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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS (Y102F) DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND (S)-2,4-DIAMINO-5-(3-METHOXY-3-(3, 4,5-TRIMETHOXYPHENYL)PROP-1-YNYL)-6-METHYLPYRIMIDINE (UCP114A)
 
Authors :  A. C. Anderson, J. M. Beierlein, N. G. Karri
Date :  18 Sep 09  (Deposition) - 29 Sep 10  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Beierlein, N. G. Karri, A. C. Anderson
Targeted Mutations In Bacillus Anthracis Dihydrofolate Reductase Condense Complex Structure-Activity Relationships
J. Med. Chem. 2010
PubMed: search

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: A, B
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE2
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BAS2083, BA_2237, DFRA, GBAA2237, GBAA_2237
    Mutation: YES
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 1392

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
15WB2Ligand/Ion5-[(3S)-3-METHOXY-3-(3,4,5-TRIMETHOXYPHENYL)PROP-1-YN-1-YL]-6-METHYLPYRIMIDINE-2,4-DIAMINE
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
15WB2Ligand/Ion5-[(3S)-3-METHOXY-3-(3,4,5-TRIMETHOXYPHENYL)PROP-1-YN-1-YL]-6-METHYLPYRIMIDINE-2,4-DIAMINE
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
15WB2Ligand/Ion5-[(3S)-3-METHOXY-3-(3,4,5-TRIMETHOXYPHENYL)PROP-1-YN-1-YL]-6-METHYLPYRIMIDINE-2,4-DIAMINE
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:7 , ALA A:8 , ILE A:15 , GLY A:16 , ASN A:19 , ASN A:20 , LEU A:21 , GLY A:44 , ARG A:45 , LYS A:46 , ASN A:47 , VAL A:63 , THR A:64 , ARG A:65 , HIS A:78 , PHE A:96 , GLY A:97 , GLY A:98 , ALA A:99 , GLN A:100 , ILE A:101 , LEU A:104 , HOH A:164 , HOH A:167 , HOH A:184 , 5WB A:208 , HOH A:213 , HOH A:220 , HOH A:235 , HOH A:248 , HOH A:254 , HOH A:316 , HOH A:348BINDING SITE FOR RESIDUE NDP A 207
2AC2SOFTWAREMET A:6 , VAL A:7 , ALA A:8 , GLU A:28 , LEU A:29 , VAL A:32 , ASN A:47 , PHE A:96 , HOH A:203 , NDP A:207BINDING SITE FOR RESIDUE 5WB A 208
3AC3SOFTWAREVAL B:7 , ALA B:8 , ILE B:15 , GLY B:16 , ASN B:19 , ASN B:20 , LEU B:21 , GLY B:44 , ARG B:45 , LYS B:46 , ASN B:47 , VAL B:63 , THR B:64 , ARG B:65 , HIS B:78 , PHE B:96 , GLY B:97 , GLY B:98 , ALA B:99 , GLN B:100 , ILE B:101 , LEU B:104 , HOH B:166 , HOH B:180 , HOH B:182 , HOH B:187 , HOH B:206 , 5WB B:208 , HOH B:211 , HOH B:212 , HOH B:229 , HOH B:295BINDING SITE FOR RESIDUE NDP B 207
4AC4SOFTWAREMET B:6 , VAL B:7 , ALA B:8 , LEU B:21 , GLU B:28 , LEU B:29 , VAL B:32 , ASN B:47 , ALA B:50 , PHE B:96 , HOH B:183 , NDP B:207BINDING SITE FOR RESIDUE 5WB B 208

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:97 -Gly A:98
2Gly B:97 -Gly B:98

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3JWK)

(-) 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:165
 aligned with Q81R22_BACAN | Q81R22 from UniProtKB/TrEMBL  Length:162

    Alignment length:165
                               1                                                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157     
         Q81R22_BACAN     - ---MIVSFMVAMDENRVIGKDNNLPWRLPSELQYVKKTTMGHPLIMGRKNYEAIGRPLPGRRNIIVTRNEGYHVEGCEVAHSVEEVFELCKNEEEIFIFGGAQIYDLFLPYVDKLYITKIHHAFEGDTFFPEMDMTNWKEVFVEKGLTDEKNPYTYYYHVYEKQQ 162
               SCOP domains d3jwka_ A: automated matches                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee...eee........hhhhhhhhhhhhh...eeeehhhhhhhh.......eeee...........eee.hhhhhhhhh....eeeeeehhhhhhhhhhhh.eeeeeee.......ee........eeeeeeee..........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jwk A  -2 HHHMRVSFMVAMDENRVIGKDNNLPWRLPSELQYVKKTTMGHPLIMGRKNYEAIGRPLPGRRNIIVTRNEGYHVEGCEVAHSVEEVFELCKNEEEIFIFGGAQIFDLFLPYVDKLYITKIHHAFEGDTFFPEMDMTNWKEVFVEKGLTDEKNPYTYYYHVYEKQQ 162
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157     


Chain B from PDB  Type:PROTEIN  Length:165
 aligned with Q81R22_BACAN | Q81R22 from UniProtKB/TrEMBL  Length:162

    Alignment length:165
                               1                                                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157     
         Q81R22_BACAN     - ---MIVSFMVAMDENRVIGKDNNLPWRLPSELQYVKKTTMGHPLIMGRKNYEAIGRPLPGRRNIIVTRNEGYHVEGCEVAHSVEEVFELCKNEEEIFIFGGAQIYDLFLPYVDKLYITKIHHAFEGDTFFPEMDMTNWKEVFVEKGLTDEKNPYTYYYHVYEKQQ 162
               SCOP domains d3jwkb_ B: automated matches                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----DHFR_1-3jwkB01 B:3-160                                                                                                                                        -- Pfam domains (1)
           Pfam domains (2) -----DHFR_1-3jwkB02 B:3-160                                                                                                                                        -- Pfam domains (2)
         Sec.struct. author ....eeeeeeeee...eee........hhhhhhhhhhhhh...eeeehhhhhhhh.......eeee...........eee.hhhhhhhhh....eeee..hhhhhhhhhhhh.eeeeeee.......ee........eeeeeeee..........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jwk B  -2 HHHMRVSFMVAMDENRVIGKDNNLPWRLPSELQYVKKTTMGHPLIMGRKNYEAIGRPLPGRRNIIVTRNEGYHVEGCEVAHSVEEVFELCKNEEEIFIFGGAQIFDLFLPYVDKLYITKIHHAFEGDTFFPEMDMTNWKEVFVEKGLTDEKNPYTYYYHVYEKQQ 162
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157
   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 3JWK)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: DHFred (95)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q81R22_BACAN | Q81R22)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0004146    dihydrofolate reductase activity    Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
    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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    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:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    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/TrEMBL
        Q81R22_BACAN | Q81R22: 2kgk 2qk8 3dat 3e0b 3fl8 3fl9 3jvx 3jw3 3jw5 3jwc 3jwf 3jwm 3s9u 3sa1 3sa2 3sai 4elb 4ele 4elf 4elg 4elh

(-) Related Entries Specified in the PDB File

3eob CRYSTAL STRUCTURE THE FAB FRAGMENT OF EFALIZUMAB IN COMPLEX WITH LFA-1 I DOMAIN, FORM II
3jvx CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 2,4-DIAMINO-5-(3-(3,4,5- TRIMETHOXYPHENYL)PROP-1-YNYL)-6-ETHYLPYRIMIDINE (UCP120A)
3jw3 CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS (F96I) DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND TRIMETHOPRIM
3jw5 CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS (Y102F) DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND TRIMETHOPRIM
3jwc CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS (Y102F) DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 2,4- DIAMINO-5-(3-(3,4,5-TRIMETHOXYPHENYL)PROP-1-YNYL)-6- ETHYLPYRIMIDINE (UCP120A)
3jwf CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS (Y102F) DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND (R)-2,4- DIAMINO-5-(3-HYDROXY-3-(3,4,5-TRIMETHOXYPHENYL)PROP-1-YNYL) -6-METHYLPYRIMIDINE (UCP113A)
3jwm CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND (S)-2,4-DIAMINO-5-(3- METHOXY-3-(3,4,5-TRIMETHOXYPHENYL)PROP-1-YNYL)-6- METHYLPYRIMIDINE (UCP114A)