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Title :   CRYSTAL STRUCTURE OF CDP-DIACYLGLYCEROL PYROPHOSPHATASE

Authors :   M. Madegowda, S. Eswaramoorthy, S. K. Burley, S. Swaminathan, New Yor Research Center For Structural Genomics (Nysgxrc)

Date :   26 Apr 07 (Deposition) - 15 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Nysgxrc, 10285A, Pfam02611, Psi-2, Phospholipid Biosynthesis, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Madegowda, S. Eswaramoorthy, S. K. Burley, S. Swaminathan
Crystal Structure Of Cdp-Diacylglycerol Pyrophosphatase.
To Be Published
PubMed: search

Molecule 1 - CDP-DIACYLGLYCEROL PYROPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.6.1.26
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PSGX4(BS)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 27-251
	Gene	:	CDH, Z5463, ECS4843
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83334
	Synonym	:	CDP-DIACYLGLYCEROL PHOSPHATIDYLHYDROLASE, CDP-DIGLYCERIDE HYDROLASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2POF)

Asymmetric Unit

No.	Residues
1	A:42	-	A:55
2	A:145	-	A:247
3	B:42	-	B:55
4	B:145	-	B:247

Asymmetric Unit

No.	Residues
1	Ser A:53	-	Pro A:54
2	Ser B:53	-	Pro B:54

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

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

(no "Exon" information available for 2POF)

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:220
 aligned with CDH_ECO57 | Q8X7A5 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:220
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
            CDH_ECO57    31 SDTLRKIVLEECLPNQQQNQNPSPCAEVKPNAGYVVLKDLNGPLQYLLMPTYRINGTESPLLTDPSTPNFFWLAWQARDFMSKKYGQPVPDRAVSLAINSRTGRTQNHFHIHISCIRPDVREQLDNNLANISSRWLPLPGGLRGHEYLARRVTESELVQRSPFMMLAEEVPEAREHMGSYGLAMVRQSDNSFVLLATQRNLLTLNRASAEEIQDHQCEIL 250
               SCOP domains d2pofa1 A:31-250 CDP-diacylglycerol pyrophosphatase CDH                                                                                                                                                                      SCOP domains
               CATH domains 2pofA00 A:31-250 HIT family -  CDH-like                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......ee.....eeeee.......eeeee........hhhhhh....hhhhhhhhhhhhhhhhhh...hhh.eeeee.hhhhh......eeeee.hhhhhhhhhhhhhhh....ee..........eeeeehhhhhhhhhhhhhhhhhh.....hhh.eeeeeee.....eeeeeee.........hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pof A  31 SDTLRKIVLEECLPNQQQNQNPSPCAEVKPNAGYVVLKDLNGPLQYLLmPTYRINGTESPLLTDPSTPNFFWLAWQARDFmSKKYGQPVPDRAVSLAINSRTGRTQNHFHIHISCIRPDVREQLDNNLANISSRWLPLPGGLRGHEYLARRVTESELVQRSPFmmLAEEVPEAREHmGSYGLAmVRQSDNSFVLLATQRNLLTLNRASAEEIQDHQCEIL 250
                                    40        50        60        70        80        90       100       110|      120       130       140       150       160       170       180       190   ||  200      |210   |   220       230       240       250
                                                                           79-MSE                         111-MSE                                                                            194-MSE      207-MSE  |                                    
                                                                                                                                                                                              195-MSE            214-MSE

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with CDH_ECO57 | Q8X7A5 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:220
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
            CDH_ECO57    31 SDTLRKIVLEECLPNQQQNQNPSPCAEVKPNAGYVVLKDLNGPLQYLLMPTYRINGTESPLLTDPSTPNFFWLAWQARDFMSKKYGQPVPDRAVSLAINSRTGRTQNHFHIHISCIRPDVREQLDNNLANISSRWLPLPGGLRGHEYLARRVTESELVQRSPFMMLAEEVPEAREHMGSYGLAMVRQSDNSFVLLATQRNLLTLNRASAEEIQDHQCEIL 250
               SCOP domains d2pofb_ B: CDP-diacylglycerol pyrophosphatase CDH                                                                                                                                                                            SCOP domains
               CATH domains 2pofB00 B:31-250 HIT family -  CDH-like                                                                                                                                                                                      CATH domains
           Pfam domains (1) CDH-2pofB01 B:31-250                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) CDH-2pofB02 B:31-250                                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......eee....eeeee.......eeeee........hhhhhh....hhhhhhhhhhhhhhhhhh...hhh.eeeee.hhhhh......eeeee.hhhhhhhhhh.........ee..........eeeeehhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeee.....eeeeeee.........hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pof B  31 SDTLRKIVLEECLPNQQQNQNPSPCAEVKPNAGYVVLKDLNGPLQYLLmPTYRINGTESPLLTDPSTPNFFWLAWQARDFmSKKYGQPVPDRAVSLAINSRTGRTQNHFHIHISCIRPDVREQLDNNLANISSRWLPLPGGLRGHEYLARRVTESELVQRSPFmmLAEEVPEAREHmGSYGLAmVRQSDNSFVLLATQRNLLTLNRASAEEIQDHQCEIL 250
                                    40        50        60        70        80        90       100       110|      120       130       140       150       160       170       180       190   ||  200      |210   |   220       230       240       250
                                                                           79-MSE                         111-MSE                                                                            194-MSE      207-MSE  |                                    
                                                                                                                                                                                              195-MSE            214-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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: HIT-like (73)

Superfamily: HIT-like (67)

Family: CDH-like (1)

Protein domain: CDP-diacylglycerol pyrophosphatase CDH (1)

Escherichia coli [TaxId: 562] (1)

1a	d2pofa1	A:31-250
1b	d2pofb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: HIT family, subunit A (33)

Homologous Superfamily: HIT family - CDH-like (1)

Escherichia coli o157:h7. Organism_taxid: 83334. Strain: o157:h7. (1)

1a	2pofA00	A:31-250
1b	2pofB00	B:31-250

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: CDH] (1)

Family: CDH (1)

Escherichia coli O157:H7 (1)

1a	CDH-2pofB01	B:31-250
1b	CDH-2pofB02	B:31-250

Asymmetric Unit(hide GO term definitions)

Chain A,B (CDH_ECO57 | Q8X7A5)

molecular function
	GO:0008715	CDP-diacylglycerol diphosphatase activity	Catalysis of the reaction: CDP-diacylglycerol + H(2)O = a phosphatidate + CMP + 2 H(+).
	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:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
	GO:0046342	CDP-diacylglycerol catabolic process	The chemical reactions and pathways resulting in the breakdown of CDP-diacylglycerol, CDP-1,2-diacylglycerol, a substance composed of diacylglycerol in glycosidic linkage with cytidine diphosphate.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0008654	phospholipid biosynthetic process	The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ser A:53 - Pro A:54	[ RasMol ]
		Ser B:53 - Pro B:54	[ RasMol ]

Biological Units
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Description

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SS Bonds (4, 4)

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