1RB3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   DIHYDROFOLATE REDUCTASE COMPLEXED WITH METHOTREXATE AND NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE (OXIDIZED FORM)

Authors :   M. R. Sawaya, J. Kraut

Date :   26 Nov 96 (Deposition) - 12 Mar 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

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

Reference :   M. R. Sawaya, J. Kraut
Loop And Subdomain Movements In The Mechanism Of Escherichia Coli Dihydrofolate Reductase: Crystallographic Evidence.
Biochemistry V. 36 586 1997
PubMed-ID: 9012674 | Reference-DOI: 10.1021/BI962337C
(for further references see the PDB file header)

Molecule 1 - DIHYDROFOLATE REDUCTASE
	Chains	:	A, B
	EC Number	:	1.5.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRWA-1
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	RT500
	Synonym	:	DHFR

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MTX	2	Ligand/Ion	METHOTREXATE
2	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:5 , ALA A:6 , ASP A:27 , LEU A:28 , PHE A:31 , LYS A:32 , ILE A:50 , ARG A:57 , ILE A:94 , TYR A:100 , THR A:113 , HOH A:409 , HOH A:550 , HOH A:551	BINDING SITE FOR RESIDUE MTX A 161
2	AC2	SOFTWARE	MET A:16 , GLY A:43 , ARG A:44 , HIS A:45 , THR A:46 , LEU A:62 , SER A:63 , SER A:64 , LYS A:76 , GLY A:96 , GLY A:97 , ARG A:98 , VAL A:99 , GLN A:102 , ASP A:122 , THR A:123 , HOH A:406 , HOH A:470 , HOH A:542	BINDING SITE FOR RESIDUE NAP A 164
3	AC3	SOFTWARE	ILE B:5 , ALA B:6 , ASP B:27 , PHE B:31 , LYS B:32 , LEU B:54 , ARG B:57 , ILE B:94 , TYR B:100 , THR B:113 , HOH B:400	BINDING SITE FOR RESIDUE MTX B 161
4	AC4	SOFTWARE	MET B:16 , GLU B:17 , GLY B:43 , ARG B:44 , HIS B:45 , THR B:46 , LEU B:62 , SER B:63 , SER B:64 , LYS B:76 , GLY B:96 , GLY B:97 , ARG B:98 , VAL B:99 , GLN B:102 , ASP B:122 , HOH B:415 , HOH B:425	BINDING SITE FOR RESIDUE NAP B 164

(no "SS Bond" information available for 1RB3)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:95	-	Gly A:96
2	Gly B:95	-	Gly B:96

Asymmetric/Biological Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DYR_ECOLI_001 *	L	28	R	DYR_ECOLI	---	---	A/B	L	28	R
2	UniProt	VAR_DYR_ECOLI_002 *	W	30	G	DYR_ECOLI	---	---	A/B	W	30	G
3	UniProt	VAR_DYR_ECOLI_003 *	E	154	K	DYR_ECOLI	---	---	A/B	E	154	K
4	UniProt	VAR_DYR_ECOLI_004 *	E	154	Q	DYR_ECOLI	---	---	A/B	E	154	Q
	* ID not provided by source

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHFR_2	PS51330	Dihydrofolate reductase (DHFR) domain profile.	DYR_ECOLI	1-158	2	A:1-158 B:1-158
2	DHFR_1	PS00075	Dihydrofolate reductase (DHFR) domain signature.	DYR_ECOLI	13-35	2	A:13-35 B:13-35

(no "Exon" information available for 1RB3)

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 d1rb3a_ A: Dihydrofolate reductase, prokaryotic type                                                                                                            SCOP domains
               CATH domains 1rb3A00 A:1-159 Dihydrofolate Reductase, subunit A                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...................hhhhhhhhhhh...eeeeehhhhhhh.......eeeee..........eee..hhhhhhhh.....eeeee.hhhhhhhhhheeeeeeeee.................eee...............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
                 1rb3 A   1 MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLDKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B 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 d1rb3b_ B: Dihydrofolate reductase, prokaryotic type                                                                                                            SCOP domains
               CATH domains 1rb3B00 B:1-159 Dihydrofolate Reductase, subunit A                                                                                                              CATH domains
           Pfam domains (1) DHFR_1-1rb3B01 B:1-158                                                                                                                                        - Pfam domains (1)
           Pfam domains (2) DHFR_1-1rb3B02 B:1-158                                                                                                                                        - Pfam domains (2)
         Sec.struct. author .eeee...................hhhhhhhhhhh...eeeeehhhhhhh.......eeeee..........eee..hhhhhhhh.....eeeee.hhhhhhhhhheeeeeeeee.................eee...............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: B:1-158 UniProt: 1-158                                                                                                                           - PROSITE (1)
                PROSITE (2) ------------DHFR_1  PDB: B:13-35   ---------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rb3 B   1 MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLDKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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(

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Protein Domains( (-)

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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: Dihydrofolate reductase, prokaryotic type (107)

Escherichia coli [TaxId: 562] (61)

1a	d1rb3a_	A:
1b	d1rb3b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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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)

Escherichia coli. Organism_taxid: 562. Strain: rt500. (23)

1a	1rb3A00	A:1-159
1b	1rb3B00	B:1-159

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DHFred (95)

Family: DHFR_1 (89)

Escherichia coli (strain K12) (24)

1a	DHFR_1-1rb3B01	B:1-158
1b	DHFR_1-1rb3B02	B:1-158

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:95 - Gly A:96	[ RasMol ]
		Gly B:95 - Gly B:96	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 1RB3)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

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Exons (0, 0)

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