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(-) Description

Title :  STRUCTURE OF COENZYME F420 DEPENDENT TETRAHYDROMETHANOPTERIN REDUCTASE FROM METHANOPYRUS KANDLERI
 
Authors :  S. Shima, E. Warkentin, W. Grabarse, R. K. Thauer, U. Ermler
Date :  12 May 00  (Deposition) - 06 Sep 00  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  (Beta, Alpha)8 Barrel, Tim Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Shima, E. Warkentin, W. Grabarse, M. Sordel, M. Wicke, R. K. Thauer, U. Ermler
Structure Of Coenzyme F(420) Dependent Methylenetetrahydromethanopterin Reductase From Two Methanogenic Archaea.
J. Mol. Biol. V. 300 935 2000
PubMed-ID: 10891279  |  Reference-DOI: 10.1006/JMBI.2000.3909

(-) Compounds

Molecule 1 - COENZYME F420-DEPENDENT N5,N10- METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
    ChainsA
    Organism ScientificMETHANOPYRUS KANDLERI
    Organism Taxid2320

 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, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:53 , THR A:56 , SER A:57 , HOH A:562BINDING SITE FOR RESIDUE MG A 361
2AC2SOFTWAREARG A:71 , ASN A:79BINDING SITE FOR RESIDUE CL A 362

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:64 -Ile A:65
2Phe A:110 -Pro A:111
3Gly A:145 -Pro A:146
4Ser A:326 -Pro A:327

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1EZW)

(-) 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:347
 aligned with MER_METKA | Q8TXY4 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:347
                                    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       
            MER_METKA     2 AEVSFGIELLPDDKPTKIAHLIKVAEDNGFEYAWICDHYNNYSYMGVLTLAAVITSKIKLGPGITNPYTRHPLITASNIATLDWISGGRAIIGMGPGDKATFDKMGLPFPCKIPIWNPEAEDEVGPATAIREVKEVIYQYLEGGPVEYEGKYVKTGTADVNARSIQGSDIPFYMGAQGPIMLKTAGEIADGVLVNASNPKDFEVAVPKIEEGAKEAGRSLDEIDVAAYTCFSIDKDEDKAIEATKIVVAFIVMGSPDVVLERHGIDTEKAEQIAEAIGKGDFGTAIGLVDEDMIEAFSIAGDPDTVVDKIEELLKAGVTQVVVGSPIGPDKEKAIELVGQEVIPHFK 348
               SCOP domains d1ezwa_ A: Coenzyme F420 dependent tetrahydromethanopterin reductase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ezwA00 A:2-348 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhh.....eee...hhhhhhhhh..................hhhhhhhhhhhhhhhhhh.......................hhhhh.eeee..hhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhh..hhhhheeeee..eee..hhhhhhhhhhhhhhhhhhh.hhhhhhhh.......hhhhhhh...hhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ezw A   2 AEVSFGIELLPDDKPTKIAHLIKVAEDNGFEYAWICDHYNNYSYMGVLTLAAVITSKIKLGPGITNPYTRHPLITASNIATLDWISGGRAIIGMGPGDKATFDKMGLPFPCKIPIWNPEAEDEVGPATAIREVKEVIYQYLEGGPVEYEGKYVKTGTADVKARSIQGSDIPFYMGAQGPIMLKTAGEIANGVLVNASNPKDFEVAVPKIEEGAKEAGRSLDEIDVAAYTCFSIDKDEDKAIEATKIVVAFIVMGSPDVVLERHGIDTEKAEQIAEAIGKGDFGTAIGLVDEDMIEAFSIAGDPDTVVDKIEELLKAGVTQVVVGSPIGPDKEKAIELVGQEVIPHFK 348
                                    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       

   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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (MER_METKA | Q8TXY4)
molecular function
    GO:0018537    coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity    Catalysis of the reaction: 5-methyltetrahydromethanopterin + coenzyme F420 + H(+) = 5,10-methylenetetrahydromethanopterin + reduced coenzyme F420.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
biological process
    GO:0015948    methanogenesis    The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes.
    GO:0019386    methanogenesis, from carbon dioxide    The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4, from other compounds, including carbon dioxide (CO2).
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1f07