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(-) Description

Title :  CRYSTAL STRUCTURE OF BIFUNCTIONAL 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE FROM THERMOPLASMA ACIDOPHILUM
 
Authors :  K. W. Hwang, M. W. Sung, W. H. Lee
Date :  14 Jun 10  (Deposition) - 20 Apr 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase, Catalyzes The Oxidation Of 5, 10-Methylenetetrahydrofolate To 5, 10- Methenyltetrahydrofolate, The Hydrolysis Of 5, 10- Methenyltetrahydrofolate To 10-Formyltetrahydrofolate, Oxidoreductase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. H. Lee, M. W. Sung, J. H. Kim, Y. K. Kim, A. Han, K. Y. Hwang
Crystal Structure Of Bifunctional 5, 10-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase From Thermoplasma Acidophilum
Biochem. Biophys. Res. Commun. V. 406 459 2011
PubMed-ID: 21333632  |  Reference-DOI: 10.1016/J.BBRC.2011.02.074

(-) Compounds

Molecule 1 - BIFUNCTIONAL PROTEIN FOLD
    ChainsA, B
    EC Number1.5.1.5, 3.5.4.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificTHERMOPLASMA ACIDOPHILUM
    Organism Taxid2303
    SynonymMETHYLENETETRAHYDROFOLATE DEHYDROGENASE, METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3NGX)

(-) Sites  (0, 0)

(no "Site" information available for 3NGX)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NGX)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:92 -Pro A:93
2Val A:249 -Pro A:250
3Asn B:92 -Pro B:93
4Val B:249 -Pro B:250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NGX)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THF_DHG_CYH_2PS00767 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2.FOLD_THEAC250-258
 
  2A:250-258
B:250-258

(-) Exons   (0, 0)

(no "Exon" information available for 3NGX)

(-) 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:275
 aligned with FOLD_THEAC | Q05213 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:275
                                    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     
           FOLD_THEAC     2 KILRGEEIAEKKAENLHGIIERSGLEPSLKLIQIGDNEAASIYARAKIRRGKKIGIAVDLEKYDDISMKDLLKRIDDLAKDPQINGIMIENPLPKGFDYYEIVRNIPYYKDVDALSPYNQGLIALNREFLVPATPRAVIDIMDYYGYHENTVTIVNRSPVVGRPLSMMLLNRNYTVSVCHSKTKDIGSMTRSSKIVVVAVGRPGFLNREMVTPGSVVIDVGINYVNDKVVGDANFEDLSEYVEAITPVPGGVGPITATNILENVVKAAEFQKNNL 276
               SCOP domains d3ngxa1 A:2-115 automated matches                                                                                 d3ngxa2 A:116-276 automated matches                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..eeeee.....hhhhhhhhh.eeee........hhhhh....eeee...eee..eee...hhhhhhh...ee......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THF_DHG_C------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngx A   2 KILRGEEIAEKKAENLHGIIERSGLEPSLKLIQIGDNEAASIYARAKIRRGKKIGIAVDLEKYDDISMKDLLKRIDDLAKDPQINGIMIENPLPKGFDYYEIVRNIPYYKDVDALSPYNQGLIALNREFLVPATPRAVIDIMDYYGYHENTVTIVNRSPVVGRPLSMMLLNRNYTVSVCHSKTKDIGSMTRSSKIVVVAVGRPGFLNREMVTPGSVVIDVGINYVNDKVVGDANFEDLSEYVEAITPVPGGVGPITATNILENVVKAAEFQKNNL 276
                                    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     

Chain B from PDB  Type:PROTEIN  Length:275
 aligned with FOLD_THEAC | Q05213 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:275
                                    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     
           FOLD_THEAC     2 KILRGEEIAEKKAENLHGIIERSGLEPSLKLIQIGDNEAASIYARAKIRRGKKIGIAVDLEKYDDISMKDLLKRIDDLAKDPQINGIMIENPLPKGFDYYEIVRNIPYYKDVDALSPYNQGLIALNREFLVPATPRAVIDIMDYYGYHENTVTIVNRSPVVGRPLSMMLLNRNYTVSVCHSKTKDIGSMTRSSKIVVVAVGRPGFLNREMVTPGSVVIDVGINYVNDKVVGDANFEDLSEYVEAITPVPGGVGPITATNILENVVKAAEFQKNNL 276
               SCOP domains d3ngxb1 B:2-115 automated matches                                                                                 d3ngxb2 B:116-276 automated matches                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) THF_DHG_CYH-3ngxB03 B:2-114                                                                                      --THF_DHG_CYH_C-3ngxB01 B:117-273                                                                                                                              --- Pfam domains (1)
           Pfam domains (2) THF_DHG_CYH-3ngxB04 B:2-114                                                                                      --THF_DHG_CYH_C-3ngxB02 B:117-273                                                                                                                              --- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhh...eeeee.....hhhhhhh...eeee........hhhhh....eeee...ee....ee...hhhhhh....ee......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THF_DHG_C------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ngx B   2 KILRGEEIAEKKAENLHGIIERSGLEPSLKLIQIGDNEAASIYARAKIRRGKKIGIAVDLEKYDDISMKDLLKRIDDLAKDPQINGIMIENPLPKGFDYYEIVRNIPYYKDVDALSPYNQGLIALNREFLVPATPRAVIDIMDYYGYHENTVTIVNRSPVVGRPLSMMLLNRNYTVSVCHSKTKDIGSMTRSSKIVVVAVGRPGFLNREMVTPGSVVIDVGINYVNDKVVGDANFEDLSEYVEAITPVPGGVGPITATNILENVVKAAEFQKNNL 276
                                    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     

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NGX)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FOLD_THEAC | Q05213)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004477    methenyltetrahydrofolate cyclohydrolase activity    Catalysis of the reaction: 5,10-methenyltetrahydrofolate + H2O = 10-formyltetrahydrofolate.
    GO:0004488    methylenetetrahydrofolate dehydrogenase (NADP+) activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH.
    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: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:0009396    folic acid-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.
    GO:0000105    histidine biosynthetic process    The chemical reactions and pathways resulting in the formation of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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: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.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    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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    Asn A:92 - Pro A:93   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        FOLD_THEAC | Q052133ngl

(-) Related Entries Specified in the PDB File

3ngl THE STRUCTURE OF 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE WITH NADP.