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Title :   CO-CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI WITH HYDROLYZED CDP

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   24 Oct 08 (Deposition) - 04 Nov 08 (Release) - 30 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

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

Keywords :   Ssgcid, Niaid, Burkholderia Pseudomallei, Isoprene Biosynthesis, Lyase, Metal-Binding, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Baugh, L. A. Gallagher, R. Patrapuvich, M. C. Clifton, A. S. Gardberg, T. E. Edwards, B. Armour, D. W. Begley, S. H. Dieterich, D. M. Dranow, J. Abendroth, J. W. Fairman, D. Fox, B. L. Staker, I. Phan, A. Gillespie, R. Choi, S. Nakazawa-Hewitt, M. T. Nguyen, A. Napuli, L. Barrett, G. W. Buchko, R. Stacy, P. J. Myler, L. J. Stewart, C. Manoil W. C. Van Voorhis
Combining Functional And Structural Genomics To Sample The Essential Burkholderia Structome.
Plos One V. 8 53851 2013
PubMed-ID: 23382856 | Reference-DOI: 10.1371/JOURNAL.PONE.0053851

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
	Chains	:	A, B, C
	EC Number	:	4.6.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	AVA0421
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ISPF, MECS, BPSL2098
	Organism Common	:	PSEUDOMONAS PSEUDOMALLEI
	Organism Scientific	:	BURKHOLDERIA PSEUDOMALLEI
	Organism Taxid	:	28450
	Strain	:	1710B
	Synonym	:	MECPS, MECDP-SYNTHASE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 6)

No.	Name	Count	Type	Full Name
1	C5P	1	Ligand/Ion	CYTIDINE-5'-MONOPHOSPHATE
2	GOL	1	Ligand/Ion	GLYCEROL
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	ZN	3	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:58 , GLY B:60 , HOH B:178 , ALA C:102 , PRO C:105 , LEU C:107 , ALA C:108 , ALA C:133 , LYS C:134 , THR C:135 , GLU C:137	BINDING SITE FOR RESIDUE C5P C 163
2	AC2	SOFTWARE	ASP A:10 , HIS A:12 , HIS A:44 , ZN A:165 , HOH A:175 , LYS B:134	BINDING SITE FOR RESIDUE GOL A 163
3	AC3	SOFTWARE	HOH A:201 , HOH C:165 , HOH C:217	BINDING SITE FOR RESIDUE MG A 164
4	AC4	SOFTWARE	ASP B:10 , HIS B:12 , HIS B:44 , HOH C:198	BINDING SITE FOR RESIDUE ZN B 163
5	AC5	SOFTWARE	HOH A:203 , ASP C:10 , HIS C:12 , HIS C:44	BINDING SITE FOR RESIDUE ZN C 164
6	AC6	SOFTWARE	ASP A:10 , HIS A:12 , HIS A:44 , GOL A:163	BINDING SITE FOR RESIDUE ZN A 165

(no "SS Bond" information available for 3F0F)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:104	-	Pro A:105
2	Ala B:104	-	Pro B:105
3	Ala C:104	-	Pro C:105

(no "SAP(SNP)/Variant" information available for 3F0F)

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPF	PS01350	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.	ISPF_BURP1	37-52	3	A:37-52 B:37-52 C:37-52
1	ISPF	PS01350		ISPF_BURPS	37-52	3	A:37-52 B:37-52 C:37-52

(no "Exon" information available for 3F0F)

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:159
 aligned with ISPF_BURP1 | Q3JRA0 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
           ISPF_BURP1     1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
               SCOP domains d3f0fa_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains 3f0fA00 A:1-159  [code=3.30.1330.50, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.....ee..ee.....ee......hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh..hhhhh..eee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f0f A   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain A from PDB  Type:PROTEIN  Length:159
 aligned with ISPF_BURPS | Q63T71 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
           ISPF_BURPS     1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
               SCOP domains d3f0fa_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains 3f0fA00 A:1-159  [code=3.30.1330.50, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.....ee..ee.....ee......hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh..hhhhh..eee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f0f A   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 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 ISPF_BURP1 | Q3JRA0 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
           ISPF_BURP1     1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
               SCOP domains d3f0fb_ B: automated matches                                                                                                                                    SCOP domains
               CATH domains 3f0fB00 B:1-159  [code=3.30.1330.50, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eee..eee....ee......hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f0f B   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 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 ISPF_BURPS | Q63T71 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
           ISPF_BURPS     1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
               SCOP domains d3f0fb_ B: automated matches                                                                                                                                    SCOP domains
               CATH domains 3f0fB00 B:1-159  [code=3.30.1330.50, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eee..eee....ee......hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f0f B   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:156
 aligned with ISPF_BURP1 | Q3JRA0 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
           ISPF_BURP1     1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
               SCOP domains d3f0fc_ C: automated matches                                                                                                                                    SCOP domains
               CATH domains 3f0fC00 C:1-159  [code=3.30.1330.50, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee...eee..eee...eeee.....hhhhhhhhhhhhhhh...hhhhhh.---......hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f0f C   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFS---PRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
                                    10        20        30        40        50        60   |   |70        80        90       100       110       120       130       140       150         
                                                                                          64  68

Chain C from PDB  Type:PROTEIN  Length:156
 aligned with ISPF_BURPS | Q63T71 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
           ISPF_BURPS     1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
               SCOP domains d3f0fc_ C: automated matches                                                                                                                                    SCOP domains
               CATH domains 3f0fC00 C:1-159  [code=3.30.1330.50, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee...eee..eee...eeee.....hhhhhhhhhhhhhhh...hhhhhh.---......hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f0f C   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFS---PRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
                                    10        20        30        40        50        60   |   |70        80        90       100       110       120       130       140       150         
                                                                                          64  68

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) (23004)

Fold: Bacillus chorismate mutase-like (324)

Superfamily: IpsF-like (56)

Family: automated matches (21)

Protein domain: automated matches (21)

Burkholderia pseudomallei [TaxId: 28450] (11)

1a	d3f0fa_	A:
1b	d3f0fb_	B:
1c	d3f0fc_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: [code=3.30.1330.50, no name defined] (46)

Pseudomonas pseudomallei (Burkholderia pseudomallei) (10)

1a	3f0fC00	C:1-159
1b	3f0fA00	A:1-159
1c	3f0fB00	B:1-159

(no "Pfam Domain" information available for 3F0F)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (ISPF_BURPS | Q63T71)

molecular function
	GO:0008685	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity	Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0019288	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
	GO:0008299	isoprenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
	GO:0016114	terpenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.

Chain A,B,C (ISPF_BURP1 | Q3JRA0)

molecular function
	GO:0008685	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity	Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0019288	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
	GO:0008299	isoprenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
	GO:0016114	terpenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:104 - Pro A:105	[ RasMol ]
		Ala B:104 - Pro B:105	[ RasMol ]
		Ala C:104 - Pro C:105	[ RasMol ]

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	3f0f
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3f0d	HIGH RESOLUTION STRUCTURE APO
3f0e	ALTERNATIVE CRYSTAL FORM APO RELATED ID: BUPSA.00122.A RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

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