2L28 - JenaLib

Title :   SOLUTION STRUCTURE OF LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE APO-FORM, 25 CONFORMERS

Authors :   V. I. Polshakov, B. Birdsall, J. Feeney

Date :   13 Aug 10 (Deposition) - 06 Apr 11 (Release) - 18 May 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (25x)
NMR Structure *: A  (1x)

Keywords :   Oxidoreductase, Dhfr, Antifolates, Co-Operative Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Feeney, B. Birdsall, N. V. Kovalevskaya, Y. D. Smurnyy, E. M. Navarro Peran, V. I. Polshakov
Nmr Structures Of Apo L. Casei Dihydrofolate Reductase And Its Complexes With Trimethoprim And Nadph: Contributions To Positive Cooperative Binding From Ligand-Induced Refolding, Conformational Changes, And Interligand Hydrophobic Interactions.
Biochemistry V. 50 3609 2011
PubMed-ID: 21410224 | Reference-DOI: 10.1021/BI200067T

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 50)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:162
 aligned with DYR_LACCA | P00381 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  
            DYR_LACCA     2 TAFLWAQDRDGLIGKDGHLPWHLPDDLHYFRAQTVGKIMVVGRRTYESFPKRPLPERTNVVLTHQEDYQAQGAVVVHDVAAVFAYAKQHPDQELVIAGGAQIFTAFKDDVDTLLVTRLAGSFEGDTKMIPLNWDDFTKVSSRTVEDTNPALTHTYEVWQKKA 163
               SCOP domains d2l28a_ A: Dihydrofolate reductase, prokaryotic type                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains DHFR_1-2l28A01 A:1-160                                                                                                                                          -- Pfam domains
         Sec.struct. author .eeeeeee...eee........hhhhhhhhhhh....eeeeehhhhhhh........eeeee...........eee.hhhhhhhhhhhh....eeeeehhhhhhhhh....eeeeeee.......ee........eeeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------DHFR_1  PDB: A:12-34   -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2l28 A   1 TAFLWAQDRDGLIGKDGHLPWHLPDDLHYFRAQTVGKIMVVGRRTYESFPKRPLPERTNVVLTHQEDYQAQGAVVVHDVAAVFAYAKQHPDQELVIAGGAQIFTAFKDDVDTLLVTRLAGSFEGDTKMIPLNWDDFTKVSSRTVEDTNPALTHTYEVWQKKA 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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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 (0, 0)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

NMR Structure(hide GO term definitions)

Chain A (DYR_LACCA | P00381)

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:0046677	response to antibiotic	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 an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	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.

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	Cis Peptide Bonds
		Arg A:52 - Pro A:53	[ RasMol ]
		Gly A:98 - Gly A:99	[ RasMol ]

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