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Title :   MYCOBACTERIUM AVIUM DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND A LIPOPHILIC ANTIFOLATE SELECTIVE FOR M. AVIUM DHFR, 6-((2,5-DIETHOXYPHENYL)AMINOMETHYL)-2,4-DIAMINO-5-METHYLPYRIDO(2,3-D)PYRIMIDINE (SRI-8686)

Authors :   A. K. W. Leung, R. C. Reynolds, D. W. Borhani

Date :   16 Nov 08 (Deposition) - 17 Nov 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Nonclassical Antifolates, One-Carbon Metabolism, Lipophilic Antifolates, Nadp, Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. W. Leung, L. J. Ross, S. Zywno-Van Ginkel, R. C. Reynolds, L. E. Seitz, V. Pathak, W. W. Barrow, E. L. White, W. J. Suling, J. R. Piper, D. W. Borhani
Structural Basis For Selective Inhibition Of Mycobacterium Avium Dihydrofolate Reductase By A Lipophilic Antifolate
To Be Published
PubMed: search

Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
	Chains	:	A
	EC Number	:	1.5.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A-MACDHFR-DEL
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET11A
	Fragment	:	RESIDUES, 1-167
	Organism Scientific	:	MYCOBACTERIUM AVIUM
	Organism Taxid	:	1764
	Other Details	:	STRAIN OBTAINED FROM THE AIDS RESEARCH AND REFERENCE REAGENT PROGRAM, DIVISION OF AIDS, NIAID, NIH, CATALOG NUMBER 1786.

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:9 , TRP A:10 , ALA A:11 , ILE A:24 , ASP A:31 , LEU A:32 , PHE A:35 , ILE A:102 , TYR A:108 , NDP A:1169 , HOH A:2087	BINDING SITE FOR RESIDUE VG9 A1168
2	AC2	SOFTWARE	TRP A:10 , ALA A:11 , ILE A:18 , GLY A:19 , GLY A:22 , ASP A:23 , ILE A:24 , GLY A:47 , ARG A:48 , ARG A:49 , THR A:50 , VAL A:69 , SER A:70 , ARG A:71 , ARG A:72 , GLY A:84 , ILE A:102 , GLY A:104 , ALA A:105 , GLN A:106 , ILE A:107 , TYR A:108 , LEU A:110 , VG9 A:1168 , HOH A:2048 , HOH A:2121 , HOH A:2122 , HOH A:2123 , HOH A:2124 , HOH A:2125 , HOH A:2126	BINDING SITE FOR RESIDUE NDP A1169

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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

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Chain A from PDB  Type:PROTEIN  Length:165
 aligned with O30463_MYCAV | O30463 from UniProtKB/TrEMBL  Length:181

    Alignment length:165
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162     
         O30463_MYCAV     3 RAEVGLVWAQSTSGVIGRGGDIPWSVPEDLTRFKEVTMGHTVIMGRRTWESLPAKVRPLPGRRNVVVSRRPDFVAEGARVAGSLEAALAYAGSDPAPWVIGGAQIYLLALPHATRCEVTEIEIDLRRDDDDALAPALDDSWVGETGEWLASRSGLRYRFHSYRRD 167
               SCOP domains d2w3wa_ A: automated matches                                                                                                                                          SCOP domains
               CATH domains 2w3wA00 A:3-167 Dihydrofolate Reductase, subunit A                                                                                                                    CATH domains
               Pfam domains --DHFR_1-2w3wA01 A:5-166                                                                                                                                            - Pfam domains
         Sec.struct. author ....eeeeeee...eee........hhhhhhhhhhhhh..eeeeehhhhhhhhhhhh.....eeeee...........eee.hhhhhhhhh......eeeehhhhhhhhhhhh.eeeeeeee.........ee........eeee...ee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w3w A   3 RAEVGLVWAQSTSGVIGRGGDIPWSVPEDLTRFKEVTMGHTVIMGRRTWESLPAKVRPLPGRRNVVVSRRPDFVAEGARVAGSLEAALAYAGSDPAPWVIGGAQIYLLALPHATRCEVTEIEIDLRRDDDDALAPALDDSWVGETGEWLASRSGLRYRFHSYRRD 167
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Legend:		→ Mismatch	(orange background)
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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (O30463_MYCAV | O30463)

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: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: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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