2BLA - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   SP21 DOUBLE MUTANT P. VIVAX DIHYDROFOLATE REDUCTASE IN COMPLEX WITH PYRIMETHAMINE

Authors :   P. Kongsaeree, P. Khongsuk, U. Leartsakulpanich, P. Chitnumsub, B. Tarnchompoo, M. D. Walkinshaw, Y. Yuthavong

Date :   02 Mar 05 (Deposition) - 07 Sep 05 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Dihydrofolate Reductase, Plasmodium Vivax, Pyrimethamine, Malaria, Drug Resistance, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Kongsaeree, P. Khongsuk, U. Leartsakulpanich, P. Chitnumsub, B. Tarnchompoo, M. D. Walkinshaw, Y. Yuthavong
Crystal Structure Of Dihydrofolate Reductase From Plasmodiu Vivax: Pyrimethamine Displacement Linked With Mutation-Induced Resistance.
Proc. Natl. Acad. Sci. Usa V. 102 13046 2005
PubMed-ID: 16135570 | Reference-DOI: 10.1073/PNAS.0501747102

Molecule 1 - DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE
	Chains	:	A
	EC Number	:	1.5.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	PLASMODIUM VIVAX
	Organism Taxid	:	5855
	Synonym	:	DIHYDROFOLATE REDUCTASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CP6	1	Ligand/Ion	5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:14 , ALA A:15 , LEU A:39 , GLY A:43 , THR A:44 , LEU A:45 , TRP A:47 , ARG A:58 , GLY A:114 , ARG A:115 , SER A:116 , ASN A:117 , TYR A:125 , LEU A:136 , SER A:137 , LYS A:138 , THR A:139 , ASP A:153 , ILE A:173 , GLY A:174 , GLY A:175 , GLN A:177 , VAL A:178 , GLU A:181 , CP6 A:302 , HOH A:403 , HOH A:418 , HOH A:424 , HOH A:470	binding site for residue NDP A 301
2	AC2	SOFTWARE	ILE A:13 , CYS A:14 , ALA A:15 , ASP A:53 , PHE A:57 , ASN A:117 , ILE A:173 , TYR A:179 , THR A:194 , NDP A:301	binding site for residue CP6 A 302
3	AC3	SOFTWARE	PHE A:57 , ARG A:58 , LEU A:128 , ARG A:131	binding site for residue MES A 303

(no "SS Bond" information available for 2BLA)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:126	-	Pro A:127
2	Gly A:174	-	Gly A:175

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DRTS_PLAVI_001 *	S	58	R	DRTS_PLAVI	---	---	A	R	58	R
2	UniProt	VAR_DRTS_PLAVI_002 *	S	117	N	DRTS_PLAVI	---	---	A	N	117	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHFR_2	PS51330	Dihydrofolate reductase (DHFR) domain profile.	DRTS_PLAVI	9-237	1	A:9-237
2	DHFR_1	PS00075	Dihydrofolate reductase (DHFR) domain signature.	DRTS_PLAVI	38-61	1	A:38-61

(no "Exon" information available for 2BLA)

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:218
 aligned with DRTS_PLAVI | O02604 from UniProtKB/Swiss-Prot  Length:623

    Alignment length:237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           DRTS_PLAVI     2 EDLSDVFDIYAICACCKVAPTSEGTKNEPFSPRTFRGLGNKGTLPWKCNSVDMKYFSSVTTYVDESKYEKLKWKRERYLRMEASQGGGDNTSGGDNTHGGDNADKLQNVVVMGRSSWESIPKQYKPLPNRINVVLSKTLTKEDVKEKVFIIDSIDDLLLLLKKLKYYKCFIIGGAQVYRECLSRNLIKQIYFTRINGAYPCDVFFPEFDESQFRVTSVSEVYNSKGTTLDFLVYSKV 238
               SCOP domains d2blaa_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2blaA00 A:2-238 Dihydrofolate Reductase, subunit A                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eeeeeeeeee..................eee.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.-------------------.......eeeeehhhhhhhhhhhh.....eeeee.............eee.hhhhhhhhhhh.....eeeeehhhhhhhhhhh....eeeeeeeeeee...ee....hhh.eeeeee...eee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------R----------------------------------------------------------N------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------DHFR_2  PDB: A:9-237 UniProt: 9-237                                                                                                                                                                                                  - PROSITE (1)
                PROSITE (2) ------------------------------------DHFR_1  PDB: A:38-61    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bla A   2 ENLSDVFDIYAICACCKVAPTSEGTKNEPFSPRTFRGLGNKGTLPWKCNSVDMKYFRSVTTYVDESKYEKLKWKRERYLRME-------------------NADKLQNVVVMGRSNWESIPKQYKPLPNRINVVLSKTLTKEDVKEKVFIIDSIDDLLLLLKKLKYYKCFIIGGAQVYRECLSRNLIKQIYFTRINGAYPCDVFFPEFDESEFRVTSVSEVYNSKGTTLDFLVYSKV 238
                                    11        21        31        41        51        61        71        81 |       -         - |     111       121       131       141       151       161       171       181       191       201       211       221       231       
                                                                                                            83                 103

Chain A from PDB  Type:PROTEIN  Length:218
 aligned with Q5U9H1_PLAVI | Q5U9H1 from UniProtKB/TrEMBL  Length:237

    Alignment length:237
                                                                                                                                                                                                                                                                     237 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     | 
         Q5U9H1_PLAVI     2 EDLSDVFDIYAICACCKVAPTSEGTKNEPFSPRTFRGLGNKGTLPWKCNSVDMKYFRSVTTYVDESKYEKLKWKRERYLRMEASQGGGDNTSGGDNTSGGDNADKLQNVVVMGRSNWESIPKQYKPLPNRINVVLSKTLTKEDVKEKVFIIDSIDDLLLLLKKLKYYKCFIIGGAQVYRECLSRNLIKQIYFTRINGAYPCDVFFPEFDESQFRVTSVSEVYNSKGTTLDFLVYSK-   -
               SCOP domains d2blaa_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2blaA00 A:2-238 Dihydrofolate Reductase, subunit A                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eeeeeeeeee..................eee.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.-------------------.......eeeeehhhhhhhhhhhh.....eeeee.............eee.hhhhhhhhhhh.....eeeeehhhhhhhhhhh....eeeeeeeeeee...ee....hhh.eeeeee...eee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------R----------------------------------------------------------N------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bla A   2 ENLSDVFDIYAICACCKVAPTSEGTKNEPFSPRTFRGLGNKGTLPWKCNSVDMKYFRSVTTYVDESKYEKLKWKRERYLRME-------------------NADKLQNVVVMGRSNWESIPKQYKPLPNRINVVLSKTLTKEDVKEKVFIIDSIDDLLLLLKKLKYYKCFIIGGAQVYRECLSRNLIKQIYFTRINGAYPCDVFFPEFDESEFRVTSVSEVYNSKGTTLDFLVYSKV 238
                                    11        21        31        41        51        61        71        81 |       -         - |     111       121       131       141       151       161       171       181       191       201       211       221       231       
                                                                                                            83                 103

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

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

Fold: Dihydrofolate reductase-like (332)

Superfamily: Dihydrofolate reductase-like (332)

Family: Dihydrofolate reductases (249)

Protein domain: automated matches (15)

Plasmodium vivax [TaxId: 5855] (4)

d2blaa_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Dihydrofolate Reductase, subunit A (200)

Homologous Superfamily: Dihydrofolate Reductase, subunit A (200)

Plasmodium vivax. Organism_taxid: 5855. (4)

2blaA00

A:2-238

(no "Pfam Domain" information available for 2BLA)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q5U9H1_PLAVI | Q5U9H1)

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: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.

Chain A (DRTS_PLAVI | O02604)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004146	dihydrofolate reductase activity	Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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.
	GO:0004799	thymidylate synthase activity	Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dUMP = 7,8-dihydrofolate + thymidylate.
	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:0006231	dTMP biosynthetic process	The chemical reactions and pathways resulting in the formation of dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate).
	GO:0006545	glycine biosynthetic process	The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:174 - Gly A:175	[ RasMol ]
		Lys A:126 - Pro A:127	[ RasMol ]

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	2bla
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	Q5U9H1_PLAVI \| Q5U9H1
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	1.5.1.3
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UniProtKB/Swiss-Prot
	DRTS_PLAVI \| O02604	:	2bl9 2blb 2blc
	Q5U9H1_PLAVI \| Q5U9H1	:	2blc

1j3i	WILD-TYPE PLASMODIUM FALCIPARUM DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE (PFDHFR-TS) COMPLEXED WITH WR99210,NADPH, AND DUMP
1j3j	DOUBLE MUTANT (C59R+S108N) PLASMODIUM FALCIPARUMDIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE (PFDHFR-TS)COMPLEXED WITH PYRIMETHAMINE, NADPH, AND DUMP
1j3k	QUADRUPLE MUTANT (N51I+C59R+S108N+I164L) PLASMODIUMFALCIPARUM DIHYDROFOLATE REDUCTASE- THYMIDYLATE SYNTHASE(PFDHFR-TS) COMPLEXED WITH WR99210, NADPH, AND DUMP
2bl9	PLASMODIUM VIVAX DIHYDROFOLATE REDUCTASE IN COMPLEX WITH PYRIMETHAMINE AND ITS DERIVATIVE
2blb	PLASMODIUM VIVAX DIHYDROFOLATE REDUCTASE IN COMPLEX WITH PYRIMETHAMINE AND ITS DERIVATIVE
2blc	SP21 DOUBLE MUTANT P. VIVAX DIHYDROFOLATE REDUCTASE IN COMPLEX WITH DES- CHLOROPYRIMETHAMINESP21

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (15, 20)

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