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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI HPPK(N55A)
 
Authors :  J. Blaszczyk, Y. Li, H. Yan, X. Ji
Date :  10 Jun 09  (Deposition) - 23 Jun 10  (Release) - 23 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.18
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha Beta, Atp-Binding, Folate Biosynthesis, Kinase, Nucleotide- Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Li, J. Blaszczyk, X. Ji, H. Yan
Pterin-Binding Site Mutation Y53A, N55A Or F123A And Activity Of E. Coli Hppk
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HPPK
    ChainsA
    EC Number2.7.6.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET17B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneB0142, FOIK, FOLK, JW0138
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK 12
    Synonym7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE, 2- AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE PYROPHOSPHOKINASE, 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  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:132 , PRO A:133 , GLU A:134 , GOL A:195 , HOH A:299 , HOH A:370 , HOH A:422BINDING SITE FOR RESIDUE ACT A 191
2AC2SOFTWAREGLU A:30 , SER A:31 , HIS A:32 , HOH A:224 , HOH A:332BINDING SITE FOR RESIDUE ACT A 192
3AC3SOFTWARELEU A:11 , PRO A:14 , HOH A:320BINDING SITE FOR RESIDUE ACT A 193
4AC4SOFTWARETYR A:53 , PHE A:123 , HOH A:284BINDING SITE FOR RESIDUE GOL A 194
5AC5SOFTWARETYR A:4 , LEU A:34 , ILE A:131 , ACT A:191 , HOH A:433BINDING SITE FOR RESIDUE GOL A 195

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:113 -Pro A:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HPPKPS00794 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature.HPPK_ECOLI89-100  1A:88-99

(-) Exons   (0, 0)

(no "Exon" information available for 3HSJ)

(-) 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:158
 aligned with HPPK_ECOLI | P26281 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           HPPK_ECOLI     2 TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW 159
               SCOP domains d3hsja_ A: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhh...eeeeee...eee..........eeeeeeeeee..hhhhhhhhhhhhhhhhh..hhhhh.....eeeeeeee....ee....ee...hhhhhhhhhhhhhhhh.........hhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------HPPK        ----------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hsj A   1 TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPDYLAAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HSJ)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HPPK_ECOLI | P26281)
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:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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: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: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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HPPK_ECOLI | P262811dy3 1eq0 1eqm 1ex8 1f9h 1g4c 1hka 1hq2 1im6 1kbr 1q0n 1rao 1rb0 1rtz 1ru1 1ru2 1tmj 1tmm 2f63 2f65 3hcx 3hd1 3hd2 3hsd 3hsg 3hsz 3ht0 3ili 3ilj 3ill 3ilo 3ip0 3kue 3kug 3kuh 3ud5 3ude 3udv 4f7v 4m5g 4m5h 4m5i 4m5j 4m5k 4m5l 4m5m 4m5n 5etk 5etl 5etm 5etn 5eto 5etp

(-) Related Entries Specified in the PDB File

1hka 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE
3hsd CRYSTAL STRUCTURE OF E. COLI HPPK(Y53A)
3hsg CRYSTAL STRUCTURE OF E. COLI HPPK(Y53A) IN COMPLEX WITH MGAMPCPP
3hsz CRYSTAL STRUCTURE OF E. COLI HPPK(F123A)
3ht0 CRYSTAL STRUCTURE OF E. COLI HPPK(F123A) IN COMPLEX WITH MGAMPCPP