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(-) Description

Title :  STRUCTURAL STUDIES OF PTERIN-BASED INHIBITORS OF DIHYDROPTEROATE SYNTHASE
 
Authors :  M. -K. Yun, S. W. White
Date :  14 Apr 09  (Deposition) - 08 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Anthracis, Folate Biosynthesis, Dihydropteroate, Pterine, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. E. Hevener, M. K. Yun, J. Qi, I. D. Kerr, K. Babaoglu, J. G. Hurdle, K. Balakrishna, S. W. White, R. E. Lee
Structural Studies Of Pterin-Based Inhibitors Of Dihydropteroate Synthase.
J. Med. Chem. V. 53 166 2010
PubMed-ID: 19899766  |  Reference-DOI: 10.1021/JM900861D

(-) Compounds

Molecule 1 - DIHYDROPTEROATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FOLP, BAO_0074
    Organism Scientific: BACILLUS ANTHRACIS STR. A2012
    Organism Taxid: 191218

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1B612Ligand/Ion2-AMINO-6-(2-HYDROXY-2-METHYLPROPYL)-8-METHYL-7,8-DIHYDROPTERIDIN-4(3H)-ONE
2SO410Ligand/IonSULFATE ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1B612Ligand/Ion2-AMINO-6-(2-HYDROXY-2-METHYLPROPYL)-8-METHYL-7,8-DIHYDROPTERIDIN-4(3H)-ONE
2SO48Ligand/IonSULFATE ION
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1B612Ligand/Ion2-AMINO-6-(2-HYDROXY-2-METHYLPROPYL)-8-METHYL-7,8-DIHYDROPTERIDIN-4(3H)-ONE
2SO412Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:101 , ASN A:120 , ILE A:122 , MET A:145 , ASP A:184 , PHE A:189 , GLY A:216 , LYS A:220 , ARG A:254 , SO4 A:279 , HOH A:315 , HOH A:319BINDING SITE FOR RESIDUE B61 A 901
02AC2SOFTWARELYS A:50 , ARG A:53BINDING SITE FOR RESIDUE SO4 A 278
03AC3SOFTWAREILE A:25 , SER A:66 , ARG A:254 , HIS A:256 , B61 A:901BINDING SITE FOR RESIDUE SO4 A 279
04AC4SOFTWARESER A:221 , ARG A:234BINDING SITE FOR RESIDUE SO4 A 280
05AC5SOFTWAREARG A:219 , HOH A:339BINDING SITE FOR RESIDUE SO4 A 281
06AC6SOFTWAREASP B:101 , ASN B:120 , ILE B:122 , MET B:145 , ASP B:184 , PHE B:189 , LEU B:214 , GLY B:216 , LYS B:220 , ARG B:254 , SO4 B:281 , HOH B:320 , HOH B:324BINDING SITE FOR RESIDUE B61 B 902
07AC7SOFTWARELYS B:50 , ARG B:53BINDING SITE FOR RESIDUE SO4 B 278
08AC8SOFTWAREARG B:219BINDING SITE FOR RESIDUE SO4 B 279
09AC9SOFTWAREARG B:201 , ASN B:202BINDING SITE FOR RESIDUE SO4 B 280
10BC1SOFTWAREARG B:254 , HIS B:256 , B61 B:902BINDING SITE FOR RESIDUE SO4 B 281
11BC2SOFTWARELEU B:229 , ARG B:263 , HOH B:293BINDING SITE FOR RESIDUE SO4 B 282
12BC3SOFTWARESER B:221 , ARG B:234BINDING SITE FOR RESIDUE SO4 B 283

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H2M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H2M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H2M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H2M)

(-) Exons   (0, 0)

(no "Exon" information available for 3H2M)

(-) 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:270
 aligned with Q81VW8_BACAN | Q81VW8 from UniProtKB/TrEMBL  Length:280

    Alignment length:274
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273    
         Q81VW8_BACAN     4 LKWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGESTRPGFAKVSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 277
               SCOP domains d3h2ma_ A: Dihydropteroate synthetase                                                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee......eeeee............hhhhhhhhhhhhhhhhhhh..eeeee...----....hhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhh...eeee.......hhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhhhhhhhhhh...ee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h2m A   1 MKWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGES----FAKVSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 274
                                    10        20        30        40        50        60     |   -|       80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    
                                                                                            66   71                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:259
 aligned with Q81VW8_BACAN | Q81VW8 from UniProtKB/TrEMBL  Length:280

    Alignment length:273
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   
         Q81VW8_BACAN     5 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGESTRPGFAKVSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 277
               SCOP domains d3h2mb_ B: Dihydropteroate sy     nthetase                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee......eeeee.....-----..hhhhhhhhhhhhhhhhhhh..eeeee.---------.hhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhh...eeee.......hhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhhhhhhhhhh...ee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h2m B   2 KWDYDLRCGEYTLNLNEKTLIMGILNVTP-----GGSYNEVDAAVRHAKEMRDEGAHIIDIGG---------VSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 274
                                    11        21        |-    |   41        51        61  |      -  |     81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   
                                                       30    36                          64        74
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H2M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H2M)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q81VW8_BACAN | Q81VW8)
molecular function
    GO:0004156    dihydropteroate synthase activity    Catalysis of the reaction: 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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.

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  3h2m
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 Related Entries

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

UniProtKB/TrEMBL
        Q81VW8_BACAN | Q81VW8: 1tws 1tww 1twz 1tx0 1tx2 3h21 3h22 3h23 3h24 3h26 3h2a 3h2c 3h2e 3h2f 3h2n 3h2o 3tya 3tyb 3tyc 3tyd 3tye 4d8a 4d8z 4d9p 4daf 4dai 4db7 4nhv 4nil 4nir 4nl1

(-) Related Entries Specified in the PDB File

1tws 1tww 1twz 1tx0 1tx2 3h21 3h22 3h23 3h24 3h26 3h2a 3h2c 3h2e 3h2f 3h2n 3h2o