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(-) Description

Title :  THREE DIMENSIONAL STRUCTURE OF BIFUNCTIONAL METHYLENETETRAHYDROFOLATE DEHYDROGENASE-CYCLOHYDROLASE FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  F. Javid-Majd, J. C. Sacchettini, Tb Structural Genomics Consortium (Tbsgc)
Date :  30 Sep 05  (Deposition) - 13 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tetrahydrofolate, Methylenetetrahydrofolate Dehydrogenase, Cyclohydrolase, Hydrolase, Oxidoreductase, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Javid-Majd, J. C. Sacchettini
Three Dimensional Structure Of Bifunctional Methylenetetrahydrofolate Dehydrogenase- Cyclohydrolase From Mycobacterium Tuberculosis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHYLENETETRAHYDROFOLATE DEHYDROGENASE- METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE
    ChainsA
    EC Number1.5.1.5, 3.5.4.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cell LineBL21-DE3-PLYSS
    Expression System PlasmidPET23A-FOLD
    Expression System StrainT7 OVEREXPRESSION SYSTEM
    Expression System Taxid562
    Expression System VectorPET23A
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid83332
    StrainH37RV

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2C2Y)

(-) Sites  (0, 0)

(no "Site" information available for 2C2Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C2Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:98 -Pro A:99
2Asn A:258 -Pro A:259

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C2Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C2Y)

(-) Exons   (0, 0)

(no "Exon" information available for 2C2Y)

(-) 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:280
 aligned with FOLD_MYCTO | P9WG80 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:280
                                    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
           FOLD_MYCTO     2 GAIMLDGKATRDEIFGDLKQRVAALDAAGRTPGLGTILVGDDPGSQAYVRGKHADCAKVGITSIRRDLPADISTATLNETIDELNANPDCTGYIVQLPLPKHLDENAALERVDPAKDADGLHPTNLGRLVLGTPAPLPCTPRGIVHLLRRYDISIAGAHVVVIGRGVTVGRPLGLLLTRRSENATVTLCHTGTRDLPALTRQADIVVAAVGVAHLLTADMVRPGAAVIDVGVSRTDDGLVGDVHPDVWELAGHVSPNPGGVGPLTRAFLLTNVVELAERR 281
               SCOP domains d2c2ya1 A:2-121 automated matches                                                                                       d2c2ya2 A:122-281 automated matches                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhh......eeeee.....hhhhhhh...eeee........hhhhh....eeee..eeee..eeee..hhhhhhh..ee.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c2y A   2 GAIMLDGKATRDEIFGDLKQRVAALDAAGRTPGLGTILVGDDPGSQAYVRGKHADCAKVGITSIRRDLPADISTATLNETIDELNANPDCTGYIVQLPLPKHLDENAALERVDPAKDADGLHPTNLGRLVLGTPAPLPCTPRGIVHLLRRYDISIAGAHVVVIGRGVTVGRPLGLLLTRRSENATVTLCHTGTRDLPALTRQADIVVAAVGVAHLLTADMVRPGAAVIDVGVSRTDDGLVGDVHPDVWELAGHVSPNPGGVGPLTRAFLLTNVVELAERR 281
                                    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

Chain A from PDB  Type:PROTEIN  Length:280
 aligned with FOLD_MYCTU | P9WG81 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:280
                                    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
           FOLD_MYCTU     2 GAIMLDGKATRDEIFGDLKQRVAALDAAGRTPGLGTILVGDDPGSQAYVRGKHADCAKVGITSIRRDLPADISTATLNETIDELNANPDCTGYIVQLPLPKHLDENAALERVDPAKDADGLHPTNLGRLVLGTPAPLPCTPRGIVHLLRRYDISIAGAHVVVIGRGVTVGRPLGLLLTRRSENATVTLCHTGTRDLPALTRQADIVVAAVGVAHLLTADMVRPGAAVIDVGVSRTDDGLVGDVHPDVWELAGHVSPNPGGVGPLTRAFLLTNVVELAERR 281
               SCOP domains d2c2ya1 A:2-121 automated matches                                                                                       d2c2ya2 A:122-281 automated matches                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhh......eeeee.....hhhhhhh...eeee........hhhhh....eeee..eeee..eeee..hhhhhhh..ee.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c2y A   2 GAIMLDGKATRDEIFGDLKQRVAALDAAGRTPGLGTILVGDDPGSQAYVRGKHADCAKVGITSIRRDLPADISTATLNETIDELNANPDCTGYIVQLPLPKHLDENAALERVDPAKDADGLHPTNLGRLVLGTPAPLPCTPRGIVHLLRRYDISIAGAHVVVIGRGVTVGRPLGLLLTRRSENATVTLCHTGTRDLPALTRQADIVVAAVGVAHLLTADMVRPGAAVIDVGVSRTDDGLVGDVHPDVWELAGHVSPNPGGVGPLTRAFLLTNVVELAERR 281
                                    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

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C2Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C2Y)

(-) Gene Ontology  (18, 32)

Asymmetric Unit(hide GO term definitions)
Chain A   (FOLD_MYCTO | P9WG80)
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.

Chain A   (FOLD_MYCTU | P9WG81)
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:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    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.
cellular component
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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.

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 Related Entries

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

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        FOLD_MYCTO | P9WG802c2x
        FOLD_MYCTU | P9WG812c2x

(-) Related Entries Specified in the PDB File

2c2x THREE DIMENSIONAL STRUCTURE OF BIFUNCTIONAL METHYLENETETRAHYDROFOLATE DEHYDROGENASE- CYCLOHYDROLASE FROM MYCOBACTERIUM TUBERCULOSIS RELATED ID: RV3356C RELATED DB: TARGETDB