1DR4 - JenaLib

Title :   CRYSTAL STRUCTURES OF ORGANOMERCURIAL-ACTIVATED CHICKEN LIVER DIHYDROFOLATE REDUCTASE COMPLEXES

Authors :   M. A. Mctigue, J. F. Davies /Ii, B. T. Kaufman, N. -H. Xuong, J. Kraut

Date :   14 Mar 92 (Deposition) - 31 Oct 93 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Mctigue, J. F. Davies Ii, B. T. Kaufman, N. -H. Xuong, J. Kraut
Crystal Structures Of Organomercurial-Activated Chicken Liver Dihydrofolate Reductase Complexes
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	HBI	1	Ligand/Ion	7,8-DIHYDROBIOPTERIN
3	HG	1	Ligand/Ion	MERCURY (II) ION
4	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HBI	1	Ligand/Ion	7,8-DIHYDROBIOPTERIN
3	HG	-1	Ligand/Ion	MERCURY (II) ION
4	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	HBI	2	Ligand/Ion	7,8-DIHYDROBIOPTERIN
3	HG	-1	Ligand/Ion	MERCURY (II) ION
4	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:11 , ASN A:13 , GLY A:15 , GLU A:141 , PHE A:142 , SER A:144 , HOH A:705	BINDING SITE FOR RESIDUE HG A 190
2	AC2	SOFTWARE	GLU A:78 , NAP A:191 , HOH A:278	BINDING SITE FOR RESIDUE CA A 200
3	AC3	SOFTWARE	VAL A:8 , ALA A:9 , ILE A:16 , GLY A:17 , GLY A:20 , ASN A:21 , LEU A:22 , GLY A:53 , LYS A:54 , LYS A:55 , THR A:56 , LEU A:75 , SER A:76 , ARG A:77 , GLU A:78 , LYS A:91 , SER A:92 , VAL A:115 , GLY A:117 , THR A:118 , ALA A:119 , VAL A:120 , TYR A:121 , HBI A:198 , CA A:200 , HOH A:220 , HOH A:318 , HOH A:392 , HOH A:393 , HOH A:493 , HOH A:648	BINDING SITE FOR RESIDUE NAP A 191
4	AC4	SOFTWARE	ILE A:7 , VAL A:8 , ALA A:9 , LEU A:22 , GLU A:30 , PHE A:34 , VAL A:115 , THR A:136 , NAP A:191 , HOH A:230 , HOH A:648	BINDING SITE FOR RESIDUE HBI A 198

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHFR_2	PS51330	Dihydrofolate reductase (DHFR) domain profile.	DYR_CHICK	3-184	1	A:3-184
2	DHFR_1	PS00075	Dihydrofolate reductase (DHFR) domain signature.	DYR_CHICK	15-38	1	A:15-38

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHFR_2	PS51330	Dihydrofolate reductase (DHFR) domain profile.	DYR_CHICK	3-184	1	A:3-184
2	DHFR_1	PS00075	Dihydrofolate reductase (DHFR) domain signature.	DYR_CHICK	15-38	1	A:15-38

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHFR_2	PS51330	Dihydrofolate reductase (DHFR) domain profile.	DYR_CHICK	3-184	2	A:3-184
2	DHFR_1	PS00075	Dihydrofolate reductase (DHFR) domain signature.	DYR_CHICK	15-38	2	A:15-38

Exons (0, 0)

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:186
 aligned with DYR_CHICK | P00378 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
            DYR_CHICK     1 VRSLNSIVAVCQNMGIGKDGNLPWPPLRNEYKYFQRMTSTSHVEGKQNAVIMGKKTWFSIPEKNRPLKDRINIVLSRELKEAPKGAHYLSKSLDDALALLDSPELKSKVDMVWIVGGTAVYKAAMEKPINHRLFVTRILHEFESDTFFPEIDYKDFKLLTEYPGVPADIQEEDGIQYKFEVYQKSV 186
               SCOP domains d1dr4a_ A: Dihydrofolate reductases, eukaryotic type                                                                                                                                       SCOP domains
               CATH domains 1dr4A00 A:1-186 Dihydrofolate Reductase, subunit A                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ...eeeeeee................hhhhhhhhhhhhhh......------hhhhhhh...........eeeeee...........eee.hhhhhhhhhhhhhhhhhh-------hhhhhhhhhhh..eeeeeeeeee.................eee........eeeee..eeeeeeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) ----------------------------------------------eeeeeee------------------------------------------------------eeeeeeeee---------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --DHFR_2  PDB: A:3-184 UniProt: 3-184                                                                                                                                                   -- PROSITE (1)
                PROSITE (2) --------------DHFR_1  PDB: A:15-38    ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dr4 A   1 VRSLNSIVAVCQNMGIGKDGNLPWPPLRNEYKYFQRMTSTSHVEGKQNAVIMGKKTWFSIPEKNRPLKDRINIVLSRELKEAPKGAHYLSKSLDDALALLDSPELKSKVDMVWIVGGTAVYKAAMEKPINHRLFVTRILHEFESDTFFPEIDYKDFKLLTEYPGVPADIQEEDGIQYKFEVYQKSV 186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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 (13, 13)

Asymmetric Unit(hide GO term definitions)

Chain A (DYR_CHICK | P00378)

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:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004146	dihydrofolate reductase activity	Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
	GO:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	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:0031427	response to methotrexate	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a methotrexate stimulus. Methotrexate is 4-amino-10-methylformic acid, a folic acid analogue that is a potent competitive inhibitor of dihydrofolate reductase.
	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.
	GO:0046653	tetrahydrofolate metabolic process	The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.

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