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(-) Description

Title :  X-RAY STRUCTURE OF THE BIFUNCTIONAL 6-HYDROXYMETHYL-7,8-DIHYDROXYPTERIN PYROPHOSPHOKINASE DIHYDROPTEROATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE
 
Authors :  M. C. Lawrence, P. Iliades, R. T. Fernley, J. Berglez, P. A. Pilling, I. G. Macreadie
Date :  11 Mar 05  (Deposition) - 17 Jan 06  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Folate Biosynthesis, Transferase, Ligase, Multifunctional Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. C. Lawrence, P. Iliades, R. T. Fernley, J. Berglez, P. A. Pilling, I. G. Macreadie
The Three-Dimensional Structure Of The Bifunctional 6-Hydroxymethyl-7, 8-Dihydropterin Pyrophosphokinase/Dihydropteroate Synthase Of Saccharomyces Cerevisiae
J. Mol. Biol. V. 348 655 2005
PubMed-ID: 15826662  |  Reference-DOI: 10.1016/J.JMB.2005.03.021

(-) Compounds

Molecule 1 - FOLIC ACID SYNTHESIS PROTEIN FOL1
    ChainsA
    EC Number2.7.6.3, 6.3.2.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET-28A
    FragmentBIFUNCTIONAL COMPONENT (HPPK-DHPS) OF TRIFUNCTIONAL ENZYME FOL1, RESIDUES 337-864
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymDIHYDRONEOPTERIN ALDOLASE, DHNA, FASA, FASB, DIHYDROPTEROATE SYNTHASE, DHPS, DIHYDROPTEROATE-PYROPHOSPHORYLASE, FASC, 2-AMINO-4- HYDROXY-6 HYDROXYMETHYLDIHYDROPTERIDINE PYROPHOSPHOKINASE, 7,8- DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE, HPPK, 6- HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE, PPPK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PMM2Ligand/IonPTERIN-6-YL-METHYL-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:597 , ARG A:598 , ASP A:636 , ASN A:655 , ILE A:657 , ASP A:755 , PHE A:760 , LEU A:801 , GLY A:803 , LYS A:807 , ARG A:842 , HIS A:844 , HOH A:2097 , HOH A:2115BINDING SITE FOR RESIDUE PMM A1865
2AC2SOFTWARESER A:379 , GLU A:380 , PRO A:381 , MET A:382 , TYR A:383 , PHE A:390 , ASN A:392 , ASP A:434 , ARG A:463 , PHE A:465 , ASN A:698 , HOH A:2009BINDING SITE FOR RESIDUE PMM A1866

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:455 -Pro A:456

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HPPKPS00794 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature.FOL1_YEAST385-396  1A:430-436
2PTERIN_BINDINGPS50972 Pterin-binding domain profile.FOL1_YEAST504-814  1A:544-854
3DHPS_1PS00792 Dihydropteroate synthase signature 1.FOL1_YEAST506-521  1A:546-561
4DHPS_2PS00793 Dihydropteroate synthase signature 2.FOL1_YEAST546-559  1A:586-599

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNL256W1YNL256W.1XIV:164624-1670982475FOL1_YEAST1-8248241A:336-864 (gaps)529

(-) 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:513
 aligned with FOL1_YEAST | P53848 from UniProtKB/Swiss-Prot  Length:824

    Alignment length:529
                                   305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815         
           FOL1_YEAST   296 TWKRAFLAFGSNIGDRFKHIQMALQLLSREKTVKLRNISSIFESEPMYFKDQTPFMNGCVEVETLLTPSELLKLCKKIEYEELQRVKHFDNGPRTIDLDIVMFLNSAGEDIIVNEPDLNIPHPRMLERTFVLEPLCELISPVHLHPVTAEPIVDHLKQLYDKQHDEDTLWKLVPLPYRSGVEPRFLKFKTATKLDEFTGETNRITVSPTYIMAIFNATPDSFSDGGEHFADIESQLNDIIKLCKDALYLHESVIIDVGGCSTRPNSIQASEEEEIRRSIPLIKAIRESTELPQDKVILSIDTYRSNVAKEAIKVGVDIINDISGGLFDSNMFAVIAENPEICYILSHTRGDISTMNRLAHYENFALGDSIQQEFVHNTDIQQLDDLKDKTVLIRNVGQEIGERYIKAIDNGVKRWQILIDPGLGFAKTWKQNLQIIRHIPILKNYSFTMNSNNSQVYVNLRNMPVLLGPSRKKFIGHITKDVDAKQRDFATGAVVASCIGFGSDMVRVHDVKNCSKSIKLADAIYKGLE 824
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2bmbA02 A:543-864 Dihydropteroate (DHP) synthetase                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhhhhhhhhhhhh..eeeeee..eeee..........eeeeeeeeee..hhhhhhhhhhhhhhhhh..---------..eeeeeeee........ee....ee...hhhhhhhhhhhhh..............hhhhhhhhhhhh.hhhh.eeeeeee........eeeeeeeee.-------..eee....eeeeeee..............hhhhhhhhhhhhhhhhhh....eeeeee...........hhhhhhhhhhhhhhhhhhh...hhh.eeeeee..hhhhhhhhhhh...eeee........hhhhhhhh....eeeee.......hhhhh...........eeeeee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhhhhhhh.eeeeeee..eeeeee......ee....hhhhhhhhh..hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------HPPK        -----------------------------------------------------------------------------------------------------------PTERIN_BINDING  PDB: A:544-854 UniProt: 504-814                                                                                                                                                                                                                                                                        ---------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DHPS_1          ------------------------DHPS_2        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:336-864 (gaps) UniProt: 1-824 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Transcript 1
                 2bmb A 336 SWKRAFLAFGSNIGDRFKHIQMALQLLSREKTVKLRNISSIFESEPMYFKDQTPFMNGCVEVETLLTPSELLKLCKKIEYEELQR---------TIDLDIVMFLNSAGEDIIVNEPDLNIPHPRMLERTFVLEPLCELISPVHLHPVTAEPIVDHLKQLYDKQHDEDTLWKLVPLPYRSGVEPRFLKFKTATK-------TNRITVSPTYIMAIFNATPDSFSDGGEHFADIESQLNDIIKLCKDALYLHESVIIDVGGCSTRPNSIQASEEEEIRRSIPLIKAIRESTELPQDKVILSIDTYRSNVAKEAIKVGVDIINDISGGLFDSNMFAVIAENPEICYILSHTRGDISTMNRLAHYENFALGDSIQQEFVHNTDIQQLDDLKDKTVLIRNVGQEIGERYIKAIDNGVKRWQILIDPGLGFAKTWKQNLQIIRHIPILKNYSFTMNSNNSQVYVNLRNMPVLLGPSRKKFIGHITKDVDAKQRDFATGAVVASCIGFGSDMVRVHDVKNCSKSIKLADAIYKGLE 864
                                   345       355       365       375       385       395       405       415    |    -    |  435       445       455       465       475       485       495       505       515       525  |      -|      545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855         
                                                                                                              420       430                                                                                               528     536                                                                                                                                                                                                                                                                                                                                        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 2BMB)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FOL1_YEAST | P53848)
molecular function
    GO:0003848    2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity    Catalysis of the reaction: 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine + ATP = (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate + AMP + 2 H(+).
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0004150    dihydroneopterin aldolase activity    Catalysis of the reaction: 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine = 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine + glycolaldehyde.
    GO:0004156    dihydropteroate synthase activity    Catalysis of the reaction: 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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.
biological process
    GO:0044237    cellular metabolic process    The chemical reactions and pathways by which individual cells transform chemical substances.
    GO:0046656    folic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of folic acid, pteroylglutamic acid.
    GO:0009396    folic acid-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.
    GO:0006760    folic acid-containing compound metabolic process    The chemical reactions and pathways involving a folic acid-containing compound, i.e. any of a group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid or L-glutamate units.
    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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0042558    pteridine-containing compound metabolic process    The chemical reactions and pathways involving any compound containing pteridine (pyrazino(2,3-dipyrimidine)), e.g. pteroic acid, xanthopterin and folic acid.
    GO:0046654    tetrahydrofolate biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005740    mitochondrial envelope    The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.
    GO:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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