3JVX - JenaLib

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Title :   CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 2,4-DIAMINO-5-(3-(3,4,5-TRIMETHOXYPHENYL) PROP-1-YNYL)-6-ETHYLPYRIMIDINE (UCP120A)

Authors :   A. C. Anderson, J. M. Beierlein, N. G. Karri

Date :   17 Sep 09 (Deposition) - 15 Sep 10 (Release) - 20 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

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

Reference :   J. M. Beierlein, N. G. Karri, A. C. Anderson
Mutational Studies Into Trimethoprim Resistance In Bacillus Anthracis Dihydrofolate Reductase
To Be Published
PubMed: search

Molecule 1 - DIHYDROFOLATE REDUCTASE
	Chains	:	A, B
	EC Number	:	1.5.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE2
	Expression System Strain	:	M15
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BAS2083, BA_2237, DFRA, GBAA2237, GBAA_2237
	Mutation	:	YES
	Organism Scientific	:	BACILLUS ANTHRACIS
	Organism Taxid	:	1392

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	EKB	2	Ligand/Ion	6-ETHYL-5-[3-(3,4,5-TRIMETHOXYPHENYL)PROP-1-YN-1-YL]PYRIMIDINE-2,4-DIAMINE
2	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	EKB	2	Ligand/Ion	6-ETHYL-5-[3-(3,4,5-TRIMETHOXYPHENYL)PROP-1-YN-1-YL]PYRIMIDINE-2,4-DIAMINE
2	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	EKB	2	Ligand/Ion	6-ETHYL-5-[3-(3,4,5-TRIMETHOXYPHENYL)PROP-1-YN-1-YL]PYRIMIDINE-2,4-DIAMINE
2	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:7 , ALA A:8 , ILE A:15 , GLY A:16 , ASN A:19 , ASN A:20 , LEU A:21 , TRP A:23 , GLY A:44 , ARG A:45 , LYS A:46 , ASN A:47 , VAL A:63 , THR A:64 , ARG A:65 , HIS A:78 , PHE A:96 , GLY A:97 , GLY A:98 , ALA A:99 , GLN A:100 , ILE A:101 , HOH A:163 , HOH A:164 , EKB A:208 , HOH A:234 , HOH A:256 , HOH A:271 , HOH A:282 , HOH A:285	BINDING SITE FOR RESIDUE NDP A 207
2	AC2	SOFTWARE	MET A:6 , VAL A:7 , ALA A:8 , ASN A:20 , LEU A:21 , TRP A:23 , GLU A:28 , VAL A:32 , ASN A:47 , ILE A:51 , PHE A:96 , TYR A:102 , THR A:115 , NDP A:207	BINDING SITE FOR RESIDUE EKB A 208
3	AC3	SOFTWARE	VAL B:7 , ALA B:8 , ILE B:15 , GLY B:16 , ASN B:19 , ASN B:20 , LEU B:21 , TRP B:23 , GLY B:44 , ARG B:45 , LYS B:46 , ASN B:47 , VAL B:63 , THR B:64 , ARG B:65 , HIS B:78 , PHE B:96 , GLY B:97 , GLY B:98 , ALA B:99 , GLN B:100 , ILE B:101 , TYR B:102 , LEU B:104 , HOH B:166 , HOH B:168 , HOH B:191 , HOH B:197 , EKB B:208 , HOH B:209 , HOH B:220 , HOH B:221 , HOH B:237	BINDING SITE FOR RESIDUE NDP B 207
4	AC4	SOFTWARE	MET B:6 , VAL B:7 , ALA B:8 , ASN B:20 , LEU B:21 , GLU B:28 , VAL B:32 , ASN B:47 , ILE B:51 , PHE B:96 , TYR B:102 , THR B:115 , NDP B:207	BINDING SITE FOR RESIDUE EKB B 208

(no "SS Bond" information available for 3JVX)

Asymmetric Unit

No.	Residues
1	Gly A:97	-	Gly A:98
2	Gly B:97	-	Gly B:98

(no "SAP(SNP)/Variant" information available for 3JVX)

(no "PROSITE Motif" information available for 3JVX)

(no "Exon" information available for 3JVX)

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:166
 aligned with Q81R22_BACAN | Q81R22 from UniProtKB/TrEMBL  Length:162

    Alignment length:166
                                1                                                                                                                                                                 
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156      
         Q81R22_BACAN     - ----MIVSFMVAMDENRVIGKDNNLPWRLPSELQYVKKTTMGHPLIMGRKNYEAIGRPLPGRRNIIVTRNEGYHVEGCEVAHSVEEVFELCKNEEEIFIFGGAQIYDLFLPYVDKLYITKIHHAFEGDTFFPEMDMTNWKEVFVEKGLTDEKNPYTYYYHVYEKQQ 162
               SCOP domains d3jvxa_ A: automated matches                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee....eee........hhhhhhhhhhhhh...eeeehhhhhhhh.......eeee...........eee.hhhhhhhhh....eeee..hhhhhhhhhhhh.eeeeeee.......ee........eeeeeeee..........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jvx A  -3 HHHHMRVSFMVAMDENRVIGKDNNLPWRLPSELQYVKKTTMGHPLIMGRKNYEAIGRPLPGRRNIIVTRNEGYHVEGCEVAHSVEEVFELCKNEEEIFIFGGAQIYDLFLPYVDKLYITKIHHAFEGDTFFPEMDMTNWKEVFVEKGLTDEKNPYTYYYHVYEKQQ 162
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with Q81R22_BACAN | Q81R22 from UniProtKB/TrEMBL  Length:162

    Alignment length:166
                                1                                                                                                                                                                 
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156      
         Q81R22_BACAN     - ----MIVSFMVAMDENRVIGKDNNLPWRLPSELQYVKKTTMGHPLIMGRKNYEAIGRPLPGRRNIIVTRNEGYHVEGCEVAHSVEEVFELCKNEEEIFIFGGAQIYDLFLPYVDKLYITKIHHAFEGDTFFPEMDMTNWKEVFVEKGLTDEKNPYTYYYHVYEKQQ 162
               SCOP domains d3jvxb_ B: automated matches                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------DHFR_1-3jvxB01 B:3-160                                                                                                                                        -- Pfam domains (1)
           Pfam domains (2) ------DHFR_1-3jvxB02 B:3-160                                                                                                                                        -- Pfam domains (2)
         Sec.struct. author .....eeeeeeeee...eee........hhhhhhhhhhhhh...eeeehhhhhhhh.......eeee...........eee.hhhhhhhhh....eeee..hhhhhhhhhhhh.eeeeeee.......ee........eeeeeeee..........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jvx B  -3 HHHHMRVSFMVAMDENRVIGKDNNLPWRLPSELQYVKKTTMGHPLIMGRKNYEAIGRPLPGRRNIIVTRNEGYHVEGCEVAHSVEEVFELCKNEEEIFIFGGAQIYDLFLPYVDKLYITKIHHAFEGDTFFPEMDMTNWKEVFVEKGLTDEKNPYTYYYHVYEKQQ 162
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Dihydrofolate reductase-like (332)

Superfamily: Dihydrofolate reductase-like (332)

Family: automated matches (76)

Protein domain: automated matches (76)

Anthrax bacillus (Bacillus anthracis) [TaxId: 1392] (20)

1a	d3jvxa_	A:
1b	d3jvxb_	B:

(no "CATH Domain" information available for 3JVX)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DHFred (95)

Family: DHFR_1 (89)

Bacillus anthracis (9)

1a	DHFR_1-3jvxB01	B:3-160
1b	DHFR_1-3jvxB02	B:3-160

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q81R22_BACAN | Q81R22)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0006760	folic acid-containing compound metabolic process	The chemical reactions and pathways involving a folic acid-containing compound, i.e. any of a group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid or L-glutamate units.
	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: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
		Gly A:97 - Gly A:98	[ RasMol ]
		Gly B:97 - Gly B:98	[ RasMol ]

Biological Units
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3eob	CRYSTAL STRUCTURE THE FAB FRAGMENT OF EFALIZUMAB IN COMPLEX WITH LFA-1 I DOMAIN, FORM II
3jv3	CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS (F96I) DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND TRIMETHOPRIM
3jv5	CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS (Y102F) DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND TRIMETHOPRIM

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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