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Title :   2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF GLYCEROL-3-PHOSPHATE DEHYDROGENASE (GPSA) FROM COXIELLA BURNETII

Authors :   G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, S. N. Pe W. F. Anderson, Center For Structural Genomics Of Infectious (Csgid)

Date :   15 Oct 09 (Deposition) - 27 Oct 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Glycerol-3-Phosphate Dehydrogenase, Gpsa, Idp01976, Nad, Oxidoreductase, Phospholipid Biosynthesis, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, S. N. Peterson, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
2. 1 Angstrom Resolution Crystal Structure Of Glycerol-3-Phosphate Dehydrogenase (Gpsa) From Coxiella Burnetii.
To Be Published
PubMed: search

Molecule 1 - GLYCEROL-3-PHOSPHATE DEHYDROGENASE [NAD(P)+]
	Chains	:	A, B
	EC Number	:	1.1.1.94
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CBU_1518, GPSA
	Organism Scientific	:	COXIELLA BURNETII
	Organism Taxid	:	227377
	Strain	:	RSA 493
	Synonym	:	NAD(P)H-DEPENDENT GLYCEROL-3-PHOSPHATE DEHYDROGENASE

		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	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER B:38 , ASP B:42 , CYS B:67	BINDING SITE FOR RESIDUE BME B 401
2	AC2	SOFTWARE	GLN B:45 , LYS B:64 , TYR B:66 , CYS B:67 , ASP B:68 , HOH B:481	BINDING SITE FOR RESIDUE EPE B 402
3	AC3	SOFTWARE	GLN A:45 , TYR A:66 , CYS A:67 , ASP A:68	BINDING SITE FOR RESIDUE EPE A 403

(no "SS Bond" information available for 3K96)

(no "Cis Peptide Bond" information available for 3K96)

(no "SAP(SNP)/Variant" information available for 3K96)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NAD_G3PDH	PS00957	NAD-dependent glycerol-3-phosphate dehydrogenase signature.	GPDA_COXBU	189-210	2	A:189-210 B:189-210

(no "Exon" information available for 3K96)

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:326
 aligned with GPDA_COXBU | Q83BJ0 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:326
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322      
           GPDA_COXBU     3 PFKHPIAILGAGSWGTALALVLARKGQKVRLWSYESDHVDEMQAEGVNNRYLPNYPFPETLKAYCDLKASLEGVTDILIVVPSFAFHEVITRMKPLIDAKTRIAWGTKGLAKGSRLLHEVVATELGQVPMAVISGPSLATEVAANLPTAVSLASNNSQFSKDLIERLHGQRFRVYKNDDMIGVELCGSVKNILAIATGISDGLKLGSNARAALITRGLTEMGRLVSVFGGKQETLTGLAGLGDLVLTCTDNQSRNRRFGLALGEGVDKKEAQQAIGQAIEGLYNTDQVHALAQKHAIEMPLTFQVHRILHEDLDPQQAVQELLERS 328
               SCOP domains d3k96a1 A:3-180 automated matches                                                                                                                                                 d3k96a2 A:181-328 automated matches                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3k96A02 A:190-328 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhh....eeee..hhhhhhhhhhhh..............eeee.hhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhh...eeeee...hhhhhhh...eeeeeee.hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NAD_G3PDH             ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k96 A   3 PFKHPIAILGAGSWGTALALVLARKGQKVRLWSYESDHVDEMQAEGVNNRYLPNYPFPETLKAYCDLKASLEGVTDILIVVPSFAFHEVITRMKPLIDAKTRIAWGTKGLAKGSRLLHEVVATELGQVPMAVISGPSLATEVAANLPTAVSLASNNSQFSKDLIERLHGQRFRVYKNDDMIGVELCGSVKNILAIATGISDGLKLGSNARAALITRGLTEMGRLVSVFGGKQETLTGLAGLGDLVLTCTDNQSRNRRFGLALGEGVDKKEAQQAIGQAIEGLYNTDQVHALAQKHAIEMPLTFQVHRILHEDLDPQQAVQELLERS 328
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322

Chain B from PDB  Type:PROTEIN  Length:325
 aligned with GPDA_COXBU | Q83BJ0 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:325
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322     
           GPDA_COXBU     3 PFKHPIAILGAGSWGTALALVLARKGQKVRLWSYESDHVDEMQAEGVNNRYLPNYPFPETLKAYCDLKASLEGVTDILIVVPSFAFHEVITRMKPLIDAKTRIAWGTKGLAKGSRLLHEVVATELGQVPMAVISGPSLATEVAANLPTAVSLASNNSQFSKDLIERLHGQRFRVYKNDDMIGVELCGSVKNILAIATGISDGLKLGSNARAALITRGLTEMGRLVSVFGGKQETLTGLAGLGDLVLTCTDNQSRNRRFGLALGEGVDKKEAQQAIGQAIEGLYNTDQVHALAQKHAIEMPLTFQVHRILHEDLDPQQAVQELLER 327
               SCOP domains d3k96b1 B:3-180 automated matches                                                                                                                                                 d3k96b2 B:181-327 automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3k96B02 B:190-327 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                CATH domains
           Pfam domains (1) ----NAD_Gly3P_dh_N-3k96B03 B:7-162                                                                                                                              -----------------NAD_Gly3P_dh_C-3k96B01 B:180-324                                                                                                                 --- Pfam domains (1)
           Pfam domains (2) ----NAD_Gly3P_dh_N-3k96B04 B:7-162                                                                                                                              -----------------NAD_Gly3P_dh_C-3k96B02 B:180-324                                                                                                                 --- Pfam domains (2)
         Sec.struct. author .....eeee..hhhhhhhhhhhhh....eeee..hhhhhhhhhhhh..............eeee.hhhhhhh...eeee..hhhhhhhhhhhhh.......eeee....ee...eehhhhhhhhhh...eeeee...hhhhhhh...eeeeeee.hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NAD_G3PDH             --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k96 B   3 PFKHPIAILGAGSWGTALALVLARKGQKVRLWSYESDHVDEMQAEGVNNRYLPNYPFPETLKAYCDLKASLEGVTDILIVVPSFAFHEVITRMKPLIDAKTRIAWGTKGLAKGSRLLHEVVATELGQVPMAVISGPSLATEVAANLPTAVSLASNNSQFSKDLIERLHGQRFRVYKNDDMIGVELCGSVKNILAIATGISDGLKLGSNARAALITRGLTEMGRLVSVFGGKQETLTGLAGLGDLVLTCTDNQSRNRRFGLALGEGVDKKEAQQAIGQAIEGLYNTDQVHALAQKHAIEMPLTFQVHRILHEDLDPQQAVQELLER 327
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 (60)

Homologous Superfamily: N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 (59)

Coxiella burnetii rsa 493. Organism_taxid: 227377. Strain: rsa 493. (1)

1a	3k96A02	A:190-328
1b	3k96B02	B:190-327

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: 6PGD_C (47)

Family: NAD_Gly3P_dh_C (11)

Coxiella burnetii (1)

1a	NAD_Gly3P_dh_C-3k96B01	B:180-324
1b	NAD_Gly3P_dh_C-3k96B02	B:180-324

Clan: NADP_Rossmann (1239)

Family: NAD_Gly3P_dh_N (11)

Coxiella burnetii (1)

2a	NAD_Gly3P_dh_N-3k96B03	B:7-162
2b	NAD_Gly3P_dh_N-3k96B04	B:7-162

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GPDA_COXBU | Q83BJ0)

molecular function
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0047952	glycerol-3-phosphate dehydrogenase [NAD(P)+] activity	Catalysis of the reaction: sn-glycerol 3-phosphate + NAD(P)+ = glycerone phosphate + NAD(P)H + H+.
	GO:0004367	glycerol-3-phosphate dehydrogenase [NAD+] activity	Catalysis of the reaction: sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH + H+.
	GO:0036439	glycerol-3-phosphate dehydrogenase [NADP+] activity	Catalysis of the reaction: glycerol 3-phosphate + NADP+ = glycerone phosphate + H+ + NADPH.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0046167	glycerol-3-phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of glycerol-3-phosphate, a phosphoric monoester of glycerol.
	GO:0046168	glycerol-3-phosphate catabolic process	The chemical reactions and pathways resulting in the breakdown of glycerol-3-phosphate, a phosphoric monoester of glycerol.
	GO:0006072	glycerol-3-phosphate metabolic process	The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
	GO:0006650	glycerophospholipid metabolic process	The chemical reactions and pathways involving glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.
	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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0009331	glycerol-3-phosphate dehydrogenase complex	An enzyme complex that catalyzes the dehydrogenation of sn-glycerol 3-phosphate to form glycerone phosphate.

Asymmetric/Biological Unit
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Ligands, Modified Residues, Ions (2, 3)

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