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Description

Title :   DHFR R67 COMPLEXED WITH NADP AND DIHYDROFOLATE

Authors :   J. M. Krahn, R. E. London

Date :   16 Oct 07 (Deposition) - 03 Jun 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.26

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Oxidoreductase, Nadp, Dihydrofolate, Asymmetric Ligand Binding, Antibiotic Resistance, Methotrexate Resistance, One-Carbon Metabolism, Plasmid, Trimethoprim Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Krahn, M. R. Jackson, E. F. Derose, E. E. Howell, R. E. London
Crystal Structure Of A Type Ii Dihydrofolate Reductase Catalytic Ternary Complex.
Biochemistry V. 46 14878 2007
PubMed-ID: 18052202 | Reference-DOI: 10.1021/BI701532R
(for further references see the PDB file header)

Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE TYPE 2
	Chains	:	A
	EC Number	:	1.5.1.3
	Organism Scientific	:	ESCHERICHIA COLI
	Strain	:	TMP-RESISTANT, CONTAINING R67 DHFR OVERPRODUCING PLASMID PLZ1
	Synonym	:	DIHYDROFOLATE REDUCTASE TYPE II

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 5)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	DHF	1	Ligand/Ion	DIHYDROFOLIC ACID
2	MRD	3	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (3, 20)

No.	Name	Count	Type	Full Name
1	DHF	4	Ligand/Ion	DIHYDROFOLIC ACID
2	MRD	12	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
3	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:67 , ILE A:68 , TYR A:69 , HOH A:547 , HOH A:550 , HOH A:575 , HOH A:581 , HOH A:596 , HOH A:603 , HOH A:605 , HOH A:608	BINDING SITE FOR RESIDUE DHF A 0
2	AC2	SOFTWARE	LYS A:32 , SER A:34 , GLY A:35 , ALA A:36 , LEU A:50 , GLY A:64 , SER A:65 , GLN A:67 , ILE A:68 , TYR A:69 , PRO A:70 , ALA A:72 , ALA A:73 , HOH A:503 , HOH A:504 , HOH A:506 , HOH A:508 , HOH A:509 , HOH A:510 , HOH A:527 , HOH A:538 , HOH A:547 , HOH A:550 , HOH A:565 , HOH A:567 , HOH A:575 , HOH A:578 , HOH A:581 , HOH A:590 , HOH A:591 , HOH A:592 , HOH A:596 , HOH A:597 , HOH A:605 , HOH A:608	BINDING SITE FOR RESIDUE NAP A 1
3	AC3	SOFTWARE	ALA A:22 , GLY A:25 , ARG A:76 , ILE A:77 , ASN A:78 , HOH A:559 , HOH A:580 , HOH A:595 , HOH A:600	BINDING SITE FOR RESIDUE MRD A 500
4	AC4	SOFTWARE	GLY A:35 , ASN A:49 , LEU A:50 , PRO A:52 , HOH A:570	BINDING SITE FOR RESIDUE MRD A 501
5	AC5	SOFTWARE	PHE A:24 , GLY A:25 , TRP A:45 , HOH A:600	BINDING SITE FOR RESIDUE MRD A 502

SS Bonds (0, 0)

(no "SS Bond" information available for 2RK1)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2RK1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2RK1)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 2RK1)

Exons (0, 0)

(no "Exon" information available for 2RK1)

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
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Chain A from PDB  Type:PROTEIN  Length:58
 aligned with DYR21_ECOLX | P00383 from UniProtKB/Swiss-Prot  Length:78

    Alignment length:58
                                    30        40        50        60        70        
           DYR21_ECOLX   21 NATFGMGDRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERIN 78
               SCOP domains d2rk1a_ A: automated matches                               SCOP domains
               CATH domains 2rk1A00 A:21-78  [code=2.30.30.60, no name defined]        CATH domains
               Pfam domains DHFR_2-2rk1A01 A:21-78                                     Pfam domains
         Sec.struct. author ........eeee......eeeeeeee.......eeeeee......eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  2rk1 A 21 NATFGMGDRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERIN 78
                                    30        40        50        60        70

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)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Electron transport accessory proteins (58)

Family: R67 dihydrofolate reductase (8)

Protein domain: automated matches (6)

Escherichia coli [TaxId: 562] (6)

d2rk1a_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: [code=2.30.30.60, no name defined] (9)

Escherichia coli. Strain: tmp-resistant, containing r67 dhfr overproducing plasmid plz1 (2)

2rk1A00

A:21-78

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: DHFR_2] (6)

Family: DHFR_2 (6)

Escherichia coli (6)

DHFR_2-2rk1A01

A:21-78

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A (DYR21_ECOLX | P00383)

molecular function
	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: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.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	DYR21_ECOLX \| P00383	:	1vie 1vif 2gqv 2p4t 2rh2 2rk2 3sfm

Related Entries Specified in the PDB File

2p4t	A MUTANT FORM OF THE SAME PROTEIN (Q67H) COMPLEXED WITH NADP. THE MUTANT HAS A HIGHER AFFINITY FOR NADP, BUT APPEARS TO BIND DIFFERENTLY.
2rh2	HIGH RESOLUTION STRUCTURE OF THE SAME PROTEIN WITH NO LIGANDS, USED AS A STARTING MODEL FOR THIS STRUCTURE.