2VEG - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   DIHYDROPTEROATE SYNTHASE FROM STREPTOCOCCUS PNEUMONIAE: COMPLEX WITH 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN MONOPHOSPHATE

Authors :   J. Derrick, C. Levy

Date :   24 Oct 07 (Deposition) - 25 Mar 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Folic Acid, Transferase, Biosynthesis, Antibiotic Resistance, Streptococcus Pneumoniae, Dihydropteroate, Folate Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Levy, D. Minnis, J. Derrick
Dihydropteroate Synthase From Streptococcus Pneumoniae: Structure, Ligand Recognition And Mechanism Of Sulfonamide Resistance.
Biochem. J. V. 412 379 2008
PubMed-ID: 18321242 | Reference-DOI: 10.1042/BJ20071598

Molecule 1 - DIHYDROPTEROATE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.5.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	1313
	Synonym	:	DHPS, DIHYDROPTEROATE PYROPHOSPHORYLASE

		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, 2)

No.	Name	Count	Type	Full Name
1	PMM	1	Ligand/Ion	PTERIN-6-YL-METHYL-MONOPHOSPHATE
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	PMM	1	Ligand/Ion	PTERIN-6-YL-METHYL-MONOPHOSPHATE
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	PMM	-1	Ligand/Ion	PTERIN-6-YL-METHYL-MONOPHOSPHATE
2	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:15 , ASN A:17 , ASP A:91 , ASN A:110 , ILE A:112 , MET A:135 , ASP A:201 , PHE A:206 , PHE A:231 , GLY A:233 , LYS A:237 , ARG A:282 , HIS A:284	BINDING SITE FOR RESIDUE PMM A1304
2	AC2	SOFTWARE	ALA A:44 , GLU A:45 , GLY A:46 , THR A:255 , GLU A:256 , ARG A:290	BINDING SITE FOR RESIDUE PO4 A1305

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

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

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PTERIN_BINDING	PS50972	Pterin-binding domain profile.	DHPS_STRR6	10-294	2	A:10-294 B:10-294
2	DHPS_1	PS00792	Dihydropteroate synthase signature 1.	DHPS_STRR6	12-27	2	A:12-20 B:12-19
3	DHPS_2	PS00793	Dihydropteroate synthase signature 2.	DHPS_STRR6	46-59	2	A:46-56 B:46-56

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PTERIN_BINDING	PS50972	Pterin-binding domain profile.	DHPS_STRR6	10-294	1	A:10-294 -
2	DHPS_1	PS00792	Dihydropteroate synthase signature 1.	DHPS_STRR6	12-27	1	A:12-20 -
3	DHPS_2	PS00793	Dihydropteroate synthase signature 2.	DHPS_STRR6	46-59	1	A:46-56 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PTERIN_BINDING	PS50972	Pterin-binding domain profile.	DHPS_STRR6	10-294	1	- B:10-294
2	DHPS_1	PS00792	Dihydropteroate synthase signature 1.	DHPS_STRR6	12-27	1	- B:12-19
3	DHPS_2	PS00793	Dihydropteroate synthase signature 2.	DHPS_STRR6	46-59	1	- B:46-56

(no "Exon" information available for 2VEG)

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:279
 aligned with DHPS_STRR6 | P59655 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:297
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       
           DHPS_STRR6     7 HAKTVICGIINVTPDSFSDGGQFFALEQALQQARKLIAEGASMLDIGGESTRPGSSYVEIEEEIQRVVPVIKAIRKESDVLISIDTWKSQVAEAALAAGADLVNDITGLMGDEKMPHVVAEARAQVVIMFNPVMARPQHPSSLIFPHFGFGQAFTEEELADFETLPIEELMEAFFERALARAAEAGIAPENILLDPGIGFGLTKKENLLLLRDLDKLHQKGYPIFLGVSRKRFVINILEENGFEVNPETELGFRNRDTASAHVTSIAARQGVEVVRVHDVASHRMAVEIASAIRLAD 303
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2vegA00 A:7-30         3 Dihydropteroate (DHP) syn     thetase                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...---------hhhhhhhhhhhhhhhhh..eeeee...-----hhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhh....eeee........hhhhhhhhhh.eeeee.hhhhhh..............--....--..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeee.......hhhhhhhhhhhhhhhhh.....eee...hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---PTERIN_BINDING  PDB: A:10-294 UniProt: 10-294                                                                                                                                                                                                                                                --------- PROSITE (1)
                PROSITE (2) -----DHPS_1          ------------------DHPS_2        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2veg A   7 HAKTVICGIINVTP---------FALEQALQQARKLIAEGASMLDIGGES-----SYVEIEEEIQRVVPVIKAIRKESDVLISIDTWKSQVAEAALAAGADLVNDITGLMGDEKMPHVVAEARAQVVIMFNPVMARPQHPSSLIFPHFGF--AFTE--LADFETLPIEELMEAFFERALARAAEAGIAPENILLDPGIGFGLTKKENLLLLRDLDKLHQKGYPIFLGVSRKRFVINILEENGFEVNPETELGFRNRDTASAHVTSIAARQGVEVVRVHDVASHRMAVEIASAIRLAD 303
                                    16   |     -   |    36        46        56     |  66        76        86        96       106       116       126       136       146       156  |  | 166       176       186       196       206       216       226       236       246       256       266       276       286       296       
                                        20        30                        56    62                                                                                           156  |  |  |                                                                                                                                          
                                                                                                                                                                                  159  |  |                                                                                                                                          
                                                                                                                                                                                     162  |                                                                                                                                          
                                                                                                                                                                                        165

Chain B from PDB  Type:PROTEIN  Length:275
 aligned with DHPS_STRR6 | P59655 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:297
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       
           DHPS_STRR6     6 NHAKTVICGIINVTPDSFSDGGQFFALEQALQQARKLIAEGASMLDIGGESTRPGSSYVEIEEEIQRVVPVIKAIRKESDVLISIDTWKSQVAEAALAAGADLVNDITGLMGDEKMPHVVAEARAQVVIMFNPVMARPQHPSSLIFPHFGFGQAFTEEELADFETLPIEELMEAFFERALARAAEAGIAPENILLDPGIGFGLTKKENLLLLRDLDKLHQKGYPIFLGVSRKRFVINILEENGFEVNPETELGFRNRDTASAHVTSIAARQGVEVVRVHDVASHRMAVEIASAIRLA 302
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2vegB00 B:6-30            2 Dihydropteroate (DHP) s      ynthetase                                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) ---------Pteri            n_bind-2vegB01 B:15-241                                                                                                                                                                                           ------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------Pteri            n_bind-2vegB02 B:15-241                                                                                                                                                                                           ------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....eeeeeee..------------hhhhhhhhhhhhhh...eeeee...------.hhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhh.....eeee........hhhhhhhhhh.eeeee.hhhhhh.............----.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhh.eeee.......hhhhhhhhhhhhhhhhh.....eee...hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTERIN_BINDING  PDB: B:10-294 UniProt: 10-294                                                                                                                                                                                                                                                -------- PROSITE (1)
                PROSITE (2) ------DHPS_1          ------------------DHPS_2        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2veg B   6 NHAKTVICGIINVT------------LEQALQQARKLIAEGASMLDIGGES------YVEIEEEIQRVVPVIKAIRKESDVLISIDTWKSQVAEAALAAGADLVNDITGLMGDEKMPHVVAEARAQVVIMFNPVMARPQHPSSLIFPHFG----FTEEELADFETLPIEELMEAFFERALARAAEAGIAPENILLDPGIGFGLTKKENLLLLRDLDKLHQKGYPIFLGVSRKRFVINILEENGFEVNPETELGFRNRDTASAHVTSIAARQGVEVVRVHDVASHRMAVEIASAIRLA 302
                                    15   |     -      | 35        45        55|      |65        75        85        95       105       115       125       135       145       155    |  165       175       185       195       205       215       225       235       245       255       265       275       285       295       
                                        19           32                      56     63                                                                                         155  160

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 '\|'

(no "SCOP Domain" information available for 2VEG)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Dihydropteroate (DHP) synthetase (30)

Streptococcus pneumoniae. Organism_taxid: 1313. (2)

1a	2vegB00	B:6-302
1b	2vegA00	A:7-303

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: Pterin_bind (18)

Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (2)

1a	Pterin_bind-2vegB01	B:15-241
1b	Pterin_bind-2vegB02	B:15-241

Asymmetric Unit(hide GO term definitions)

Chain A,B (DHPS_STRR6 | P59655)

molecular function
	GO:0004156	dihydropteroate synthase activity	Catalysis of the reaction: 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0044237	cellular metabolic process	The chemical reactions and pathways by which individual cells transform chemical substances.
	GO:0046656	folic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of folic acid, pteroylglutamic acid.
	GO:0009396	folic acid-containing compound biosynthetic process	The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.
	GO:0042558	pteridine-containing compound metabolic process	The chemical reactions and pathways involving any compound containing pteridine (pyrazino(2,3-dipyrimidine)), e.g. pteroic acid, xanthopterin and folic acid.
	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: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
	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
		PMM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2veg)

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2veg
		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
	DHPS_STRR6 \| P59655
		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)
	2.5.1.15
		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

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	DHPS_STRR6 \| P59655
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	DHPS_STRR6 \| P59655	:	2vef

2vef	DIHYDROPTEROATE SYNTHASE FROM STREPTOCOCCUS PNEUMONIAE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File