3K74 - JenaLib

Title :   DISRUPTION OF PROTEIN DYNAMICS BY AN ALLOSTERIC EFFECTOR ANTIBODY

Authors :   D. Oyen, V. Srinivasan, J. Steyaert, J. Barlow

Date :   12 Oct 09 (Deposition) - 20 Oct 10 (Release) - 18 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A,B

Keywords :   Immunoglobulin, Protein-Nanobody Complex, Antibiotic Resistance, Methotrexate Resistance, Nadp, One-Carbon Metabolism, Oxidoreductase, Trimethoprim Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Oyen, V. Srinivasan, J. Steyaert, J. N. Barlow
Constraining Enzyme Conformational Change By An Antibody Leads To Hyperbolic Inhibition.
J. Mol. Biol. V. 407 138 2011
PubMed-ID: 21238460 | Reference-DOI: 10.1016/J.JMB.2011.01.017

Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
	Chains	:	A
	EC Number	:	1.5.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	B0048, DHFR, FOLA, JW0047, TMRA
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Strain	:	RT500

Molecule 2 - NANOBODY
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHEN6
	Expression System Strain	:	WK6
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LAMA
	Organism Scientific	:	LAMA GLAMA
	Organism Taxid	:	9844

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

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_ECOLI | P0ABQ4 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
            DYR_ECOLI     1 MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR 159
               SCOP domains d3k74a_ A: Dihydrofolate reductase, prokaryotic type                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains DHFR_1-3k74A01 A:1-158                                                                                                                                        - Pfam domains
         Sec.struct. author .eeeeeeehhh.ee.hhhhh...hhhhhhhhhhhhh..eeeeehhhhhhhh......eeeee..........eee.hhhhhhhhhh....eee..hhhhhhhhhhhh.eeeeeee.......ee....hhh.eeeeeeeee.........eeeeeeee. Sec.struct. author
             SAPs(SNPs) (1) ---------------------------R-G---------------------------------------------------------------------------------------------------------------------------K----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------Q----- SAPs(SNPs) (2)
                PROSITE (1) DHFR_2  PDB: A:1-158 UniProt: 1-158                                                                                                                           - PROSITE (1)
                PROSITE (2) ------------DHFR_1  PDB: A:13-35   ---------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k74 A   1 MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains d3k74b_ B: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...ee.....eeeeeee...hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.......ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3k74 B 162 QLQESGGGLVQPGGSLRLSCAASGFTFNNYWMYWVRRAPGKGLEWVSMINPGGIITKYAESVKGRFTISRDNAKNTLYLQMNSLTSEDTAVYYCAKDWATGLAKKGQGTQVTVSS 276
                                   171       181       191       201       211       221       231       241       251       261       271

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 (2, 2)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DYR_ECOLI | P0ABQ4)

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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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