3RE3 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE FROM FRANCISELLA TULARENSIS

Authors :   Y. Kim, M. Makowska-Grzyska, K. Kwon, W. F. Anderson, A. Joachimiak, Ce Structural Genomics Of Infectious Diseases (Csgid)

Date :   02 Apr 11 (Deposition) - 27 Apr 11 (Release) - 27 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (3x)
Biol. Unit 2: B,C,D  (1x)
Biol. Unit 3: A,B,C,D  (3x)

Keywords :   Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha-Beta Half Sandwich, Cytosol, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, M. Makowska-Grzyska, K. Kwon, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of 2-C-Methyl-D-Erythritol 2, 4-Cyclodiphosphate Synthase From Francisella Tularensis
To Be Published
PubMed: search

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
	Chains	:	A, B, C, D
	EC Number	:	4.6.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21 MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	FTT_1128, ISPF
	Organism Scientific	:	FRANCISELLA TULARENSIS SUBSP. TULARENSIS
	Organism Taxid	:	177416
	Strain	:	SCHU S4
	Synonym	:	MECDP-SYNTHASE, MECPS

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (3x)	:	A
Biological Unit 2 (1x)	:		B	C	D
Biological Unit 3 (3x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 28)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
4	NA	3	Ligand/Ion	SODIUM ION
5	PO4	3	Ligand/Ion	PHOSPHATE ION
6	POP	2	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 1 (3, 18)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
4	NA	-1	Ligand/Ion	SODIUM ION
5	PO4	3	Ligand/Ion	PHOSPHATE ION
6	POP	3	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 2 (4, 17)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
4	NA	-1	Ligand/Ion	SODIUM ION
5	PO4	2	Ligand/Ion	PHOSPHATE ION
6	POP	1	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 3 (4, 69)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MPD	6	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MSE	48	Mod. Amino Acid	SELENOMETHIONINE
4	NA	-1	Ligand/Ion	SODIUM ION
5	PO4	9	Ligand/Ion	PHOSPHATE ION
6	POP	6	Ligand/Ion	PYROPHOSPHATE 2-

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:10 , VAL A:11 , HIS A:12 , GLY A:40 , VAL A:42 , HIS A:45 , GLU A:138	BINDING SITE FOR RESIDUE POP A 163
02	AC2	SOFTWARE	ARG A:4 , GLY A:53 , ALA A:54 , ASN A:96 , ILE A:97 , ASN A:131	BINDING SITE FOR RESIDUE NA A 165
03	AC3	SOFTWARE	GLY A:141 , ARG A:145 , PO4 A:161	BINDING SITE FOR RESIDUE CL A 160
04	AC4	SOFTWARE	GLY A:141 , PHE A:142 , CL A:160 , HOH A:187	BINDING SITE FOR RESIDUE PO4 A 161
05	AC5	SOFTWARE	ASP B:10 , VAL B:11 , HIS B:12 , ASP B:39 , GLY B:40 , VAL B:42 , HIS B:45 , HOH B:165 , THR C:136 , GLU C:138 , HOH C:171	BINDING SITE FOR RESIDUE POP B 161
06	AC6	SOFTWARE	ASN B:96 , ILE B:97 , ASN B:131 , ARG D:4 , GLY D:53	BINDING SITE FOR RESIDUE NA B 160
07	AC7	SOFTWARE	HIS B:152 , HIS C:152 , HOH C:170 , HIS D:152	BINDING SITE FOR RESIDUE PO4 C 162
08	AC8	SOFTWARE	GLY B:141 , PHE B:142 , GLY C:141 , PHE C:142 , HOH C:169 , PHE D:142 , PO4 D:162	BINDING SITE FOR RESIDUE MPD C 163
09	AC9	SOFTWARE	ARG C:4 , GLY C:53 , ALA C:54 , ASN D:96 , ILE D:97 , ASN D:131	BINDING SITE FOR RESIDUE NA C 161
10	BC1	SOFTWARE	ASP C:10 , VAL C:11 , HIS C:45 , HOH C:166 , THR D:135 , THR D:136 , GLU D:138	BINDING SITE FOR RESIDUE MPD C 160
11	BC2	SOFTWARE	GLY B:141 , ARG B:145 , GLY C:141 , ARG C:145 , MPD C:163 , GLY D:141 , PHE D:142 , ARG D:145	BINDING SITE FOR RESIDUE PO4 D 162
12	BC3	SOFTWARE	ASP D:10	BINDING SITE FOR RESIDUE CL D 160

(no "SS Bond" information available for 3RE3)

Asymmetric Unit

No.	Residues
1	Ala A:105	-	Pro A:106
2	Ala B:105	-	Pro B:106
3	Ala C:105	-	Pro C:106
4	Ala D:105	-	Pro D:106

(no "SAP(SNP)/Variant" information available for 3RE3)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPF	PS01350	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.	ISPF_FRATT	38-53	4	A:39-53 B:39-53 C:39-53 D:40-53

Biological Unit 1 (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_FRATT	38-53	3	A:39-53 - - -

Biological Unit 2 (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_FRATT	38-53	3	- B:39-53 C:39-53 D:40-53

Biological Unit 3 (1, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPF	PS01350	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.	ISPF_FRATT	38-53	12	A:39-53 B:39-53 C:39-53 D:40-53

(no "Exon" information available for 3RE3)

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:148
 aligned with ISPF_FRATT | Q5NFU1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:161
                              1                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
           ISPF_FRATT     - --MSFRIGHGYDVHKFTSAKQNIIIGGVEIAYHLGLEAHSDGDVLIHALCDAILGALGLGDIGKHFLDTDNQFKNIDSKFFLAEIKKMLDKKQYSISNIDCTIIAQAPKMLPHIEKMRACLANILEIQISQINIKATTTERLGFIGREEGIATHVVCLLYR 159
               SCOP domains d3re3a_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee.......eee..eee....------..hhhhhhhhhhhhhhh...hhhhhh-------...hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3re3 A  -1 NAmSFRIGHGYDVHKFTSAKQNIIIGGVEIAYHL------DGDVLIHALCDAILGALGLGDIGKHF-------KNIDSKFFLAEIKKmLDKKQYSISNIDCTIIAQAPKmLPHIEKmRACLANILEIQISQINIKATTTERLGFIGREEGIATHVVCLLYR 159
                              |      8        18        28   |     -|       48        58     |   -   |    78       |88        98       108      |118       128       138       148       158 
                              |                             32     39                       64      72            86-MSE               108-MSE  |                                            
                              1-MSE                                                                                                           115-MSE

Chain B from PDB  Type:PROTEIN  Length:144
 aligned with ISPF_FRATT | Q5NFU1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
           ISPF_FRATT     1 MSFRIGHGYDVHKFTSAKQNIIIGGVEIAYHLGLEAHSDGDVLIHALCDAILGALGLGDIGKHFLDTDNQFKNIDSKFFLAEIKKMLDKKQYSISNIDCTIIAQAPKMLPHIEKMRACLANILEIQISQINIKATTTERLGFIGREEGIATHVVCLLYR 159
               SCOP domains d3re3b_ B: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.......eee..eee...-------..hhhhhhhhhhhhhhh...hhhhh.--------..hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3re3 B   1 mSFRIGHGYDVHKFTSAKQNIIIGGVEIAYH-------DGDVLIHALCDAILGALGLGDIGKHF--------NIDSKFFLAEIKKmLDKKQYSISNIDCTIIAQAPKmLPHIEKmRACLANILEIQISQINIKATTTERLGFIGREEGIATHVVCLLYR 159
                            |       10        20        30|       40        50        60   |     -  |     80     |  90       100       110    |  120       130       140       150         
                            1-MSE                        31      39                       64       73           86-MSE               108-MSE  |                                            
                                                                                                                                            115-MSE

Chain C from PDB  Type:PROTEIN  Length:147
 aligned with ISPF_FRATT | Q5NFU1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
           ISPF_FRATT     1 MSFRIGHGYDVHKFTSAKQNIIIGGVEIAYHLGLEAHSDGDVLIHALCDAILGALGLGDIGKHFLDTDNQFKNIDSKFFLAEIKKMLDKKQYSISNIDCTIIAQAPKMLPHIEKMRACLANILEIQISQINIKATTTERLGFIGREEGIATHVVCLLYR 159
               SCOP domains d3re3c_ C: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.....eeeee..eeeee....----..hhhhhhhhhhhhhhhh..hhhhhh--------..hhhhhhhhhhhhhhh...eeeeeeeeee........hhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3re3 C   1 mSFRIGHGYDVHKFTSAKQNIIIGGVEIAYHLGL----DGDVLIHALCDAILGALGLGDIGKHF--------NIDSKFFLAEIKKmLDKKQYSISNIDCTIIAQAPKmLPHIEKmRACLANILEIQISQINIKATTTERLGFIGREEGIATHVVCLLYR 159
                            |       10        20        30   |    40        50        60   |     -  |     80     |  90       100       110    |  120       130       140       150         
                            1-MSE                           34   39                       64       73           86-MSE               108-MSE  |                                            
                                                                                                                                            115-MSE

Chain D from PDB  Type:PROTEIN  Length:144
 aligned with ISPF_FRATT | Q5NFU1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:160
                             1                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
           ISPF_FRATT     - -MSFRIGHGYDVHKFTSAKQNIIIGGVEIAYHLGLEAHSDGDVLIHALCDAILGALGLGDIGKHFLDTDNQFKNIDSKFFLAEIKKMLDKKQYSISNIDCTIIAQAPKMLPHIEKMRACLANILEIQISQINIKATTTERLGFIGREEGIATHVVCLLYR 159
               SCOP domains d3re3d_ D: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---YgbB-3re3D01 D:3-159                                                                                                                                          Pfam domains (1)
           Pfam domains (2) ---YgbB-3re3D02 D:3-159                                                                                                                                          Pfam domains (2)
           Pfam domains (3) ---YgbB-3re3D03 D:3-159                                                                                                                                          Pfam domains (3)
           Pfam domains (4) ---YgbB-3re3D04 D:3-159                                                                                                                                          Pfam domains (4)
         Sec.struct. author ..eeeeeeeeeeee.......eee..eee...--------.hhhhhhhhhhhhhhh...hhhhhh--------..hhhhhhhhhhhhhhhh..eeeeeeeeee........hhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3re3 D   0 AmSFRIGHGYDVHKFTSAKQNIIIGGVEIAYH--------GDVLIHALCDAILGALGLGDIGKHF--------NIDSKFFLAEIKKmLDKKQYSISNIDCTIIAQAPKmLPHIEKmRACLANILEIQISQINIKATTTERLGFIGREEGIATHVVCLLYR 159
                             |       9        19        29 |       -|       49        59    |    -   |    79      | 89        99       109     | 119       129       139       149       159
                             1-MSE                        31       40                      64       73           86-MSE               108-MSE  |                                            
                                                                                                                                             115-MSE

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) (23004)

Fold: Bacillus chorismate mutase-like (324)

Superfamily: IpsF-like (56)

Family: automated matches (21)

Protein domain: automated matches (21)

Francisella tularensis [TaxId: 177416] (1)

1a	d3re3a_	A:
1b	d3re3b_	B:
1c	d3re3c_	C:
1d	d3re3d_	D:

(no "CATH Domain" information available for 3RE3)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: YgbB] (24)

Family: YgbB (24)

Francisella tularensis subsp. tularensis (1)

1a	YgbB-3re3D01	D:3-159
1b	YgbB-3re3D02	D:3-159
1c	YgbB-3re3D03	D:3-159
1d	YgbB-3re3D04	D:3-159

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ISPF_FRATT | Q5NFU1)

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.

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	Cis Peptide Bonds
		Ala A:105 - Pro A:106	[ RasMol ]
		Ala B:105 - Pro B:106	[ RasMol ]
		Ala C:105 - Pro C:106	[ RasMol ]
		Ala D:105 - Pro D:106	[ RasMol ]

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	3re3
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Description

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Ligands, Modified Residues, Ions (6, 28)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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