3N9W - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE (ISPD) IN COMPLEX WITH 1,2-PROPANEDIOL

Authors :   J. Behnen, A. Heine, G. Klebe

Date :   31 May 10 (Deposition) - 25 May 11 (Release) - 15 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Ygbp, Cytidylyltransferase, Deoxyxylulose-5-Phosphate Pathway (Dxp), Isoprenoid Biosynthesis, 1, 2-Propanediol, Fbld, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Behnen, H. Koster, G. Neudert, T. Craan, A. Heine, G. Klebe
Experimental And Computational Active Site Mapping As A Starting Point To Fragment-Based Lead Discovery.
Chemmedchem V. 7 248 2012
PubMed-ID: 22213702 | Reference-DOI: 10.1002/CMDC.201100490

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.7.7.60
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP CYTIDYLYLTRANSFERASE, MCT, CDP-ME SYNTHASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	PGO	2	Ligand/Ion	S-1,2-PROPANEDIOL
2	PGR	1	Ligand/Ion	R-1,2-PROPANEDIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:106 , ARG A:109 , ALA A:163 , THR A:165 , ASP A:190	BINDING SITE FOR RESIDUE PGO A 3002
2	AC2	SOFTWARE	ALA A:135 , ARG A:138 , HIS A:162 , ALA A:209	BINDING SITE FOR RESIDUE PGO A 3003
3	AC3	SOFTWARE	ASP A:139 , THR A:140 , ASP B:106 , ARG B:109 , ALA B:163 , LYS B:213	BINDING SITE FOR RESIDUE PGR B 3001

(no "SS Bond" information available for 3N9W)

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 3N9W)

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_ECOLI	102-109	2	A:102-109 B:102-109

(no "Exon" information available for 3N9W)

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:195
 aligned with ISPD_ECOLI | Q46893 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:223
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225   
           ISPD_ECOLI     6 LDVCAVVPAAGFGRRMQTECPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVDGGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLT 228
               SCOP domains d3n9wa_ A:                   automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..------------------hhhhhhhhhhhhhh...eeeeeeee----------hhhhh..eeeee...hhhhhhhhhhh......eeee........hhhhhhhhhhhhhh....eeeeee....eeee......eeeee....eeeeeeeeeeehhhhhhhhhhhhhh.....hhhhhhhhhh...eeee.........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ISPD    ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n9w A   6 LDVCAVVPAA------------------NQTILEHSVHALLAHPRVKRVVIAI----------PLANHPQITVVDGGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLT 228
                                    15         -        35        45        55  |      -   |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225   
                                    15                 34                      58         69

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with ISPD_ECOLI | Q46893 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:230
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235
           ISPD_ECOLI     6 LDVCAVVPAAGFGRRMQTECPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVDGGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLTRTIHQEN 235
               SCOP domains d3n9wb_ B:           automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --IspD-3n9w          B01 B:8-229                                                                                                                                                                                                ------ Pfam domains (1)
           Pfam domains (2) --IspD-3n9w          B02 B:8-229                                                                                                                                                                                                ------ Pfam domains (2)
         Sec.struct. author ..eeeeeee..----------....ee..eehhhhhhhhhh....eeeeeeee.....hhhhhhhhhh..eeeee...hhhhhhhhhhh......eeee........hhhhhhhhhhhhhhh...eeeeee....eeee......eeee.....eeeeeeeeeeehhhhhhhhhhhhhh......hhhhhhhh....eeee...........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n9w B   6 LDVCAVVPAAG----------KQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVDGGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLTRTIHQEN 235
                                    15|        - |      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235
                                     16         27

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: Cytidylytransferase (43)

Protein domain: automated matches (7)

Escherichia coli K-12 [TaxId: 83333] (2)

1a	d3n9wa_	A:
1b	d3n9wb_	B:

(no "CATH Domain" information available for 3N9W)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GT-A (172)

Family: IspD (16)

Escherichia coli (strain K12) (3)

1a	IspD-3n9wB01	B:8-229
1b	IspD-3n9wB02	B:8-229

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ISPD_ECOLI | Q46893)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		PGO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PGR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Thr A:165 - Pro A:166	[ RasMol ]
		Thr B:165 - Pro B:166	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3n9w
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ISPD_ECOLI \| Q46893
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.7.60
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ISPD_ECOLI \| Q46893
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ISPD_ECOLI \| Q46893	:	1h3m 1i52 1ini 1inj 1vgt 1vgu

(no "Related Entries Specified in the PDB File" available for 3N9W)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

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

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File