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Title :   CRYSTAL STRUCTURE OF HUMAN GLYCEROL-3-PHOSPHATE DEHYDROGENASE 1-LIKE PROTEIN

Authors :   J. Uppenberg, C. Smee, V. Hozjan, K. Kavanagh, G. Bunkoczi, E. Papagrig A. C. W. Pike, E. Ugochukwu, C. Umeano, F. Von Delft, J. Weigelt, C. H. Arrowsmith, A. Edwards, M. Sundstrom, U. Oppermann, Structural Consortium (Sgc)

Date :   19 Apr 07 (Deposition) - 01 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.51

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

Keywords :   Dehydrogenase, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Uppenberg, C. Smee, V. Hozjan, K. Kavanagh, G. Bunkoczi, E. Papagrigoriou, A. C. W. Pike, E. Ugochukwu, C. Umeano, F. Von Delft J. Weigelt, C. H. Arrowsmith, A. Edwards, M. Sundstrom, U. Oppermann
Crystal Structure Of Human Glycerol-3-Phosphate Dehydrogenase 1-Like Protein.
To Be Published
PubMed: search

Molecule 1 - GLYCEROL-3-PHOSPHATE DEHYDROGENASE 1-LIKE PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	GPD1L
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Tissue	:	BRAIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3	PO4	3	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:206 , ASN A:207 , THR A:266 , GLY A:270 , ARG A:271 , ASN A:272 , HOH A:507 , HOH A:566	BINDING SITE FOR RESIDUE PO4 A 501
2	AC2	SOFTWARE	LYS B:206 , ASN B:207 , THR B:266 , GLY B:270 , ARG B:271 , ASN B:272 , HOH B:602 , HOH B:604 , HOH B:610 , HOH B:643	BINDING SITE FOR RESIDUE PO4 B 502
3	AC3	SOFTWARE	LYS A:22 , HIS A:69 , LYS A:70 , LYS A:320	BINDING SITE FOR RESIDUE PO4 A 503
4	AC4	SOFTWARE	LYS B:22 , LYS B:70	BINDING SITE FOR RESIDUE CL B 601
5	AC5	SOFTWARE	GLY A:14 , ASN A:15 , TRP A:16 , GLY A:17 , PHE A:43 , TYR A:65 , PHE A:99 , ARG A:102 , ILE A:121 , LYS A:122 , ASN A:153 , ALA A:155 , ARG A:271 , GLY A:296 , GLN A:297 , LYS A:298 , HOH A:506 , HOH A:566 , HOH A:567 , HOH A:574 , HOH A:575 , HOH A:576 , HOH A:582 , HOH A:588	BINDING SITE FOR RESIDUE NAD A 401
6	AC6	SOFTWARE	GLY B:14 , ASN B:15 , TRP B:16 , GLY B:17 , PHE B:43 , TYR B:65 , VAL B:94 , PRO B:96 , PHE B:99 , LEU B:120 , ILE B:121 , LYS B:122 , ASN B:153 , ILE B:154 , ALA B:155 , ARG B:271 , GLY B:296 , GLN B:297 , LYS B:298 , GLN B:300 , HOH B:604 , HOH B:610 , HOH B:619 , HOH B:643	BINDING SITE FOR RESIDUE NAD B 401

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

(no "Cis Peptide Bond" information available for 2PLA)

Asymmetric/Biological Unit (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_044044	E	83	K	GPD1L_HUMAN	Disease (SIDS)	72552292	A/B	E	83	K
2	UniProt	VAR_044045	I	124	V	GPD1L_HUMAN	Disease (SIDS)	72552293	A/B	I	124	V
3	UniProt	VAR_032114	L	178	F	GPD1L_HUMAN	Polymorphism	35447795	A/B	L	178	F
4	UniProt	VAR_044046	R	273	C	GPD1L_HUMAN	Disease (SIDS)	72552294	A/B	R	273	C
5	UniProt	VAR_044047	A	280	V	GPD1L_HUMAN	Disease (BRGDA2)	72552291	A/B	A	280	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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

Asymmetric/Biological Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000282541	2a	ENSE00001134616	chr3:32148003-32148250	248	GPD1L_HUMAN	1-16	16	2	A:4-16 B:4-16	13 13
1.3	ENST00000282541	3	ENSE00001721944	chr3:32169568-32169745	178	GPD1L_HUMAN	16-75	60	2	A:16-75 B:16-75	60 60
1.4	ENST00000282541	4	ENSE00001635877	chr3:32180079-32180219	141	GPD1L_HUMAN	76-122	47	2	A:76-122 B:76-122	47 47
1.5b	ENST00000282541	5b	ENSE00001650240	chr3:32181720-32181858	139	GPD1L_HUMAN	123-169	47	2	A:123-169 B:123-169	47 47
1.6b	ENST00000282541	6b	ENSE00001777860	chr3:32188114-32188226	113	GPD1L_HUMAN	169-206	38	2	A:169-206 B:169-206	38 38
1.7d	ENST00000282541	7d	ENSE00001665323	chr3:32200368-32200601	234	GPD1L_HUMAN	207-284	78	2	A:207-284 B:207-284	78 78
1.8b	ENST00000282541	8b	ENSE00001075713	chr3:32201060-32201166	107	GPD1L_HUMAN	285-320	36	2	A:285-320 B:285-320	36 36
1.9c	ENST00000282541	9c	ENSE00001134607	chr3:32207306-32210205	2900	GPD1L_HUMAN	320-351	32	2	A:320-346 B:320-346	27 27

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:343
 aligned with GPD1L_HUMAN | Q8N335 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:343
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343   
          GPD1L_HUMAN     4 APLKVCIVGSGNWGSAVAKIIGNNVKKLQKFASTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHKLPENVVAMSNLSEAVQDADLLVFVIPHQFIHRICDEITGRVPKKALGITLIKGIDEGPEGLKLISDIIREKMGIDISVLMGANIANEVAAEKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKNIVAVGAGFCDGLRCGDNTKAAVIRLGLMEMIAFARIFCKGQVSTATFLESCGVADLITTCYGGRNRRVAEAFARTGKTIEELEKEMLNGQKLQGPQTSAEVYRILKQKGLLDKFPLFTAVYQICYESRPVQEMLSCLQS 346
               SCOP domains d2plaa1 A:4-195 automated matches                                                                                                                                                               d2plaa2 A:196-346 automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhhhh........eeee....ee..eehhhhhhhhh..............eeee.hhhhhhh...eeee..hhhhhhhhhhhhh.......eeee....eeee..eeeehhhhhhhhhh.eeeeee...hhhhhhh...eeeeee..hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------K----------------------------------------V-----------------------------------------------------F----------------------------------------------------------------------------------------------C------V------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a    -----------------------------------------------------------Exon 1.4  PDB: A:76-122 UniProt: 76-122        Exon 1.5b  PDB: A:123-169 UniProt: 123-169     -------------------------------------Exon 1.7d  PDB: A:207-284 UniProt: 207-284                                    Exon 1.8b  PDB: A:285-320           -------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.3  PDB: A:16-75 UniProt: 16-75                       ---------------------------------------------------------------------------------------------Exon 1.6b  PDB: A:169-206             -----------------------------------------------------------------------------------------------------------------Exon 1.9c  PDB: A:320-346   Transcript 1 (2)
                 2pla A   4 APLKVCIVGSGNWGSAVAKIIGNNVKKLQKFASTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHKLPENVVAMSNLSEAVQDADLLVFVIPHQFIHRICDEITGRVPKKALGITLIKGIDEGPEGLKLISDIIREKMGIDISVLMGANIANEVAAEKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKNIVAVGAGFCDGLRCGDNTKAAVIRLGLMEMIAFARIFCKGQVSTATFLESCGVADLITTCYGGRNRRVAEAFARTGKTIEELEKEMLNGQKLQGPQTSAEVYRILKQKGLLDKFPLFTAVYQICYESRPVQEMLSCLQS 346
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343

Chain B from PDB  Type:PROTEIN  Length:343
 aligned with GPD1L_HUMAN | Q8N335 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:343
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343   
          GPD1L_HUMAN     4 APLKVCIVGSGNWGSAVAKIIGNNVKKLQKFASTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHKLPENVVAMSNLSEAVQDADLLVFVIPHQFIHRICDEITGRVPKKALGITLIKGIDEGPEGLKLISDIIREKMGIDISVLMGANIANEVAAEKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKNIVAVGAGFCDGLRCGDNTKAAVIRLGLMEMIAFARIFCKGQVSTATFLESCGVADLITTCYGGRNRRVAEAFARTGKTIEELEKEMLNGQKLQGPQTSAEVYRILKQKGLLDKFPLFTAVYQICYESRPVQEMLSCLQS 346
               SCOP domains d2plab1 B:4-195 automated matches                                                                                                                                                               ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---NAD_Gly3P_dh_N-2plaB03 B:7-176                                                                                                                                            -----------------NAD_Gly3P_dh_C-2plaB01 B:194-344                                                                                                                       -- Pfam domains (1)
           Pfam domains (2) ---NAD_Gly3P_dh_N-2plaB04 B:7-176                                                                                                                                            -----------------NAD_Gly3P_dh_C-2plaB02 B:194-344                                                                                                                       -- Pfam domains (2)
         Sec.struct. author ....eeee..hhhhhhhhhhhhhhhhh.......eeee....ee..eehhhhhhhhh..............eeee.hhhhhhh...eeee..hhhhhhhhhhhhh.......eeee....eee....eeehhhhhhhhhh.eeeeee...hhhhhhh...eeeeee..hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------K----------------------------------------V-----------------------------------------------------F----------------------------------------------------------------------------------------------C------V------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a    -----------------------------------------------------------Exon 1.4  PDB: B:76-122 UniProt: 76-122        Exon 1.5b  PDB: B:123-169 UniProt: 123-169     -------------------------------------Exon 1.7d  PDB: B:207-284 UniProt: 207-284                                    Exon 1.8b  PDB: B:285-320           -------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.3  PDB: B:16-75 UniProt: 16-75                       ---------------------------------------------------------------------------------------------Exon 1.6b  PDB: B:169-206             -----------------------------------------------------------------------------------------------------------------Exon 1.9c  PDB: B:320-346   Transcript 1 (2)
                 2pla B   4 APLKVCIVGSGNWGSAVAKIIGNNVKKLQKFASTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHKLPENVVAMSNLSEAVQDADLLVFVIPHQFIHRICDEITGRVPKKALGITLIKGIDEGPEGLKLISDIIREKMGIDISVLMGANIANEVAAEKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKNIVAVGAGFCDGLRCGDNTKAAVIRLGLMEMIAFARIFCKGQVSTATFLESCGVADLITTCYGGRNRRVAEAFARTGKTIEELEKEMLNGQKLQGPQTSAEVYRILKQKGLLDKFPLFTAVYQICYESRPVQEMLSCLQS 346
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343

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 '\|'

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: 6PGD_C (47)

Family: NAD_Gly3P_dh_C (11)

Homo sapiens (Human) (4)

1a	NAD_Gly3P_dh_C-2plaB01	B:194-344
1b	NAD_Gly3P_dh_C-2plaB02	B:194-344

Clan: NADP_Rossmann (1239)

Family: NAD_Gly3P_dh_N (11)

Homo sapiens (Human) (4)

2a	NAD_Gly3P_dh_N-2plaB03	B:7-176
2b	NAD_Gly3P_dh_N-2plaB04	B:7-176

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GPD1L_HUMAN | Q8N335)

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:0004367	glycerol-3-phosphate dehydrogenase [NAD+] activity	Catalysis of the reaction: sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH + H+.
	GO:0044325	ion channel binding	Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
	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.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0017080	sodium channel regulator activity	Modulates the activity of a sodium channel.
biological process
	GO:0019674	NAD metabolic process	The chemical reactions and pathways involving nicotinamide adenine dinucleotide (NAD), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
	GO:0006734	NADH metabolic process	The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
	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: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:0033137	negative regulation of peptidyl-serine phosphorylation	Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-serine.
	GO:0090038	negative regulation of protein kinase C signaling	Any process that decreases the frequency, rate, or extent of a series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound.
	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:0006654	phosphatidic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
	GO:2000010	positive regulation of protein localization to cell surface	Any process that activates or increases the frequency, rate or extent of protein localization to the cell surface.
	GO:0010765	positive regulation of sodium ion transport	Any process that increases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0002027	regulation of heart rate	Any process that modulates the frequency or rate of heart contraction.
	GO:2000649	regulation of sodium ion transmembrane transporter activity	Any process that modulates the frequency, rate or extent of sodium ion transmembrane transporter activity.
	GO:0060373	regulation of ventricular cardiac muscle cell membrane depolarization	Any process that modulates the establishment or extent of a membrane potential in the depolarizing direction away from the resting potential in a ventricular cardiomyocyte.
	GO:0019432	triglyceride biosynthetic process	The chemical reactions and pathways resulting in the formation of a triglyceride, any triester of glycerol.
	GO:0086005	ventricular cardiac muscle cell action potential	An action potential that occurs in a ventricular cardiac muscle cell.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0009331	glycerol-3-phosphate dehydrogenase complex	An enzyme complex that catalyzes the dehydrogenation of sn-glycerol 3-phosphate to form glycerone phosphate.
	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/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 10)

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Exons (8, 16)

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