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(-) Description

Title :  5,10-METHYLENETETRAHYDROFOLATE REDUCTASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  Y. Nakajima, I. Miyahara, K. Hirotsu, Riken Structural Genomics/Pr Initiative (Rsgi)
Date :  20 Jan 04  (Deposition) - 03 Feb 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  5, 10-Methylenetetrahydrofolate Reductase, Methylenetetrahydrofolate Reductase, Flavoprotein, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Nakajima, I. Miyahara, K. Hirotsu
Crystal Structure Of 5, 10-Methylenetetrahydrofolate Reductase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 5,10-METHYLENETETRAHYDROFOLATE REDUCTASE
    Chains: A
    EC Number: 1.7.99.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1DIO6Ligand/Ion1,4-DIETHYLENE DIOXIDE
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:49 , TYR A:50 , HIS A:77 , THR A:79 , LEU A:104 , LEU A:106 , ARG A:107 , GLY A:108 , ASP A:109 , TYR A:126 , ALA A:127 , ALA A:147 , TYR A:149 , HIS A:153 , GLU A:155 , SER A:156 , HIS A:165 , LYS A:169 , ILE A:178 , GLN A:180 , PRO A:243 , TYR A:272 , HOH A:501 , HOH A:521 , HOH A:523 , HOH A:528 , HOH A:545 , HOH A:671BINDING SITE FOR RESIDUE FAD A 300
2AC2SOFTWAREPRO A:13 , LEU A:14 , VAL A:269 , PHE A:271BINDING SITE FOR RESIDUE DIO A 301
3AC3SOFTWAREGLY A:82 , PRO A:111 , ARG A:118 , PRO A:119 , HIS A:120 , PRO A:121 , ARG A:290 , HOH A:674BINDING SITE FOR RESIDUE DIO A 302
4AC4SOFTWAREALA A:62 , TRP A:63 , ARG A:66BINDING SITE FOR RESIDUE DIO A 303
5AC5SOFTWAREARG A:164 , ALA A:198 , ASP A:241BINDING SITE FOR RESIDUE DIO A 304
6AC6SOFTWARELYS A:235 , HIS A:239 , ALA A:245 , GLU A:248BINDING SITE FOR RESIDUE DIO A 305
7AC7SOFTWAREARG A:219 , LEU A:262 , GLU A:263BINDING SITE FOR RESIDUE DIO A 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V93)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V93)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V93)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V93)

(-) Exons   (0, 0)

(no "Exon" information available for 1V93)

(-) 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:292
 aligned with Q9RA47_THETH | Q9RA47 from UniProtKB/TrEMBL  Length:229

    Alignment length:292
                                                                                                                                                                                                                                                              229                                                               
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        |-         -         -         -         -         -         -  
         Q9RA47_THETH     1 MKIRDLLKARRGPLFSFEFFPPKDPEGEEALFRTLEELKAFRPAFVSITYGAMGSTRERSVAWAQRIQSLGLNPLAHLTVAGQSRKEVAEVLHRFVESGVENLLALRGDPPRGERVFRPHPEGFRYAAELVALIRERYGDRVSVGGAAYPEGHPESESLEADLRHFKAKVEAGLDFAITQLFFNNAHYFGFLERARRAGIGIPILPGIMPVTSYRQSAASPRSAGRASP---------------------------------------------------------------   -
               SCOP domains d1v93a_ A: Methylenetetrahydrofolate reductase                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1v93A00 A:1-292  [code=3.20.20.220, no name defined]                                                                                                                                                                                                                                                 CATH domains
               Pfam domains -MTHFR-1v93A01 A:2-216                                                                                                                                                                                                  ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeee....................hhhhhhhhhhhhhhhhheeeeee.........hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v93 A   1 MKIRDLLKARRGPLFSFEFFPPKDPEGEEALFRTLEELKAFRPAFVSITYGAMGSTRERSVAWAQRIQSLGLNPLAHLTVAGQSRKEVAEVLHRFVESGVENLLALRGDPPRGERVFRPHPEGFRYAAELVALIRERYGDRVSVGGAAYPEGHPESESLEADLRHFKAKVEAGLDFAITQLFFNNAHYFGFLERARRAGIGIPILPGIMPVTSYRQLRRFTEVCGASIPGPLLAKLERHQDDPKAVLEIGVEHAVRQVAELLEAGVEGVHFYTLNKSPATRMVLERLGLRPA 292
                                    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
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: FAD_oxidored (7)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9RA47_THETH | Q9RA47)
molecular function
    GO:0004489    methylenetetrahydrofolate reductase (NAD(P)H) activity    Catalysis of the reaction: 5-methyltetrahydrofolate + NAD(P)+ = 5,10-methylenetetrahydrofolate + NAD(P)H + H+.
    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: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.
biological process
    GO:0006555    methionine metabolic process    The chemical reactions and pathways involving methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    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.
    GO:0035999    tetrahydrofolate interconversion    The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.

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