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Title :   SYNTHESIS OF CDP-ACTIVATED RIBITOL FOR TEICHOIC ACID PRECURSORS IN STREPTOCOCCUS PNEUMONIAE

Authors :   S. Baur, J. Marles-Wright, S. Buckenmaier, R. J. Lewis, W. Vollmer

Date :   23 Apr 08 (Deposition) - 30 Dec 08 (Release) - 10 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Transferase, Nucleotidyltransferase, Tari Spr1149 Cdp Ribitol Streptococcus Pneumoniae Techoic Transferase, Isoprene Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Baur, J. Marles-Wright, S. Buckenmaier, R. J. Lewis, W. Vollmer
Synthesis Of Cdp-Activated Ribitol For Teichoic Acid Precursors In Streptococcus Pneumoniae.
J. Bacteriol. V. 191 1200 2009
PubMed-ID: 19074383 | Reference-DOI: 10.1128/JB.01120-08

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
	Atcc	:	12214
	Chains	:	A, B
	EC Number	:	2.7.7.60
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	1313
	Strain	:	R36A
	Synonym	:	TARI

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 8)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	CA	2	Ligand/Ion	CALCIUM ION
3	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL
4	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:97 , HOH A:2075 , HOH A:2076 , HOH B:2029 , HOH B:2030 , HOH B:2034	BINDING SITE FOR RESIDUE CA A1234
2	AC2	SOFTWARE	HIS A:54 , GLY A:55 , LYS A:80 , HOH A:2161	BINDING SITE FOR RESIDUE PEG A1235
3	AC3	SOFTWARE	ASP A:134 , LEU A:181 , LYS A:203 , GLY A:204 , LYS A:205	BINDING SITE FOR RESIDUE 1PE A1236
4	AC4	SOFTWARE	ARG A:100 , PRO A:101 , LEU B:102 , LYS B:176	BINDING SITE FOR RESIDUE PG4 A1237
5	AC5	SOFTWARE	GLY A:204 , ASP A:206 , PHE B:154	BINDING SITE FOR RESIDUE PEG A1238
6	AC6	SOFTWARE	THR A:119 , LEU A:120 , ARG A:121 , SER A:186 , GLU A:188 , HOH A:2088	BINDING SITE FOR RESIDUE PEG A1239
7	AC7	SOFTWARE	HOH A:2127 , HOH A:2132	BINDING SITE FOR RESIDUE CA A1240
8	AC8	SOFTWARE	ASP B:134 , ASP B:177 , LEU B:181 , LYS B:203 , GLY B:204 , LYS B:205 , HOH B:2078	BINDING SITE FOR RESIDUE P6G B1233

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

Asymmetric/Biological Unit

No.	Residues
1	Thr A:169	-	Pro A:170
2	Thr B:169	-	Pro B:170

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

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.	TARI_STRR6	108-115	2	A:108-115 B:108-115

(no "Exon" information available for 2VSH)

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:223
 aligned with TARI_STRR6 | Q8DPI2 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:234
                             1                                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229    
           TARI_STRR6     - -MIYAGILAGGTGTRMGISNLPKQFLELGDRPILIHTIEKFVLEPSIEKIVVGVHGDWVSHAEDLVDKYLPLYKERIIITKGGADRNTSIKNIIEAIDAYRPLTPEDIVVTHDSVRPFITLRMIQDNIQLAQNHDAVDTVVEAVDTIVESTNGQFITDIPNRAHLYQGQTPQTFRCKDFMDLYGSLSDEEKEILTDACKIFVIKGKDVALAKGEYSNLKITTVTDLKIAKSMIE 233
               SCOP domains d2vsha_ A:            automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.-----------hhhh.ee..eehhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhhhhhh.eeeeeee....eee...........hhh.eeeeeeeeeeehhhhhhhhhh.hhhhhhhh.hhhhhhhhh...eeeee.........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ISPD    ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vsh A   0 HMIYAGILAG-----------PKQFLELGDRPILIHTIEKFVLEPSIEKIVVGVHGDWVSHAEDLVDKYLPLYKERIIITKGGADRNTSIKNIIEAIDAYRPLTPEDIVVTHDSVRPFITLRMIQDNIQLAQNHDAVDTVVEAVDTIVESTNGQFITDIPNRAHLYQGQTPQTFRCKDFMDLYGSLSDEEKEILTDACKIFVIKGKDVALAKGEYSNLKITTVTDLKIAKSMIE 233
                                     9         - |      29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229    
                                     9          21

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with TARI_STRR6 | Q8DPI2 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:233
                             1                                                                                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229   
           TARI_STRR6     - -MIYAGILAGGTGTRMGISNLPKQFLELGDRPILIHTIEKFVLEPSIEKIVVGVHGDWVSHAEDLVDKYLPLYKERIIITKGGADRNTSIKNIIEAIDAYRPLTPEDIVVTHDSVRPFITLRMIQDNIQLAQNHDAVDTVVEAVDTIVESTNGQFITDIPNRAHLYQGQTPQTFRCKDFMDLYGSLSDEEKEILTDACKIFVIKGKDVALAKGEYSNLKITTVTDLKIAKSMI 232
               SCOP domains d2vshb_ B:            automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.-----------hhhh.ee..eehhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhhhhh..eeeeeee....eee...........hhh.eeeeeeeeeeehhhhhhhhhh.hhhhhhhh.hhhhhhhhh...eeeee.........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ISPD    --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vsh B   0 HMIYAGILAG-----------PKQFLELGDRPILIHTIEKFVLEPSIEKIVVGVHGDWVSHAEDLVDKYLPLYKERIIITKGGADRNTSIKNIIEAIDAYRPLTPEDIVVTHDSVRPFITLRMIQDNIQLAQNHDAVDTVVEAVDTIVESTNGQFITDIPNRAHLYQGQTPQTFRCKDFMDLYGSLSDEEKEILTDACKIFVIKGKDVALAKGEYSNLKITTVTDLKIAKSMI 232
                                     9         - |      29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229   
                                     9          21

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)

Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313] (2)

1a	d2vsha_	A:
1b	d2vshb_	B:

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

(no "Pfam Domain" information available for 2VSH)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TARI_STRR6 | Q8DPI2)

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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Thr A:169 - Pro A:170	[ RasMol ]
		Thr B:169 - Pro B:170	[ RasMol ]

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	2vsh
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	TARI_STRR6 \| Q8DPI2	:	2vsi

2vsi	SYNTHESIS OF CDP-ACTIVATED RIBITOL FOR TEICHOIC ACID PRECURSORS IN STREPTOCOCCUS PNEUMONIAE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 8)

Sites (8, 8)

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)

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Pfam Domains (0, 0)

Gene Ontology (7, 7)

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