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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDRONEOPTERIN ALDOLASE FROM S. AUREUS IN COMPLEX WITH (1S,2R)-NEOPTERIN AT 1.50 ANGSTROM RESOLUTION
 
Authors :  J. Blaszczyk, X. Ji, H. Yan
Date :  20 Oct 06  (Deposition) - 04 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Dihydroneopterin Aldolase, Dhna, Substrate Complex, Monapterin, Neopterin, 7, 8-Dihydroneopterin, Drug Design, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Blaszczyk, Y. Li, J. Gan, H. Yan, X. Ji
Structural Basis For The Aldolase And Epimerase Activities Of Staphylococcus Aureus Dihydroneopterin Aldolase.
J. Mol. Biol. V. 368 161 2007
PubMed-ID: 17331536  |  Reference-DOI: 10.1016/J.JMB.2007.02.009

(-) Compounds

Molecule 1 - DIHYDRONEOPTERIN ALDOLASE
    Chains: A, B, C, D
    EC Number: 4.1.2.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Strain: PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FOLB
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: DHNA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NEU4Ligand/IonL-NEOPTERIN
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1NEU8Ligand/IonL-NEOPTERIN

(-) Sites  (0, 0)

(no "Site" information available for 2NM2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NM2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NM2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NM2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NM2)

(-) Exons   (0, 0)

(no "Exon" information available for 2NM2)

(-) 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:121
 aligned with FOLB_STAAU | P56740 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
           FOLB_STAAU     1 MQDTIFLKGMRFYGYHGALSAENEIGQIFKVDVTLKVDLSEAGRTDNVIDTVHYGEVFEEVKSIMEGKAVNLLEHLAERIANRINSQYNRVMETKVRITKENPPIPGHYDGVGIEIVRENK 121
               SCOP domains d2nm2a_ A: 7,8-dihydroneopterin aldolase                                                                                  SCOP domains
               CATH domains 2nm2A00 A:1-121  [code=3.30.1130.10, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee......hhhhhheeeeeeeeee..hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....eeeeeeee..........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nm2 A   1 MQDTIFLKGMRFYGYHGALSAENEIGQIFKVDVTLKVDLSEAGRTDNVIDTVHYGEVFEEVKSIMEGKAVNLLEHLAERIANRINSQYNRVMETKVRITKENPPIPGHYDGVGIEIVRENK 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with FOLB_STAAU | P56740 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
           FOLB_STAAU     1 MQDTIFLKGMRFYGYHGALSAENEIGQIFKVDVTLKVDLSEAGRTDNVIDTVHYGEVFEEVKSIMEGKAVNLLEHLAERIANRINSQYNRVMETKVRITKENPPIPGHYDGVGIEIVRENK 121
               SCOP domains d2nm2b_ B: 7,8-dihydroneopterin aldolase                                                                                  SCOP domains
               CATH domains 2nm2B00 B:1-121  [code=3.30.1130.10, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee......hhhhhheeeeeeeeee.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.......eeeeeeee...........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nm2 B   1 MQDTIFLKGMRFYGYHGALSAENEIGQIFKVDVTLKVDLSEAGRTDNVIDTVHYGEVFEEVKSIMEGKAVNLLEHLAERIANRINSQYNRVMETKVRITKENPPIPGHYDGVGIEIVRENK 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain C from PDB  Type:PROTEIN  Length:121
 aligned with FOLB_STAAU | P56740 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
           FOLB_STAAU     1 MQDTIFLKGMRFYGYHGALSAENEIGQIFKVDVTLKVDLSEAGRTDNVIDTVHYGEVFEEVKSIMEGKAVNLLEHLAERIANRINSQYNRVMETKVRITKENPPIPGHYDGVGIEIVRENK 121
               SCOP domains d2nm2c_ C: 7,8-dihydroneopterin aldolase                                                                                  SCOP domains
               CATH domains 2nm2C00 C:1-121  [code=3.30.1130.10, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee....hhhhhhhheeeeeeeeee..hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nm2 C   1 MQDTIFLKGMRFYGYHGALSAENEIGQIFKVDVTLKVDLSEAGRTDNVIDTVHYGEVFEEVKSIMEGKAVNLLEHLAERIANRINSQYNRVMETKVRITKENPPIPGHYDGVGIEIVRENK 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain D from PDB  Type:PROTEIN  Length:121
 aligned with FOLB_STAAU | P56740 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
           FOLB_STAAU     1 MQDTIFLKGMRFYGYHGALSAENEIGQIFKVDVTLKVDLSEAGRTDNVIDTVHYGEVFEEVKSIMEGKAVNLLEHLAERIANRINSQYNRVMETKVRITKENPPIPGHYDGVGIEIVRENK 121
               SCOP domains d2nm2d_ D: 7,8-dihydroneopterin aldolase                                                                                  SCOP domains
               CATH domains 2nm2D00 D:1-121  [code=3.30.1130.10, no name defined]                                                                     CATH domains
           Pfam domains (1) ----FolB-2nm2D01 D:5-118                                                                                              --- Pfam domains (1)
           Pfam domains (2) ----FolB-2nm2D02 D:5-118                                                                                              --- Pfam domains (2)
           Pfam domains (3) ----FolB-2nm2D03 D:5-118                                                                                              --- Pfam domains (3)
           Pfam domains (4) ----FolB-2nm2D04 D:5-118                                                                                              --- Pfam domains (4)
         Sec.struct. author ....eeeeeeeeee......hhhhhheeeeeeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....eeeeeeeeee...........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nm2 D   1 MQDTIFLKGMRFYGYHGALSAENEIGQIFKVDVTLKVDLSEAGRTDNVIDTVHYGEVFEEVKSIMEGKAVNLLEHLAERIANRINSQYNRVMETKVRITKENPPIPGHYDGVGIEIVRENK 121
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: THBO-biosyn (64)
(-)
Family: FolB (15)
(-)
Staphylococcus aureus (10)
1aFolB-2nm2D01D:5-118
1bFolB-2nm2D02D:5-118
1cFolB-2nm2D03D:5-118
1dFolB-2nm2D04D:5-118

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (FOLB_STAAU | P56740)
molecular function
    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:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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.
biological process
    GO:0046656    folic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of folic acid, pteroylglutamic acid.
    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: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
        FOLB_STAAU | P56740: 1dhn 1rri 1rrw 1rry 1rs2 1rs4 1rsd 1rsi 1u68 2dhn 2nm3

(-) Related Entries Specified in the PDB File

1dhn CRYSTAL STRUCTURE OF APO-DHNA FROM S.AUREUS
1nbu CRYSTAL STRUCTURE OF COMPLEX OF DHNA FROM M.TUBERCULOSIS WITH 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN
1rri CRYSTAL STRUCTURE OF COMPLEX OF DHNA FROM S.AUREUS WITH 3- (5-AMINO-7-HYDROXY-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-2-YL)- BENZOIC ACID
1rrw CRYSTAL STRUCTURE OF COMPLEX OF DHNA FROM S.AUREUS WITH 9- METHYLGUANINE
1rry CRYSTAL STRUCTURE OF COMPLEX OF DHNA FROM S.AUREUS WITH 2- AMINO-4-HYDROXYPYRIMIDINE-5-CARBOXYLIC ACID ETHYL ESTER
1rs2 CRYSTAL STRUCTURE OF COMPLEX OF DHNA FROM S.AUREUS WITH 8- AMINO-1,3-DIMETHYL-3,7-DIHYDROPURINE-2,6-DIONE
1rs4 CRYSTAL STRUCTURE OF COMPLEX OF DHNA FROM S.AUREUS WITH 3- (5-AMINO-7-HYDROXY-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-2-YL)-N- (3,5-DICHLOROBENZYL)-BENZAMIDE
1rsd CRYSTAL STRUCTURE OF COMPLEX OF DHNA FROM S.AUREUS WITH 3- (5-AMINO-7-HYDROXY-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-2-YL)-N- [2-(2-(HYDROXYMETHYL-PHENYLSULFANYL)-BENZYL]-BENZAMIDE
1rsi CRYSTAL STRUCTURE OF COMPLEX OF DHNA FROM S.AUREUS WITH 2- AMINO-5-BROMO-6-PHENYLPYRIMIDIN-4-OL
1u68 CRYSTAL STRUCTURE OF COMPLEX OF DHNA FROM S.AUREUS WITH 2- AMINO-7,8-DIHYDRO-6-(1,2,3-TRIHYDROXYPROPYL)-4(1H)- PTERIDINONE
2dhn CRYSTAL STRUCTURE OF COMPLEX OF DHNA FROM S.AUREUS WITH 6- HYDROXYMETHYL-7,8-DIHYDROPTERIN