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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF ISPD FROM MYCOBACTERIUM SMEGMATIS 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 :   1.49

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 1-219
	Organism Scientific	:	MYCOBACTERIUM SMEGMATIS
	Organism Taxid	:	1772
	Strain	:	MC2
	Synonym	:	4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP CYTIDYLYL TRANSFERASE, CDP-ME SYNTHETASE, ISPD

		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 , HOH A:2259 , HOH A:2260 , HOH A:2264	BINDING SITE FOR RESIDUE MG A 300
2	AC2	SOFTWARE	PRO A:8 , ALA A:9 , ALA A:10 , GLY A:11 , SER A:12 , GLY A:13 , GLU A:14 , ARG A:15 , LYS A:22 , GLY A:76 , VAL A:77 , ASP A:78 , ARG A:79 , SER A:82 , ASP A:100 , ALA A:101 , ALA A:102 , LYS A:204 , MG A:300 , HOH A:2044 , HOH A:2122 , HOH A:2259 , HOH A:2260 , HOH A:2261 , HOH A:2262 , HOH A:2263 , HOH A:2264 , HOH A:2265 , HOH A:2266	BINDING SITE FOR RESIDUE CTP A 301
3	AC3	SOFTWARE	CTP B:301 , HOH B:2198 , HOH B:2201 , HOH B:2203	BINDING SITE FOR RESIDUE MG B 300
4	AC4	SOFTWARE	PRO B:8 , ALA B:9 , ALA B:10 , GLY B:11 , SER B:12 , GLY B:13 , GLU B:14 , ARG B:15 , LYS B:22 , GLY B:76 , VAL B:77 , ASP B:78 , ARG B:79 , SER B:82 , ASP B:100 , ALA B:101 , ALA B:102 , LYS B:204 , MG B:300 , HOH B:2195 , HOH B:2197 , HOH B:2198 , HOH B:2199 , HOH B:2200 , HOH B:2201 , HOH B:2202 , HOH B:2203	BINDING SITE FOR RESIDUE CTP B 301

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

Asymmetric/Biological Unit

No.	Residues
1	Thr A:158	-	Pro A:159
2	Thr B:158	-	Pro B:159

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

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

(no "Exon" information available for 2XWL)

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 A0R560_MYCS2 | A0R560 from UniProtKB/TrEMBL  Length:222

    Alignment length:221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 
         A0R560_MYCS2     2 ATVAVVPAAGSGERLRAGRPKAFVTLGGTPLLEHALSGLRASGVIDRIVIAVPPALTDESKLVFGGEDSVIVSGGVDRTESVALALEAAGDAEFVLVHDAARALTPPALIARVVAALKEGHSAVVPGLAPADTIKAVDANGAVLGTPERAGLRAVQTPQGFHADVLRRAYARATAGGVTDDASLVEQLGTPVQIVDGDPLAFKITTPLDLVLAEAVLARGA 222
               SCOP domains d2xwla_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhh...hhhh.ee..eehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhh....eeeee...hhhhhhhhhhh......eeee........hhhhhhhhhhhhhhh..eeeeee.....eeee.....eee..hhh.eeee...eeeehhhhhhhhh........hhhhhhhh.....eeee.hhhhh...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xwl A   2 ATVAVVPAAGSGERLRAGRPKAFVTLGGTPLLEHALSGLRASGVIDRIVIAVPPALTDESKLVFGGEDSVIVSGGVDRTESVALALEAAGDAEFVLVHDAARALTPPALIARVVAALKEGHSAVVPGLAPADTIKAVDANGAVLGTPERAGLRAVQTPQGFHADVLRRAYARATAGGVTDDASLVEQLGTPVQIVDGDPLAFKITTPLDLVLAEAVLAHHH 222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with A0R560_MYCS2 | A0R560 from UniProtKB/TrEMBL  Length:222

    Alignment length:222
                                                                                                                                                                                                                                                      222 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221| 
         A0R560_MYCS2     2 ATVAVVPAAGSGERLRAGRPKAFVTLGGTPLLEHALSGLRASGVIDRIVIAVPPALTDESKLVFGGEDSVIVSGGVDRTESVALALEAAGDAEFVLVHDAARALTPPALIARVVAALKEGHSAVVPGLAPADTIKAVDANGAVLGTPERAGLRAVQTPQGFHADVLRRAYARATAGGVTDDASLVEQLGTPVQIVDGDPLAFKITTPLDLVLAEAVLARGA-   -
               SCOP domains d2xwlb_ B: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -IspD-2xwlB01 B:3-219                                                                                                                                                                                                     ---- Pfam domains (1)
           Pfam domains (2) -IspD-2xwlB02 B:3-219                                                                                                                                                                                                     ---- Pfam domains (2)
         Sec.struct. author .eeeeee............hhhh.ee..eehhhhhhhhhhhh....eeeeeehhhhhhhhhhhhh...eeeee...hhhhhhhhhhh......eeee........hhhhhhhhhhhhhhh..eeeeee.....eeee.....eee..hhh.eeee...eeeehhhhhhhhh........hhhhhhhh.....eeee.hhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xwl B   2 ATVAVVPAAGSGERLRAGRPKAFVTLGGTPLLEHALSGLRASGVIDRIVIAVPPALTDESKLVFGGEDSVIVSGGVDRTESVALALEAAGDAEFVLVHDAARALTPPALIARVVAALKEGHSAVVPGLAPADTIKAVDANGAVLGTPERAGLRAVQTPQGFHADVLRRAYARATAGGVTDDASLVEQLGTPVQIVDGDPLAFKITTPLDLVLAEAVLAHHHH 223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

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 smegmatis [TaxId: 1772] (1)

1a	d2xwla_	A:
1b	d2xwlb_	B:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GT-A (172)

Family: IspD (16)

Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (2)

1a	IspD-2xwlB01	B:3-219
1b	IspD-2xwlB02	B:3-219

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (A0R560_MYCS2 | A0R560)

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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:158 - Pro A:159	[ RasMol ]
		Thr B:158 - Pro B:159	[ RasMol ]

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	2xwl
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	2.7.7.60
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	A0R560_MYCS2 \| A0R560	:	2xwm

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

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)

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Exons (0, 0)

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