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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ISPD FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH CTP AND MG

Authors :   C. Bjorkelid, T. Bergfors, T. Unge, T. A. Jones

Date :   04 Nov 10 (Deposition) - 27 Apr 11 (Release) - 01 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Transferase, Mep Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Bjorkelid, T. Bergfors, L. M. Henriksson, A. L. Stern, T. Unge, S. L. Mowbray, T. A. Jones
Structural And Functional Studies On Mycobacterial Ispd Enzymes
Acta Crystallogr. , Sect. D V. 67 403 2011
PubMed-ID: 21543842 | Reference-DOI: 10.1107/S0907444911006160

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.7.7.60
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEXP5CT/TOPO
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	AI
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-229
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP CYTIDYLYLTRANSFERASE, MCT, ISPD, CDP-ME SYNTHETASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CTP	2	Ligand/Ion	CYTIDINE-5'-TRIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CTP A:301	BINDING SITE FOR RESIDUE MG A 300
2	AC2	SOFTWARE	PRO A:13 , ALA A:14 , ALA A:15 , GLY A:16 , SER A:17 , GLY A:18 , GLU A:19 , ARG A:20 , LYS A:27 , GLY A:80 , SER A:81 , ASN A:82 , ARG A:83 , THR A:86 , ASP A:107 , ALA A:108 , ALA A:109 , LYS A:215 , MG A:300	BINDING SITE FOR RESIDUE CTP A 301
3	AC3	SOFTWARE	CTP B:301	BINDING SITE FOR RESIDUE MG B 300
4	AC4	SOFTWARE	PRO B:13 , ALA B:14 , ALA B:15 , GLY B:16 , SER B:17 , GLY B:18 , GLU B:19 , ARG B:20 , LYS B:27 , GLY B:80 , SER B:81 , ASN B:82 , ARG B:83 , THR B:86 , ASP B:107 , ALA B:108 , ALA B:109 , LYS B:215 , MG B:300	BINDING SITE FOR RESIDUE CTP B 301

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

Asymmetric/Biological Unit

No.	Residues
1	Thr A:165	-	Pro A:166
2	Thr B:165	-	Pro B:166

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPD	PS01295	4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.	ISPD_MYCTO	103-110	2	A:103-110 B:103-110
1	ISPD	PS01295		ISPD_MYCTU	103-110	2	A:103-110 B:103-110

(no "Exon" information available for 2XWN)

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:221
 aligned with ISPD_MYCTO | P9WKG8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:227
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       
           ISPD_MYCTO     5 AGEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
               SCOP domains d2xwna_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhh...hhhh.ee..eehhhhhhhhhhh.....eeeeeehhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh.......eeee........hhhhhhhhhhhhhh...eeeeee.....eeee.....eee..hhh.eeee...eeeehhhhhhhhh...------...hhhhhhhhh...eeeee.hhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xwn A   5 AGEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGS------EYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVHH 231
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       | -    |  194       204       214       224       
                                                                                                                                                                                                           182    189

Chain A from PDB  Type:PROTEIN  Length:221
 aligned with ISPD_MYCTU | P9WKG9 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:227
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       
           ISPD_MYCTU     5 AGEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
               SCOP domains d2xwna_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhh...hhhh.ee..eehhhhhhhhhhh.....eeeeeehhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh.......eeee........hhhhhhhhhhhhhh...eeeeee.....eeee.....eee..hhh.eeee...eeeehhhhhhhhh...------...hhhhhhhhh...eeeee.hhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xwn A   5 AGEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGS------EYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVHH 231
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       | -    |  194       204       214       224       
                                                                                                                                                                                                           182    189

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with ISPD_MYCTO | P9WKG8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:227
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       
           ISPD_MYCTO     5 AGEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
               SCOP domains d2xwnb_ B: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---IspD-2xwnB01 B:8-229                                                                                                                                                                                                          -- Pfam domains (1)
           Pfam domains (2) ---IspD-2xwnB02 B:8-229                                                                                                                                                                                                          -- Pfam domains (2)
         Sec.struct. author ...eeeeee............hhhh.ee..eehhhhhhhhhhh.....eeeeeehhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh.......eeee........hhhhhhhhhhhhhh...eeeeee....eeeee.....eee......eeee...eeeehhhhhhhhh............hhhhhhhhh...eeeee.hhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xwn B   5 AGEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVHH 231
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with ISPD_MYCTU | P9WKG9 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:227
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       
           ISPD_MYCTU     5 AGEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
               SCOP domains d2xwnb_ B: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---IspD-2xwnB01 B:8-229                                                                                                                                                                                                          -- Pfam domains (1)
           Pfam domains (2) ---IspD-2xwnB02 B:8-229                                                                                                                                                                                                          -- Pfam domains (2)
         Sec.struct. author ...eeeeee............hhhh.ee..eehhhhhhhhhhh.....eeeeeehhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh.......eeee........hhhhhhhhhhhhhh...eeeeee....eeeee.....eee......eeee...eeeehhhhhhhhh............hhhhhhhhh...eeeee.hhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xwn B   5 AGEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVHH 231
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224

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: Nucleotide-diphospho-sugar transferases (408)

Superfamily: Nucleotide-diphospho-sugar transferases (408)

Family: automated matches (48)

Protein domain: automated matches (48)

Mycobacterium tuberculosis [TaxId: 83332] (7)

1a	d2xwna_	A:
1b	d2xwnb_	B:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GT-A (172)

Family: IspD (16)

Mycobacterium tuberculosis (4)

1a	IspD-2xwnB01	B:8-229
1b	IspD-2xwnB02	B:8-229

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ISPD_MYCTU | P9WKG9)

molecular function
	GO:0050518	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity	Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.
	GO:0002135	CTP binding	Interacting selectively and non-covalently with CTP, cytidine 5'-triphosphate.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	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:0051484	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway that contributes to terpenoid biosynthesis. 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.
cellular component
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B (ISPD_MYCTO | P9WKG8)

molecular function
	GO:0050518	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity	Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	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: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
		Thr A:165 - Pro A:166	[ RasMol ]
		Thr B:165 - Pro B:166	[ RasMol ]

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	2xwn
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	ISPD_MYCTO \| P9WKG8
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	ISPD_MYCTU \| P9WKG9
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	2.7.7.60
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	ISPD_MYCTO \| P9WKG8
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UniProtKB/Swiss-Prot
	ISPD_MYCTO \| P9WKG8	:	3okr 3q7u 3q80
	ISPD_MYCTU \| P9WKG9	:	3okr 3q7u 3q80

2xwl	CRYSTAL STRUCTURE OF ISPD FROM MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH CTP AND MG
2xwm	CRYSTAL STRUCTURE OF ISPD FROM MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH CMP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (15, 22)

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