3LG4 - JenaLib

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Title :   STAPHYLOCOCCUS AUREUS V31Y, F92I MUTANT DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 5-[(3S)-3-(5-METHOXY-2',6'-DIMETHYLBIPHENYL-3-YL)BUT-1-YN-1-YL]-6-METHYLPYRIMIDINE-2,4-DIAMINE

Authors :   K. M. Frey, A. C. Anderson

Date :   08 Jul 10 (Deposition) - 28 Jul 10 (Release) - 27 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.15

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

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

Reference :   K. M. Frey, I. Georgiev, B. R. Donald, A. C. Anderson
Predicting Resistance Mutations Using Protein Design Algorithms.
Proc. Natl. Acad. Sci. Usa V. 107 13707 2010
PubMed-ID: 20643959 | Reference-DOI: 10.1073/PNAS.1002162107

Molecule 1 - DIHYDROFOLATE REDUCTASE
	Chains	:	A, B
	EC Number	:	1.5.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET41
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DFRA, DFRB, FOLA
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Synonym	:	DHFR

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	52V	2	Ligand/Ion	5-[(3S)-3-(5-METHOXY-2',6'-DIMETHYLBIPHENYL-3-YL)BUT-1-YN-1-YL]-6-METHYLPYRIMIDINE-2,4-DIAMINE
2	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	52V	1	Ligand/Ion	5-[(3S)-3-(5-METHOXY-2',6'-DIMETHYLBIPHENYL-3-YL)BUT-1-YN-1-YL]-6-METHYLPYRIMIDINE-2,4-DIAMINE
2	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	52V	1	Ligand/Ion	5-[(3S)-3-(5-METHOXY-2',6'-DIMETHYLBIPHENYL-3-YL)BUT-1-YN-1-YL]-6-METHYLPYRIMIDINE-2,4-DIAMINE
2	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:6 , ALA A:7 , ILE A:14 , GLY A:15 , ASN A:18 , GLN A:19 , LEU A:20 , GLY A:43 , ARG A:44 , LYS A:45 , THR A:46 , LEU A:62 , THR A:63 , SER A:64 , HIS A:77 , ILE A:92 , GLY A:94 , GLN A:95 , THR A:96 , GLU A:100 , THR A:121 , 52V A:202	BINDING SITE FOR RESIDUE NDP A 201
2	AC2	SOFTWARE	LEU A:5 , VAL A:6 , ALA A:7 , GLN A:19 , LEU A:20 , ASP A:27 , LEU A:28 , TYR A:31 , SER A:49 , ILE A:50 , ILE A:92 , NDP A:201 , THR B:66 , SER B:67	BINDING SITE FOR RESIDUE 52V A 202
3	AC3	SOFTWARE	VAL B:6 , ALA B:7 , ILE B:14 , GLY B:15 , ASN B:18 , GLN B:19 , LEU B:20 , GLY B:43 , ARG B:44 , LYS B:45 , THR B:46 , LEU B:62 , THR B:63 , SER B:64 , HIS B:77 , ILE B:79 , ILE B:92 , GLY B:93 , GLY B:94 , GLN B:95 , THR B:96 , LEU B:97 , GLU B:100 , THR B:121 , 52V B:202	BINDING SITE FOR RESIDUE NDP B 201
4	AC4	SOFTWARE	LEU B:5 , VAL B:6 , ALA B:7 , LEU B:20 , ASP B:27 , LEU B:28 , TYR B:31 , SER B:49 , ILE B:50 , ILE B:92 , NDP B:201	BINDING SITE FOR RESIDUE 52V B 202

(no "SS Bond" information available for 3LG4)

Asymmetric Unit

No.	Residues
1	Gly A:93	-	Gly A:94
2	Gly B:93	-	Gly B:94

(no "SAP(SNP)/Variant" information available for 3LG4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHFR_2	PS51330	Dihydrofolate reductase (DHFR) domain profile.	DYR_STAAU	2-157	2	A:1-156 B:1-156
2	DHFR_1	PS00075	Dihydrofolate reductase (DHFR) domain signature.	DYR_STAAU	14-36	2	A:13-35 B:13-35

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHFR_2	PS51330	Dihydrofolate reductase (DHFR) domain profile.	DYR_STAAU	2-157	1	A:1-156 -
2	DHFR_1	PS00075	Dihydrofolate reductase (DHFR) domain signature.	DYR_STAAU	14-36	1	A:13-35 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHFR_2	PS51330	Dihydrofolate reductase (DHFR) domain profile.	DYR_STAAU	2-157	1	- B:1-156
2	DHFR_1	PS00075	Dihydrofolate reductase (DHFR) domain signature.	DYR_STAAU	14-36	1	- B:13-35

(no "Exon" information available for 3LG4)

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:157
 aligned with DYR_STAAU | P0A017 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
            DYR_STAAU     2 TLSILVAHDLQRVIGFENQLPWHLPNDLKHVKKLSTGHTLVMGRKTFESIGKPLPNRRNVVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIFGGQTLFEEMIDKVDDMYITVIEGKFRGDTFFPPYTFEDWEVASSVEGKLDEKNTIPHTFLHLIRK 158
               SCOP domains d3lg4a_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eee........hhhhhhhhhhhhh..eeeeehhhhhhhh......eeeee...........eee..hhhhhh....eee..hhhhhhhhh....eeeeeee.......ee....hhh.eeeeeeee..........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) DHFR_2  PDB: A:1-156 UniProt: 2-157                                                                                                                         - PROSITE (1)
                PROSITE (2) ------------DHFR_1  PDB: A:13-35   -------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lg4 A   1 TLSILVAHDLQRVIGFENQLPWHLPNDLKHYKKLSTGHTLVMGRKTFESIGKPLPNRRNVVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIIGGQTLFEEMIDKVDDMYITVIEGKFRGDTFFPPYTFEDWEVASSVEGKLDEKNTIPHTFLHLIRK 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with DYR_STAAU | P0A017 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
            DYR_STAAU     2 TLSILVAHDLQRVIGFENQLPWHLPNDLKHVKKLSTGHTLVMGRKTFESIGKPLPNRRNVVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIFGGQTLFEEMIDKVDDMYITVIEGKFRGDTFFPPYTFEDWEVASSVEGKLDEKNTIPHTFLHLIRK 158
               SCOP domains d3lg4b_ B: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DHFR_1-3lg4B01 B:1-156                                                                                                                                      - Pfam domains (1)
           Pfam domains (2) DHFR_1-3lg4B02 B:1-156                                                                                                                                      - Pfam domains (2)
         Sec.struct. author .eeeeeee....eee........hhhhhhhhhhhhh..eeeeehhhhhhhh......eeeee...........eee..hhhhhh....eee..hhhhhhhhh....eeeeeee.......ee....hhh.eeeeeeee..........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) DHFR_2  PDB: B:1-156 UniProt: 2-157                                                                                                                         - PROSITE (1)
                PROSITE (2) ------------DHFR_1  PDB: B:13-35   -------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lg4 B   1 TLSILVAHDLQRVIGFENQLPWHLPNDLKHYKKLSTGHTLVMGRKTFESIGKPLPNRRNVVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIIGGQTLFEEMIDKVDDMYITVIEGKFRGDTFFPPYTFEDWEVASSVEGKLDEKNTIPHTFLHLIRK 157
                                    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 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: Dihydrofolate reductases (249)

Protein domain: automated matches (15)

Staphylococcus aureus [TaxId: 1280] (5)

1a	d3lg4a_	A:
1b	d3lg4b_	B:

(no "CATH Domain" information available for 3LG4)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DHFred (95)

Family: DHFR_1 (89)

Staphylococcus aureus (7)

1a	DHFR_1-3lg4B01	B:1-156
1b	DHFR_1-3lg4B02	B:1-156

Asymmetric Unit(hide GO term definitions)

Chain A,B (DYR_STAAU | P0A017)

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: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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:93 - Gly A:94	[ RasMol ]
		Gly B:93 - Gly B:94	[ RasMol ]

Biological Units
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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 (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (8, 8)

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