2W9T - JenaLib

Title :   STAPHYLOCOCCUS AUREUS S1:DHFR

Authors :   H. H. Soutter, J. R. Miller

Date :   28 Jan 09 (Deposition) - 24 Mar 09 (Release) - 29 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

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

Reference :   H. Heaslet, M. Harris, K. Fahnoe, R. Sarver, H. Putz, J. Chang, C. Subramanyam, G. Barreiro, J. R. Miller
Structural Comparison Of Chromosomal And Exogenous Dihydrofolate Reductase From Staphylococcus Aureus In Complex With The Potent Inhibitor Trimethoprim.
Proteins V. 76 706 2009
PubMed-ID: 19280600 | Reference-DOI: 10.1002/PROT.22383

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

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

Exons (0, 0)

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
	(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 DYRA_STAAU | P13955 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:159
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151         
           DYRA_STAAU     2 TLSIIVAHDKQRVIGYQNQLPWHLPNDLKHIKQLTTGNTLVMARKTFNSIGKPLPNRRNVVLTNQASFHHEGVDVINSLDEIKELSGHVFIFGGQTLYEAMIDQVDDMYITVIDGKFQGDTFFPPYTFENWEVESSVEGQLDEKNTIPHTFLHLVRRKG 160
               SCOP domains d2w9ta_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains 2w9tA00 A:1-159 Dihydrofolate Reductase, subunit A                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...............hhhhhhhhhhhhh..eeeeehhhhhhhh......eeeee..........eeee.hhhhh......eeee.hhhhhhhhh....eeeeeee.................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
                 2w9t A   1 TLSIIVAHDKQRVIGYQNQLPWHLPNDLKHIKQLTTGNTLVMARKTFESIGKPLPNRRNVVLTNQASFHHEGVDVINSLDEIKELSGHVFIFGGQTLYEAMIDQVDDMYITVIDGKFQGDTFFPPYTFEDWEVESSVEGQLDEKNTIPHTFLHLVRRKG 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 DYRA_STAAU | P13955 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:159
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151         
           DYRA_STAAU     2 TLSIIVAHDKQRVIGYQNQLPWHLPNDLKHIKQLTTGNTLVMARKTFNSIGKPLPNRRNVVLTNQASFHHEGVDVINSLDEIKELSGHVFIFGGQTLYEAMIDQVDDMYITVIDGKFQGDTFFPPYTFENWEVESSVEGQLDEKNTIPHTFLHLVRRKG 160
               SCOP domains d2w9tb_ B: automated matches                                                                                                                                    SCOP domains
               CATH domains 2w9tB00 B:1-159 Dihydrofolate Reductase, subunit A                                                                                                              CATH domains
           Pfam domains (1) DHFR_1-2w9tB01 B:1-156                                                                                                                                      --- Pfam domains (1)
           Pfam domains (2) DHFR_1-2w9tB02 B:1-156                                                                                                                                      --- Pfam domains (2)
         Sec.struct. author .eeeeeee...............hhhhhhhhhhhhh..eeeeehhhhhhhh......eeeee..........eeee..hhhhhh....eeee.hhhhhhhhh....eeeeeee.................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
                 2w9t B   1 TLSIIVAHDKQRVIGYQNQLPWHLPNDLKHIKQLTTGNTLVMARKTFESIGKPLPNRRNVVLTNQASFHHEGVDVINSLDEIKELSGHVFIFGGQTLYEAMIDQVDDMYITVIDGKFQGDTFFPPYTFEDWEVESSVEGQLDEKNTIPHTFLHLVRRKG 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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DYRA_STAAU | P13955)

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: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: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.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2w9t)

	Sites
(no "Sites" information available for 2w9t)

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

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2w9t
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	DYRA_STAAU \| P13955
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.5.1.3
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description