1DG5 - JenaLib

Title :   DIHYDROFOLATE REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH AND TRIMETHOPRIM

Authors :   R. Li, R. Sirawaraporn, P. Chitnumsub, W. Sirawaraporn, J. Wooden, F. Athappilly, S. Turley, W. G. Hol

Date :   23 Nov 99 (Deposition) - 09 Mar 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Dihydrofolate Reductase, Structure-Based Inhibitor Design, Folateanalogs, Rossmann Fold, Nicotinamide Adenine Dinucleotide, Trimethoprim, Tuberculosis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Li, R. Sirawaraporn, P. Chitnumsub, W. Sirawaraporn, J. Wooden, F. Athappilly, S. Turley, W. G. Hol
Three-Dimensional Structure Of M. Tuberculosis Dihydrofolat Reductase Reveals Opportunities For The Design Of Novel Tuberculosis Drugs.
J. Mol. Biol. V. 295 307 2000
PubMed-ID: 10623528 | Reference-DOI: 10.1006/JMBI.1999.3328
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:6 , ALA A:7 , ILE A:14 , GLY A:15 , GLY A:18 , ASP A:19 , GLY A:43 , ARG A:44 , ARG A:45 , THR A:46 , SER A:49 , LEU A:65 , SER A:66 , ARG A:67 , GLN A:68 , GLY A:80 , ILE A:94 , GLY A:95 , GLY A:96 , GLY A:97 , GLN A:98 , VAL A:99 , TYR A:100 , LEU A:102 , ALA A:126 , TOP A:201 , GOL A:202 , HOH A:228 , HOH A:236 , HOH A:259 , HOH A:264 , HOH A:276	BINDING SITE FOR RESIDUE NDP A 200
2	AC2	SOFTWARE	ILE A:5 , TRP A:6 , ASP A:27 , PHE A:31 , SER A:49 , LEU A:50 , ILE A:94 , TYR A:100 , NDP A:200 , GOL A:203	BINDING SITE FOR RESIDUE TOP A 201
3	AC3	SOFTWARE	ARG A:45 , GLN A:98 , GLY A:124 , ALA A:126 , GLY A:148 , LEU A:149 , NDP A:200 , HOH A:210 , HOH A:215	BINDING SITE FOR RESIDUE GOL A 202
4	AC4	SOFTWARE	PHE A:31 , ARG A:60 , TOP A:201 , HOH A:304	BINDING SITE FOR RESIDUE GOL A 203
5	AC5	SOFTWARE	ALA A:101 , ALA A:128 , PRO A:129 , VAL A:130 , ARG A:150 , HOH A:207 , HOH A:299 , HOH A:305	BINDING SITE FOR RESIDUE GOL A 204

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

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

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:159
 aligned with DYR_MYCTO | P9WNX0 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:159
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152         
            DYR_MYCTO     3 MVGLIWAQATSGVIGRGGDIPWRLPEDQAHFREITMGHTIVMGRRTWDSLPAKVRPLPGRRNVVLSRQADFMASGAEVVGSLEEALTSPETWVIGGGQVYALALPYATRCEVTEVDIGLPREAGDALAPVLDETWRGETGEWRFSRSGLRYRLYSYHRS 161
               SCOP domains d1dg5a_ A: Dihydrofolate reductase, prokaryotic type                                                                                                            SCOP domains
               CATH domains 1dg5A00 A:1-159 Dihydrofolate Reductase, subunit A                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...eee........hhhhhhhhhhhhh..eeeeehhhhhhh..........eeeee...........eee.hhhhhh....eeeeehhhhhhhhhhhh.eeeeeeee.........ee........eeee...ee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) DHFR_2  PDB: A:1-158 UniProt: 3-160                                                                                                                           - PROSITE (2)
                PROSITE (3) ------------DHFR_1  PDB: A:13-35   ---------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dg5 A   1 MVGLIWAQATSGVIGRGGDIPWRLPEDQAHFREITMGHTIVMGRRTWDSLPAKVRPLPGRRNVVLSRQADFMASGAEVVGSLEEALTSPETWVIGGGQVYALALPYATRCEVTEVDIGLPREAGDALAPVLDETWRGETGEWRFSRSGLRYRLYSYHRS 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain A from PDB  Type:PROTEIN  Length:159
 aligned with DYR_MYCTU | P9WNX1 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:159
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152         
            DYR_MYCTU     3 MVGLIWAQATSGVIGRGGDIPWRLPEDQAHFREITMGHTIVMGRRTWDSLPAKVRPLPGRRNVVLSRQADFMASGAEVVGSLEEALTSPETWVIGGGQVYALALPYATRCEVTEVDIGLPREAGDALAPVLDETWRGETGEWRFSRSGLRYRLYSYHRS 161
               SCOP domains d1dg5a_ A: Dihydrofolate reductase, prokaryotic type                                                                                                            SCOP domains
               CATH domains 1dg5A00 A:1-159 Dihydrofolate Reductase, subunit A                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...eee........hhhhhhhhhhhhh..eeeeehhhhhhh..........eeeee...........eee.hhhhhh....eeeeehhhhhhhhhhhh.eeeeeeee.........ee........eeee...ee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) DHFR_2  PDB: A:1-158 UniProt: 3-160                                                                                                                           - PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------DHFR_1  PDB: A:13-35   ---------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dg5 A   1 MVGLIWAQATSGVIGRGGDIPWRLPEDQAHFREITMGHTIVMGRRTWDSLPAKVRPLPGRRNVVLSRQADFMASGAEVVGSLEEALTSPETWVIGGGQVYALALPYATRCEVTEVDIGLPREAGDALAPVLDETWRGETGEWRFSRSGLRYRLYSYHRS 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (9, 17)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DYR_MYCTO | P9WNX0)

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: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.

Chain A (DYR_MYCTU | P9WNX1)

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:0070401	NADP+ binding	Interacting selectively and non-covalently with the oxidized form, NADP+, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0004146	dihydrofolate reductase activity	Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
	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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