTWAREILE A:437 , GLY A:438 , SER A:439 , GLU A:490 , MSE A:496 , MSE A:557 , ASP A:605 , CYS A:733 , GLY A:734BINDING SITE FOR RESIDUE MET A 772
8AC8SOFTWAREARG A:15 , LYS A:18 , ASN A:116 , SER A:517 , ARG A:521 , CYS A:522 , TRP A:567 , HOH A:898BINDING SITE FOR RESIDUE C2F A 773

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U1J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U1J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U1J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U1J)

(-) Exons   (0, 0)

(no "Exon" information available for 1U1J)

(-) 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:746
 aligned with METE1_ARATH | O50008 from UniProtKB/Swiss-Prot  Length:765

    Alignment length:759
                                    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       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751         
          METE1_ARATH     2 ASHIVGYPRMGPKRELKFALESFWDGKSTAEDLQKVSADLRSSIWKQMSAAGTKFIPSNTFAHYDQVLDTTAMLGAVPPRYGYTGGEIGLDVYFSMARGNASVPAMEMTKWFDTNYHYIVPELGPEVNFSYASHKAVNEYKEAKALGVDTVPVLVGPVSYLLLSKAAKGVDKSFELLSLLPKILPIYKEVITELKAAGATWIQLDEPVLVMDLEGQKLQAFTGAYAELESTLSGLNVLVETYFADIPAEAYKTLTSLKGVTAFGFDLVRGTKTLDLVKAGFPEGKYLFAGVVDGRNIWANDFAASLSTLQALEGIVGKDKLVVSTSCSLLHTAVDLINETKLDDEIKSWLAFAAQKVVEVNALAKALAGQKDEALFSANAAALASRRSSPRVTNEGVQKAAAALKGSDHRRATNVSARLDAQQKKLNLPILPTTTIGSFPQTVELRRVRREYKAKKVSEEDYVKAIKEEIKKVVDLQEELDIDVLVHGEPERNDMVEYFGEQLSGFAFTANGWVQSYGSRCVKPPVIYGDVSRPKAMTVFWSAMAQSMTSRPMKGMLTGPVTILNWSFVRNDQPRHETCYQIALAIKDEVEDLEKGGIGVIQIDEAALREGLPLRKSEHAFYLDWAVHSFRITNCGVQDSTQIHTHMCYSHFNDIIHSIIDMDADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSSEEIADRVNKMLAVLEQNILWVNPDCGLKTRKYTEVKPALKNMVDAAKLIRSQ 760
               SCOP domains d1u1ja1 A:2-395 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase MetE                                                                                                                                                                                                                                                                                                                d1u1ja2 A:396-760 5-methyltetrahydropteroyltriglutam             ate--homocysteine methyltransferase MetE                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1u1jA01 A:2-389,A:511-525  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                                                                      1u1jA02 A:390-510,A:526-760  [code=3.20.20.210, no name de             fined]                                            1u1jA01        1u1jA02 A:390-510,A:526-760  [code=3.20.20.210, no name defined]                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....ee......hhhhhhhhhh...hhhhh......hhhhhhhhhhh........eee......eee..ee..........hhhhhhhhhhhhh....eeeeehhhhhhhh.ee........hhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh..hhhhhhhhhhhhhhh.......eeeee......hhhhhhhhh......eeeee.....hhhhhhhhh.....eeeeeee........hhhhhhhhhhhhhhhh....eeeee..hhhhh..hhhhh...hhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhh.............hhhhhhhhhhhhh....................-------------.hhhhhhhhhhhhhhhhhhh................hhhhhh....ee......eeee..eee...ee...........hhhhhhhh.......eeeeehhhhhhhh.ee....hhhhhhhhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhhhhh......eeeee........hhhhhhh....eee........hhhhhhh.......ee.............hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u1j A   2 ASHIVGYPRmGPKRELKFALESFWDGKSTAEDLQKVSADLRSSIWKQmSAAGTKFIPSNTFAHYDQVLDTTAmLGAVPPRYGYTGGEIGLDVYFSmARGNASVPAmEmTKWFDTNYHYIVPELGPEVNFSYASHKAVNEYKEAKALGVDTVPVLVGPVSYLLLSKAAKGVDKSFELLSLLPKILPIYKEVITELKAAGATWIQLDEPVLVmDLEGQKLQAFTGAYAELESTLSGLNVLVETYFADIPAEAYKTLTSLKGVTAFGFDLVRGTKTLDLVKAGFPEGKYLFAGVVDGRNIWANDFAASLSTLQALEGIVGKDKLVVSTSCSLLHTAVDLINETKLDDEIKSWmAFAAQKVVEVNALAKALAGQKDEALFSANAAALASRRSSPRVTNEGVQKAAAALKGSDHRRATNVSARLDAQQKKLNLPILPTTTIGSFPQTVELR-------------EDYVKAIKEEIKKVVDLQEELDIDVLVHGEPERNDmVEYFGEQLSGFAFTANGWVQSYGSRCVKPPVIYGDVSRPKAmTVFWSAmAQSmTSRPmKGmLTGPVTILNWSFVRNDQPRHETCYQIALAIKDEVEDLEKGGIGVIQIDEAALREGLPLRKSEHAFYLDWAVHSFRITNCGVQDSTQIHTHmCYSHFNDIIHSIIDmDADVITIENSRSDEKLLSVFREGVKYGAGIGPGVYDIHSPRIPSSEEIADRVNKmLAVLEQNILWVNPDCGLKTRKYTEVKPALKNmVDAAKLIRSQ 760
                                    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       391       401       411       421       431       441     |   -       461       471       481       491    |  501       511       521       531      |541   |   551  |  | 561       571       581       591       601       611       621       631       641      |651       661 |     671       681       691       701       711      |721       731       741       751         
                                    11-MSE                                49-MSE                   74-MSE                 97-MSE   107-MSE                                                                                                  212-MSE                                                                                                                                    351-MSE                                                                                         447           461                                496-MSE                                   538-MSE  |   |    |  |                                                                                        648-MSE        663-MSE                                                718-MSE                         750-MSE      
                                                                                                                                     109-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                             545-MSE    |  |                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             549-MSE|  |                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  554-MSE                                                                                                                                                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     557-MSE                                                                                                                                                                                                       

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1U1J)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (METE1_ARATH | O50008)
molecular function
    GO:0003871    5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity    Catalysis of the reaction: 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate.
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008705    methionine synthase activity    Catalysis of the reaction: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0050667    homocysteine metabolic process    The chemical reactions and pathways involving homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid. Homocysteine is an important intermediate in the metabolic reactions of its S-methyl derivative, methionine.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0046686    response to cadmium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus.
    GO:0009651    response to salt stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
    GO:0010043    response to zinc ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a zinc ion stimulus.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0048046    apoplast    The cell membranes and intracellular regions in a plant are connected through plasmodesmata, and plants may be described as having two major compartments: the living symplast and the non-living apoplast. The apoplast is external to the plasma membrane and includes cell walls, intercellular spaces and the lumen of dead structures such as xylem vessels. Water and solutes pass freely through it.
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0009506    plasmodesma    A fine cytoplasmic channel, found in all higher plants, that connects the cytoplasm of one cell to that of an adjacent cell.
    GO:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        METE1_ARATH | O500081u1h 1u1u 1u22

(-) Related Entries Specified in the PDB File

1u1h 1u1u 1u22