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(-) Description

Title :  CRYSTAL STRUCTURE OF B. ANTHRACIS DHPS WITH COMPOUND 17
 
Authors :  D. Hammoudeh, R. E. Lee, S. W. White
Date :  11 Jan 12  (Deposition) - 28 Mar 12  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Biol. Unit 3:  A (2x),B (2x)
Keywords :  Tim Barrel, Transferase, Dhps Inhibitors, Paba, Pterin, Dhpp, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhao, D. Hammoudeh, M. K. Yun, J. Qi, S. W. White, R. E. Lee
Structure-Based Design Of Novel Pyrimido[4, 5-C]Pyridazine Derivatives As Dihydropteroate Synthase Inhibitors With Increased Affinity.
Chemmedchem V. 7 861 2012
PubMed-ID: 22416048  |  Reference-DOI: 10.1002/CMDC.201200049

(-) Compounds

Molecule 1 - DIHYDROPTEROATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FOLP
    Organism Common: ANTHRAX
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 191218
    Strain: A2012

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B
Biological Unit 3 (2x): A (2x)B (2x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
2Z172Ligand/Ion(3R)-3-(7-AMINO-1-METHYL-4,5-DIOXO-1,4,5,6-TETRAHYDROPYRIMIDO[4,5-C]PYRIDAZIN-3-YL)BUTANOIC ACID
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
2Z172Ligand/Ion(3R)-3-(7-AMINO-1-METHYL-4,5-DIOXO-1,4,5,6-TETRAHYDROPYRIMIDO[4,5-C]PYRIDAZIN-3-YL)BUTANOIC ACID
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
2Z172Ligand/Ion(3R)-3-(7-AMINO-1-METHYL-4,5-DIOXO-1,4,5,6-TETRAHYDROPYRIMIDO[4,5-C]PYRIDAZIN-3-YL)BUTANOIC ACID
Biological Unit 3 (2, 12)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
2Z172Ligand/Ion(3R)-3-(7-AMINO-1-METHYL-4,5-DIOXO-1,4,5,6-TETRAHYDROPYRIMIDO[4,5-C]PYRIDAZIN-3-YL)BUTANOIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:50 , ARG A:53BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWAREASN A:27 , ARG A:219BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREARG A:154 , ASN A:155 , ASP B:4 , HOH B:407BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWARESER A:221 , ARG A:234BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREASP A:101 , ASN A:120 , ILE A:122 , ILE A:143 , MET A:145 , ASP A:184 , PHE A:189 , LEU A:214 , GLY A:216 , LYS A:220 , ARG A:254BINDING SITE FOR RESIDUE Z17 A 306
06AC6SOFTWARESER B:221 , ARG B:234BINDING SITE FOR RESIDUE SO4 B 301
07AC7SOFTWARELYS B:50 , ARG B:53BINDING SITE FOR RESIDUE SO4 B 302
08AC8SOFTWAREASN B:27 , ARG B:219BINDING SITE FOR RESIDUE SO4 B 303
09AC9SOFTWAREGLU B:198 , ARG B:201 , ASN B:202BINDING SITE FOR RESIDUE SO4 B 304
10BC1SOFTWAREASN B:15 , ASN B:17BINDING SITE FOR RESIDUE SO4 B 305
11BC2SOFTWAREASP B:101 , ASN B:120 , ILE B:122 , MET B:145 , ASP B:184 , PHE B:189 , GLY B:216 , LYS B:220 , ARG B:254 , HOH B:405BINDING SITE FOR RESIDUE Z17 B 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D9P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4D9P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D9P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D9P)

(-) Exons   (0, 0)

(no "Exon" information available for 4D9P)

(-) 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:264
 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 d4d9pa_ A: Dihydropteroate synthetase                                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee......eeeee............hhhhhhhhhhhhhhhhhhh..eeee..---------.hhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh..eeee.......hhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhh.hhh.eeee.......hhhhhhhhhhhhhhhhhhh...ee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d9p A   2 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGG---------VSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 274
                                    11        21        31        41        51        61  |      -  |     81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   
                                                                                         64        74                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:261
 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 d4d9pb_ B: Dihydropteroate s     ynthetase                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee......eeeee....-----...hhhhhhhhhhhhhhhhhh...eeee....-------.hhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh..eeee.......hhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhhhhhhhhhh...ee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d9p B   2 KWDYDLRCGEYTLNLNEKTLIMGILNVT-----DGGSYNEVDAAVRHAKEMRDEGAHIIDIGGES-------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   
                                                      29    35                             66      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 4D9P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D9P)

(-) 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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  2.5.1.15
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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 3h2m 3h2n 3h2o 3tya 3tyb 3tyc 3tyd 3tye 4d8a 4d8z 4daf 4dai 4db7 4nhv 4nil 4nir 4nl1

(-) Related Entries Specified in the PDB File

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4dai
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