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(-) Description

Title :  THE BIFUNCTIONAL DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE FROM STREPTOCOCCUS PNEUMONIAE
 
Authors :  A. Garcon, C. Levy, J. P. Derrick
Date :  28 Feb 06  (Deposition) - 21 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Lyase/Transferase, Aldolase, Folate Biosynthesis, Pyrophosphokinase, Lyase, Multifunctional Enzyme, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Garcon, C. Levy, J. P. Derrick
Crystal Structure Of The Bifunctional Dihydroneopterin Aldolase/6-Hydroxymethyl-7, 8- Dihydropterin Pyrophosphokinase From Streptococcus Pneumoniae.
J. Mol. Biol. V. 360 644 2006
PubMed-ID: 16781731  |  Reference-DOI: 10.1016/J.JMB.2006.05.038

(-) Compounds

Molecule 1 - DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8- DIHYDROPTERIN SYNTHASE
    Chains: A, B, C, D
    EC Number: 4.1.2.25, 2.7.6.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Synonym: DIHYDRONEOPTERIN ALDOLASE, DHNA, 2-AMINO-4- HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE PYROPHOSPHOKINASE, 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN PYROPHOSPHOKINASE, 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE, HPPK, PPPK

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2CG8)

(-) Sites  (0, 0)

(no "Site" information available for 2CG8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CG8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:230 -Pro A:231
2Leu B:230 -Pro B:231
3Leu C:230 -Pro C:231
4Leu D:230 -Pro D:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CG8)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HPPKPS00794 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature.SULD_STRR6205-216
 
 
 		  4A:211-216
B:209-216
C:210-216
D:207-216
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HPPKPS00794 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature.SULD_STRR6205-216
 
 
 		  8A:211-216
B:209-216
C:210-216
D:207-216

(-) Exons   (0, 0)

(no "Exon" information available for 2CG8)

(-) 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:241
 aligned with SULD_STRR6 | P59657 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:268
                                    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        
           SULD_STRR6     1 MDQLQIKDLEMFAYHGLFPSEKELGQKFIVSAILSYDMTKAATDLDLTASVHYGELCQQWTTWFQETSEDLIETVAYKLVERTFESYPLVQEMKLELKKPWAPVHLSLDTCSVTIHRRKQRAFIALGSNMGDKQANLKQAIDKLRARGIHILKESSVLATEPWGGVEQDSFANQVVEVETWLPAQDLLETLLAIESELGRVREVHWGPRLIDLDLLFVEDQILYTDDLILPHPYIAERLFVLESLQEIAPHFIHPILKQPIRNLYDAL 268
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee....hhhhhhhheeeeeeeeeee.hhhhhh-------.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....eeeeeeee...........eeeeeeee.eeeeeeeee...hhhhhhhhhhhhhhhh..eeeee.....----------..eeeeeeeee..hhhhhhhhhhhhhhhh..----------.eeeeeee...............hhhhhhhhhhhhhhhh..........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HPPK        ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cg8 A   1 MDQLQIKDLEMFAYHGLFPSEKELGQKFIVSAILSYDMTKAAT-------VHYGELCQQWTTWFQETSEDLIETVAYKLVERTFESYPLVQEMKLELKKPWAPVHLSLDTCSVTIHRRKQRAFIALGSNMGDKQANLKQAIDKLRARGIHILKESSVLA----------SFANQVVEVETWLPAQDLLETLLAIESELGR----------IDLDLLFVEDQILYTDDLILPHPYIAERLFVLESLQEIAPHFIHPILKQPIRNLYDAL 268
                                    10        20        30        40  |      -|       60        70        80        90       100       110       120       130       140       150        |-       170       180       190       200         -|      220       230       240       250       260        
                                                                     43      51                                                                                                         159        170                           200        211                                                         


Chain B from PDB  Type:PROTEIN  Length:248
 aligned with SULD_STRR6 | P59657 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:268
                                    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        
           SULD_STRR6     1 MDQLQIKDLEMFAYHGLFPSEKELGQKFIVSAILSYDMTKAATDLDLTASVHYGELCQQWTTWFQETSEDLIETVAYKLVERTFESYPLVQEMKLELKKPWAPVHLSLDTCSVTIHRRKQRAFIALGSNMGDKQANLKQAIDKLRARGIHILKESSVLATEPWGGVEQDSFANQVVEVETWLPAQDLLETLLAIESELGRVREVHWGPRLIDLDLLFVEDQILYTDDLILPHPYIAERLFVLESLQEIAPHFIHPILKQPIRNLYDAL 268
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee....hhhhhhhheeeeeeeeeee.hhhhhhh----...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....eeeeeee...........eeeeeeeee.eeeeeeeee...hhhhhhhhhhhhhhhh..eeeee...ee.--------...eeeeeeeee..hhhhhhhhhhhhhhhh..--------...eeeeeee...............hhhhhhhhhhhhhhhh..........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HPPK        ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cg8 B   1 MDQLQIKDLEMFAYHGLFPSEKELGQKFIVSAILSYDMTKAATD----ASVHYGELCQQWTTWFQETSEDLIETVAYKLVERTFESYPLVQEMKLELKKPWAPVHLSLDTCSVTIHRRKQRAFIALGSNMGDKQANLKQAIDKLRARGIHILKESSVLAT--------DSFANQVVEVETWLPAQDLLETLLAIESELGR--------RLIDLDLLFVEDQILYTDDLILPHPYIAERLFVLESLQEIAPHFIHPILKQPIRNLYDAL 268
                                    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        
                                                                      44   49                                                                                                            160      169                            200      209                                                           


Chain C from PDB  Type:PROTEIN  Length:249
 aligned with SULD_STRR6 | P59657 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:268
                                    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        
           SULD_STRR6     1 MDQLQIKDLEMFAYHGLFPSEKELGQKFIVSAILSYDMTKAATDLDLTASVHYGELCQQWTTWFQETSEDLIETVAYKLVERTFESYPLVQEMKLELKKPWAPVHLSLDTCSVTIHRRKQRAFIALGSNMGDKQANLKQAIDKLRARGIHILKESSVLATEPWGGVEQDSFANQVVEVETWLPAQDLLETLLAIESELGRVREVHWGPRLIDLDLLFVEDQILYTDDLILPHPYIAERLFVLESLQEIAPHFIHPILKQPIRNLYDAL 268
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee....hhhhhhhheeeeeeeeeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....eeeeeee.............eeeeeee.eeeeeeeee...hhhhhhhhhhhhhhhh..eeeee.....----------..eeeeeeeee..hhhhhhhhhhhhhhh...---------..eeeeeee...............hhhhhhhhhhhhhhhh..........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HPPK        ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cg8 C   1 MDQLQIKDLEMFAYHGLFPSEKELGQKFIVSAILSYDMTKAATDLDLTASVHYGELCQQWTTWFQETSEDLIETVAYKLVERTFESYPLVQEMKLELKKPWAPVHLSLDTCSVTIHRRKQRAFIALGSNMGDKQANLKQAIDKLRARGIHILKESSVLA----------SFANQVVEVETWLPAQDLLETLLAIESELGR---------LIDLDLLFVEDQILYTDDLILPHPYIAERLFVLESLQEIAPHFIHPILKQPIRNLYDAL 268
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        |-       170       180       190       200       210       220       230       240       250       260        
                                                                                                                                                                                        159        170                           200       210                                                          


Chain D from PDB  Type:PROTEIN  Length:248
 aligned with SULD_STRR6 | P59657 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:268
                                    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        
           SULD_STRR6     1 MDQLQIKDLEMFAYHGLFPSEKELGQKFIVSAILSYDMTKAATDLDLTASVHYGELCQQWTTWFQETSEDLIETVAYKLVERTFESYPLVQEMKLELKKPWAPVHLSLDTCSVTIHRRKQRAFIALGSNMGDKQANLKQAIDKLRARGIHILKESSVLATEPWGGVEQDSFANQVVEVETWLPAQDLLETLLAIESELGRVREVHWGPRLIDLDLLFVEDQILYTDDLILPHPYIAERLFVLESLQEIAPHFIHPILKQPIRNLYDAL 268
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee....hhhhhhhheeeeeeeeeee.hhhhhhh----...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....eeeeeee...........eeeeeeeee.eeeeeeeee...hhhhhhhhhhhhhhhh..eeeee....-----------..eeeeeeeee..hhhhhhhhhhhhhhhh...-----.....eeeeeee...............hhhhhhhhhhhhhhhh..........hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HPPK        ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cg8 D   1 MDQLQIKDLEMFAYHGLFPSEKELGQKFIVSAILSYDMTKAATD----ASVHYGELCQQWTTWFQETSEDLIETVAYKLVERTFESYPLVQEMKLELKKPWAPVHLSLDTCSVTIHRRKQRAFIALGSNMGDKQANLKQAIDKLRARGIHILKESSVL-----------SFANQVVEVETWLPAQDLLETLLAIESELGRV-----GPRLIDLDLLFVEDQILYTDDLILPHPYIAERLFVLESLQEIAPHFIHPILKQPIRNLYDAL 268
                                    10        20        30        40   |    50        60        70        80        90       100       110       120       130       140       150       | -       170       180       190       200|     |210       220       230       240       250       260        
                                                                      44   49                                                                                                          158         170                            201   207
   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  (0, 0)

(no "SCOP Domain" information available for 2CG8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CG8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CG8)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (SULD_STRR6 | P59657)
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: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: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: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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