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Title :   CRYSTAL STRUCTURE OF BURKHOLDERIA CENOCEPACIA DIHYDROPTEROATE SYNTHASE COMPLEXED WITH 7,8-DIHYDROPTEROATE.

Authors :   R. E. Morgan, G. O. Batot, J. M. Dement, V. A. Rao, T. C. Eadsforth, W. N. Hu

Date :   17 Jan 11 (Deposition) - 26 Jan 11 (Release) - 25 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A,B

Keywords :   Transferase, Folate Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. E. Morgan, G. O. Batot, J. M. Dement, V. A. Rao, T. C. Eadsforth, W. N. Hunter
Crystal Structures Of Burkholderia Cenocepacia Dihydropteroate Synthase In The Apo-Form And Complexed With The Product 7, 8-Dihydropteroate.
Bmc Struct. Biol. V. 11 21 2011
PubMed-ID: 21554707 | Reference-DOI: 10.1186/1472-6807-11-21

Molecule 1 - DIHYDROPTEROATE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.5.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET15BTEV
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BURKHOLDERIA CENOCEPACIA
	Organism Taxid	:	95486
	Other Details	:	BELGIAN CO-ORDINATED COLLECTIONS OF MICRO- ORGANISMS, BACTERIA COLLECTION (BCCM/LMG)
	Strain	:	LMG 16656
	Synonym	:	DHPS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 20)

No.	Name	Count	Type	Full Name
1	78H	2	Ligand/Ion	7,8-DIHYDROPTEROATE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	EDO	16	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:68 , ARG A:69 , ASP A:101 , ASN A:120 , MET A:144 , ASP A:191 , PHE A:196 , GLY A:229 , LYS A:233 , SER A:234 , ARG A:268 , EDO A:1304 , HOH A:2099 , HOH A:2100 , HOH A:2152	BINDING SITE FOR RESIDUE 78H A1293
02	AC2	SOFTWARE	VAL A:201 , ASP A:202 , HOH A:2055	BINDING SITE FOR RESIDUE CL A1294
03	AC3	SOFTWARE	ALA A:199 , ASP A:203 , EDO A:1301 , HOH A:2104 , HOH A:2154	BINDING SITE FOR RESIDUE EDO A1295
04	AC4	SOFTWARE	ALA A:254 , CYS A:258	BINDING SITE FOR RESIDUE EDO A1296
05	AC5	SOFTWARE	ARG A:126 , MET A:146 , LEU A:147 , GLY A:148 , PHE A:170 , HOH A:2153	BINDING SITE FOR RESIDUE EDO A1297
06	AC6	SOFTWARE	ARG A:109 , ASP A:132 , LYS A:198 , ALA A:199 , VAL A:200	BINDING SITE FOR RESIDUE EDO A1298
07	AC7	SOFTWARE	ALA A:173 , ARG A:174	BINDING SITE FOR RESIDUE EDO A1299
08	AC8	SOFTWARE	VAL B:249	BINDING SITE FOR RESIDUE EDO A1300
09	AC9	SOFTWARE	ASP A:162 , VAL A:163 , ASP A:202 , ASP A:203 , EDO A:1295 , HOH A:2154	BINDING SITE FOR RESIDUE EDO A1301
10	BC1	SOFTWARE	PHE A:4 , LEU A:5 , ALA A:7 , ARG A:222 , ALA A:223 , HOH A:2115	BINDING SITE FOR RESIDUE EDO A1302
11	BC2	SOFTWARE	GLU A:51 , ILE A:54 , ALA A:55	BINDING SITE FOR RESIDUE EDO A1303
12	BC3	SOFTWARE	ILE A:26 , ARG A:268 , HIS A:270 , 78H A:1293 , HOH A:2156	BINDING SITE FOR RESIDUE EDO A1304
13	BC4	SOFTWARE	ARG A:69 , ILE A:122 , TRP A:123 , MET A:153 , VAL A:155	BINDING SITE FOR RESIDUE EDO A1305
14	BC5	SOFTWARE	THR B:68 , ARG B:69 , ASP B:101 , ASN B:120 , MET B:144 , ASP B:191 , PHE B:196 , GLY B:229 , LYS B:233 , SER B:234 , ARG B:268 , EDO B:1297 , HOH B:2090 , HOH B:2146 , HOH B:2148	BINDING SITE FOR RESIDUE 78H B1293
15	BC6	SOFTWARE	ARG B:109 , VAL B:201 , ASP B:202 , HOH B:2041	BINDING SITE FOR RESIDUE CL B1294
16	BC7	SOFTWARE	ARG B:109 , ASP B:132 , LYS B:198 , ALA B:199 , VAL B:200 , HOH B:2147	BINDING SITE FOR RESIDUE EDO B1295
17	BC8	SOFTWARE	ARG B:69 , ARG B:232 , HIS B:270 , EDO B:1297 , HOH B:2148	BINDING SITE FOR RESIDUE EDO B1296
18	BC9	SOFTWARE	SER B:234 , ARG B:248 , 78H B:1293 , EDO B:1296	BINDING SITE FOR RESIDUE EDO B1297
19	CC1	SOFTWARE	ARG B:126 , ALA B:173 , ARG B:174 , HOH B:2051 , HOH B:2149	BINDING SITE FOR RESIDUE EDO B1298
20	CC2	SOFTWARE	ARG B:126 , MET B:146 , LEU B:147 , GLY B:148 , HOH B:2066	BINDING SITE FOR RESIDUE EDO B1299

(no "SS Bond" information available for 2Y5S)

Asymmetric/Biological Unit

No.	Residues
1	Ser B:2	-	Thr B:3

(no "SAP(SNP)/Variant" information available for 2Y5S)

(no "PROSITE Motif" information available for 2Y5S)

(no "Exon" information available for 2Y5S)

Asymmetric/Biological 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:280
 aligned with B4E5F5_BURCJ | B4E5F5 from UniProtKB/TrEMBL  Length:292

    Alignment length:290
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
         B4E5F5_BURCJ     3 PFLPAPLQCGRFELTFERPLVMGILNATPDSFSDGGRFLARDDALRRAERMIAEGADLLDIGGESTRPGAPPVPLDEELARVIPLVEALRPLNVPLSIDTYKPAVMRAALAAGADLINDIWGFRQPGAIDAVRDGNSGLCAMHMLGEPQTMQVGEPDYGDVVTDVRDFLAARAQALRDAGVAAERICVDPGFGFGKAVVDDNYALLAALPDTAPARPDGRAYPILAGMSRKSMLGAVIGGKPPLERVAASVAAALCAVERGAAIVRVHDVAATVDALSVWNAVRAAARQR 292
               SCOP domains d2y5sa_ A: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee.....eeeeeee...----------..hhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh..eeee.......hhhhhhh....eeeee...ee....ee......hhhhhhhhhhhhhhhhhhhh..hhh.eeee.........hhhhhhhhhhhhhhh...........eee...hhhhhh.....hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y5s A   3 TFLPAPLQCGRFELTFERPLVMGILNATP----------ARDDALRRAERMIAEGADLLDIGGESTRPGAPPVPLDEELARVIPLVEALRPLNVPLSIDTYKPAVMRAALAAGADLINDIWGFRQPGAIDAVRDGNSGLCAMHMLGEPQTMQVGEPDYGDVVTDVRDFLAARAQALRDAGVAAERICVDPGFGFGKAVVDDNYALLAALPDTAPARPDGRAYPILAGMSRKSMLGAVIGGKPPLERVAASVAAALCAVERGAAIVRVHDVAATVDALSVWNAVRAAARQR 292
                                    12        22        |-        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
                                                       31         42

Chain B from PDB  Type:PROTEIN  Length:281
 aligned with B4E5F5_BURCJ | B4E5F5 from UniProtKB/TrEMBL  Length:292

    Alignment length:291
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291 
         B4E5F5_BURCJ     2 SPFLPAPLQCGRFELTFERPLVMGILNATPDSFSDGGRFLARDDALRRAERMIAEGADLLDIGGESTRPGAPPVPLDEELARVIPLVEALRPLNVPLSIDTYKPAVMRAALAAGADLINDIWGFRQPGAIDAVRDGNSGLCAMHMLGEPQTMQVGEPDYGDVVTDVRDFLAARAQALRDAGVAAERICVDPGFGFGKAVVDDNYALLAALPDTAPARPDGRAYPILAGMSRKSMLGAVIGGKPPLERVAASVAAALCAVERGAAIVRVHDVAATVDALSVWNAVRAAARQR 292
               SCOP domains d2y5sb_ B: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------Pterin          _bind-2y5sB01 B:26-237                                                                                                                                                                              ------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------Pterin          _bind-2y5sB02 B:26-237                                                                                                                                                                              ------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......eee..eee.....eeeeeee...----------hhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhh...eeee.......hhhhhhh....eeeee.................hhhhhhhhhhhhhhhhhhhh..hhh.eeee.........hhhhhhhhhhhhhhh...........ee....hhhhhh.....hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y5s B   2 STFLPAPLQCGRFELTFERPLVMGILNATP----------ARDDALRRAERMIAEGADLLDIGGESTRPGAPPVPLDEELARVIPLVEALRPLNVPLSIDTYKPAVMRAALAAGADLINDIWGFRQPGAIDAVRDGNSGLCAMHMLGEPQTMQVGEPDYGDVVTDVRDFLAARAQALRDAGVAAERICVDPGFGFGKAVVDDNYALLAALPDTAPARPDGRAYPILAGMSRKSMLGAVIGGKPPLERVAASVAAALCAVERGAAIVRVHDVAATVDALSVWNAVRAAARQR 292
                                    11        21        31         -|       51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291 
                                                        31         42

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/Biological 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: automated matches (3)

Protein domain: automated matches (3)

Burkholderia cenocepacia [TaxId: 95486] (2)

1a	d2y5sa_	A:
1b	d2y5sb_	B:

(no "CATH Domain" information available for 2Y5S)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: Pterin_bind (18)

Burkholderia cepacia (strain J2315 / LMG 16656) (Burkholderia cenocepacia (strain J2315)) (2)

1a	Pterin_bind-2y5sB01	B:26-237
1b	Pterin_bind-2y5sB02	B:26-237

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (B4E5F5_BURCJ | B4E5F5)

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/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ser B:2 - Thr B:3	[ RasMol ]

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	2y5s
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	B4E5F5_BURCJ \| B4E5F5	:	2y5j

2y5j	CRYSTAL STRUCTURE OF BURKHOLDERIA CENOCEPACIA DIHYDROPTEROATE SYNTHASE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 20)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (8, 8)

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