3TYB - 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 IN COMPLEX WITH PHBA AND DHP+

Authors :   M. -K. Yun, S. W. White

Date :   24 Sep 11 (Deposition) - 14 Mar 12 (Release) - 14 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Anthracis, Folate Biosynthesis, Dihydropteroate, Pterine, Tim Barrel, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. K. Yun, Y. Wu, Z. Li, Y. Zhao, M. B. Waddell, A. M. Ferreira, R. E. Lee, D. Bashford, S. W. White
Catalysis And Sulfa Drug Resistance In Dihydropteroate Synthase.
Science V. 335 1110 2012
PubMed-ID: 22383850 | Reference-DOI: 10.1126/SCIENCE.1214641

Molecule 1 - DIHYDROPTEROATE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.5.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	FOLP, BAS0071, BA_0071, GBAA_0071
	Organism Common	:	ANTHRAX,ANTHRAX BACTERIUM
	Organism Scientific	:	BACILLUS ANTHRACIS
	Organism Taxid	:	191218
	Strain	:	A2012

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	PHB	2	Ligand/Ion	P-HYDROXYBENZOIC ACID
2	SO4	8	Ligand/Ion	SULFATE ION
3	XHP	2	Ligand/Ion	2-AMINO-6-METHYLIDENE-6,7-DIHYDROPTERIDIN-4(3H)-ONE

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	PHB	2	Ligand/Ion	P-HYDROXYBENZOIC ACID
2	SO4	6	Ligand/Ion	SULFATE ION
3	XHP	2	Ligand/Ion	2-AMINO-6-METHYLIDENE-6,7-DIHYDROPTERIDIN-4(3H)-ONE

Biological Unit 2 (3, 14)

No.	Name	Count	Type	Full Name
1	PHB	2	Ligand/Ion	P-HYDROXYBENZOIC ACID
2	SO4	10	Ligand/Ion	SULFATE ION
3	XHP	2	Ligand/Ion	2-AMINO-6-METHYLIDENE-6,7-DIHYDROPTERIDIN-4(3H)-ONE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:101 , ASN A:120 , ILE A:122 , MET A:145 , ASP A:184 , PHE A:189 , LEU A:214 , GLY A:216 , LYS A:220 , ARG A:254 , SO4 A:279 , HOH A:291 , PHB A:901	BINDING SITE FOR RESIDUE XHP A 701
02	AC2	SOFTWARE	THR A:67 , LYS A:220 , SER A:221 , XHP A:701	BINDING SITE FOR RESIDUE PHB A 901
03	AC3	SOFTWARE	LYS A:50 , ARG A:53	BINDING SITE FOR RESIDUE SO4 A 278
04	AC4	SOFTWARE	ILE A:25 , ARG A:254 , HIS A:256 , XHP A:701	BINDING SITE FOR RESIDUE SO4 A 279
05	AC5	SOFTWARE	ARG A:219	BINDING SITE FOR RESIDUE SO4 A 280
06	AC6	SOFTWARE	ASP B:101 , ASN B:120 , ILE B:122 , ASP B:184 , PHE B:189 , GLY B:216 , LYS B:220 , ARG B:254 , SO4 B:278 , PHB B:902	BINDING SITE FOR RESIDUE XHP B 702
07	AC7	SOFTWARE	SER B:66 , GLY B:188 , LYS B:220 , SER B:221 , HOH B:287 , XHP B:702	BINDING SITE FOR RESIDUE PHB B 902
08	AC8	SOFTWARE	ARG B:254 , HIS B:256 , XHP B:702	BINDING SITE FOR RESIDUE SO4 B 278
09	AC9	SOFTWARE	LYS B:50 , ARG B:53	BINDING SITE FOR RESIDUE SO4 B 279
10	BC1	SOFTWARE	ARG B:201 , ASN B:202	BINDING SITE FOR RESIDUE SO4 B 280
11	BC2	SOFTWARE	SER B:221 , ARG B:234 , HOH B:287	BINDING SITE FOR RESIDUE SO4 B 281
12	BC3	SOFTWARE	ARG B:219	BINDING SITE FOR RESIDUE SO4 B 282

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

Asymmetric Unit

No.	Residues
1	Thr B:29	-	Pro B:30

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

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

(no "Exon" information available for 3TYB)

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:265
 aligned with Q81VW8_BACAN | Q81VW8 from UniProtKB/TrEMBL  Length:280

    Alignment length:274
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273    
         Q81VW8_BACAN     4 LKWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGESTRPGFAKVSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 277
               SCOP domains d3tyba_ A: Dihydropteroate syn   thetase                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee......eeeeee....---....hhhhhhhhhhhhhhhhhh...eeee.....------.hhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh..eeee.......hhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhh.hhh.eeee.......hhhhhhhhhhhhhhhhhhh...ee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tyb A   1 MKWDYDLRCGEYTLNLNEKTLIMGILNVTP---SDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGEST------VSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 274
                                    10        20        30   |    40        50        60      |  -   |    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    
                                                        30  34                               67     74

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with Q81VW8_BACAN | Q81VW8 from UniProtKB/TrEMBL  Length:280

    Alignment length:273
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   
         Q81VW8_BACAN     5 KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKEMRDEGAHIIDIGGESTRPGFAKVSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 277
               SCOP domains d3tybb_ B: Dihydropteroate sy    nthetase                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee......eeeeee....----...hhhhhhhhhhhhhhhhhhh..eeee....--------.hhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhhh..eeee........hhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhh..hhh.eeee.......hhhhhhhhhhhhhhhhhhh...ee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tyb B   2 KWDYDLRCGEYTLNLNEKTLIMGILNVTP----DGGSYNEVDAAVRHAKEMRDEGAHIIDIGGES--------SVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQAIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADMIADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLGYPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKEMSRMAKMMDAMIGK 274
                                    11        21        |-   |    41        51        61    |    -   |    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   
                                                       30   35                             66       75

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: TIM beta/alpha-barrel (3956)

Superfamily: Dihydropteroate synthetase-like (59)

Family: Dihydropteroate synthetase (40)

Protein domain: Dihydropteroate synthetase (34)

Anthrax bacillus (Bacillus anthracis) [TaxId: 1392] (28)

1a	d3tyba_	A:
1b	d3tybb_	B:

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

(no "Pfam Domain" information available for 3TYB)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q81VW8_BACAN | Q81VW8)

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: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
		PHB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		XHP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Thr B:29 - Pro B:30	[ RasMol ]

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
	3tyb
		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
	Q81VW8_BACAN \| Q81VW8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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
	Q81VW8_BACAN \| Q81VW8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

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