1X0X - JenaLib

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Title :   CO-STRUCTURE OF HOMO SAPIENS GLYCEROL-3-PHOSPHATE DEHYDROGENASE 1 COMPLEX WITH NAD

Authors :   Z. Rao, X. Ou

Date :   31 Mar 05 (Deposition) - 11 Apr 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

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

Keywords :   Nad, Co-Enzyme, Gpd1, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Ou, C. Ji, X. Han, X. Zhao, X. Li, Y. Mao, L. L. Wong, M. Bartlam, Z. Rao
Crystal Structures Of Human Glycerol 3-Phosphate Dehydrogenase 1 (Gpd1)
J. Mol. Biol. V. 357 858 2006
PubMed-ID: 16460752 | Reference-DOI: 10.1016/J.JMB.2005.12.074

Molecule 1 - GLYCEROL-3-PHOSPHATE DEHYDROGENASE [NAD+], CYTOPLASMIC
	Chains	:	A
	EC Number	:	1.1.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	DE3(BL21)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GPD-C, GPDH-C

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	SO4	10	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:20 , HIS A:67 , LYS A:68	BINDING SITE FOR RESIDUE SO4 A 1001
2	AC2	SOFTWARE	LYS A:204 , ASN A:205 , THR A:264 , GLY A:268 , ARG A:269 , ASN A:270 , HOH A:2010 , HOH A:2022 , HOH A:2039 , HOH A:2049 , HOH A:2076 , HOH A:2134	BINDING SITE FOR RESIDUE SO4 A 1002
3	AC3	SOFTWARE	LYS A:240 , VAL A:247 , SER A:248 , SER A:249 , HOH A:2175 , HOH A:2179	BINDING SITE FOR RESIDUE SO4 A 1003
4	AC4	SOFTWARE	ARG A:271 , LYS A:272 , HOH A:2017	BINDING SITE FOR RESIDUE SO4 A 1004
5	AC5	SOFTWARE	ASN A:13 , GLN A:295 , HOH A:2065 , HOH A:2096 , HOH A:2211	BINDING SITE FOR RESIDUE SO4 A 1005
6	AC6	SOFTWARE	SER A:11 , GLY A:12 , ASN A:13 , TRP A:14 , GLY A:15 , PHE A:41 , TYR A:63 , VAL A:93 , PRO A:94 , PHE A:97 , ILE A:119 , LYS A:120 , ASN A:151 , ALA A:153 , ARG A:269 , GLY A:294 , GLN A:295 , LYS A:296 , GLN A:298 , HOH A:2007 , HOH A:2011 , HOH A:2012 , HOH A:2022 , HOH A:2023 , HOH A:2039 , HOH A:2044 , HOH A:2087 , HOH A:2134 , HOH A:2135	BINDING SITE FOR RESIDUE NAD A 2001

(no "SS Bond" information available for 1X0X)

(no "Cis Peptide Bond" information available for 1X0X)

Asymmetric Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029492	I	54	V	GPDA_HUMAN	Polymorphism	2232202	A	I	54	V
2	UniProt	VAR_029493	A	113	P	GPDA_HUMAN	Polymorphism	1128867	A	A	113	P
3	UniProt	VAR_067425	E	124	K	GPDA_HUMAN	Polymorphism	34783513	A	E	124	K
4	UniProt	VAR_049220	V	197	A	GPDA_HUMAN	Polymorphism	2232207	A	V	197	A
5	UniProt	VAR_067426	T	223	I	GPDA_HUMAN	Polymorphism	200251017	A	T	223	I
6	UniProt	VAR_071967	R	229	P	GPDA_HUMAN	Disease (HTGTI)	199673455	A	R	229	P

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

Biological Unit 1 (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029492	I	54	V	GPDA_HUMAN	Polymorphism	2232202	A	I	54	V
2	UniProt	VAR_029493	A	113	P	GPDA_HUMAN	Polymorphism	1128867	A	A	113	P
3	UniProt	VAR_067425	E	124	K	GPDA_HUMAN	Polymorphism	34783513	A	E	124	K
4	UniProt	VAR_049220	V	197	A	GPDA_HUMAN	Polymorphism	2232207	A	V	197	A
5	UniProt	VAR_067426	T	223	I	GPDA_HUMAN	Polymorphism	200251017	A	T	223	I
6	UniProt	VAR_071967	R	229	P	GPDA_HUMAN	Disease (HTGTI)	199673455	A	R	229	P

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

Biological Unit 2 (6, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_029492	I	54	V	GPDA_HUMAN	Polymorphism	2232202	A	I	54	V
2	UniProt	VAR_029493	A	113	P	GPDA_HUMAN	Polymorphism	1128867	A	A	113	P
3	UniProt	VAR_067425	E	124	K	GPDA_HUMAN	Polymorphism	34783513	A	E	124	K
4	UniProt	VAR_049220	V	197	A	GPDA_HUMAN	Polymorphism	2232207	A	V	197	A
5	UniProt	VAR_067426	T	223	I	GPDA_HUMAN	Polymorphism	200251017	A	T	223	I
6	UniProt	VAR_071967	R	229	P	GPDA_HUMAN	Disease (HTGTI)	199673455	A	R	229	P

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NAD_G3PDH	PS00957	NAD-dependent glycerol-3-phosphate dehydrogenase signature.	GPDA_HUMAN	201-222	1	A:201-222

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NAD_G3PDH	PS00957	NAD-dependent glycerol-3-phosphate dehydrogenase signature.	GPDA_HUMAN	201-222	1	A:201-222

Biological Unit 2 (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_HUMAN	201-222	2	A:201-222

Asymmetric Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000301149	1	ENSE00001239163	chr12:50497801-50497874	74	GPDA_HUMAN	1-14	14	1	A:1-14	14
1.2	ENST00000301149	2	ENSE00001194139	chr12:50498357-50498534	178	GPDA_HUMAN	14-73	60	1	A:14-73	60
1.3	ENST00000301149	3	ENSE00001194132	chr12:50499331-50499471	141	GPDA_HUMAN	74-120	47	1	A:74-120	47
1.4	ENST00000301149	4	ENSE00001680723	chr12:50500071-50500209	139	GPDA_HUMAN	121-167	47	1	A:121-167	47
1.5	ENST00000301149	5	ENSE00001194124	chr12:50500588-50500700	113	GPDA_HUMAN	167-204	38	1	A:167-204	38
1.6	ENST00000301149	6	ENSE00001728210	chr12:50501350-50501583	234	GPDA_HUMAN	205-282	78	1	A:205-282	78
1.7	ENST00000301149	7	ENSE00001194116	chr12:50501807-50501913	107	GPDA_HUMAN	283-318	36	1	A:283-318	36
1.8	ENST00000301149	8	ENSE00001239159	chr12:50503206-50505091	1886	GPDA_HUMAN	318-349	32	1	A:318-349	32

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:350
 aligned with GPDA_HUMAN | P21695 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:350
                             1                                                                                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349
           GPDA_HUMAN     - -MASKKVCIVGSGNWGSAIAKIVGGNAAQLAQFDPRVTMWVFEEDIGGKKLTEIINTQHENVKYLPGHKLPPNVVAVPDVVQAAEDADILIFVVPHQFIGKICDQLKGHLKANATGISLIKGVDEGPNGLKLISEVIGERLGIPMSVLMGANIASEVADEKFCETTIGCKDPAQGQLLKELMQTPNFRITVVQEVDTVEICGALKNVVAVGAGFCDGLGFGDNTKAAVIRLGLMEMIAFAKLFCSGPVSSATFLESCGVADLITTCYGGRNRKVAEAFARTGKSIEQLEKELLNGQKLQGPETARELYSILQHKGLVDKFPLFMAVYKVCYEGQPVGEFIHCLQNHPEHM 349
               SCOP domains d1x0xa1 A:0-193 automated matches                                                                                                                                                                 d1x0xa2 A:194-349 automated matches                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----NAD_Gly3P_dh_N-1x0xA02 A:5-174                                                                                                                                            -----------------NAD_Gly3P_dh_C-1x0xA01 A:192-342                                                                                                                       ------- Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhhhhhhhh......eeee....ee..eehhhhhhhhh..............eeee.hhhhhhh...eeee..hhhhhhhhhhhhh.......eeee.....eee..eeehhhhhhhhhhh..eeeee...hhhhhhh...eeeeee..hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------V----------------------------------------------------------P----------K------------------------------------------------------------------------A-------------------------I-----P------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NAD_G3PDH             ------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -Exon 1.1      -----------------------------------------------------------Exon 1.3  PDB: A:74-120 UniProt: 74-120        Exon 1.4  PDB: A:121-167 UniProt: 121-167      -------------------------------------Exon 1.6  PDB: A:205-282 UniProt: 205-282                                     Exon 1.7  PDB: A:283-318            ------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.2  PDB: A:14-73 UniProt: 14-73                       ---------------------------------------------------------------------------------------------Exon 1.5  PDB: A:167-204              -----------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:318-349         Transcript 1 (2)
                 1x0x A   0 SMASKKVCIVGSGNWGSAIAKIVGGNAAQLAQFDPRVTMWVFEEDIGGKKLTEIINTQHENVKYLPGHKLPPNVVAVPDVVQAAEDADILIFVVPHQFIGKICDQLKGHLKANATGISLIKGVDEGPNGLKLISEVIGERLGIPMSVLMGANIASEVADEKFCETTIGCKDPAQGQLLKELMQTPNFRITVVQEVDTVEICGALKNVVAVGAGFCDGLGFGDNTKAAVIRLGLMEMIAFAKLFCSGPVSSATFLESCGVADLITTCYGGRNRKVAEAFARTGKSIEQLEKELLNGQKLQGPETARELYSILQHKGLVDKFPLFMAVYKVCYEGQPVGEFIHCLQNHPEHM 349
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349

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 1X0X)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: 6PGD_C (47)

Family: NAD_Gly3P_dh_C (11)

Homo sapiens (Human) (4)

NAD_Gly3P_dh_C-1x0xA01

A:192-342

Clan: NADP_Rossmann (1239)

Family: NAD_Gly3P_dh_N (11)

Homo sapiens (Human) (4)

NAD_Gly3P_dh_N-1x0xA02

A:5-174

Asymmetric Unit(hide GO term definitions)

Chain A (GPDA_HUMAN | P21695)

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:0004368	glycerol-3-phosphate dehydrogenase activity	Catalysis of the reaction: sn-glycerol 3-phosphate + a quinone = glycerone phosphate + a quinol.
	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.
biological process
	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:0006116	NADH oxidation	A metabolic process that results in the oxidation of reduced nicotinamide adenine dinucleotide, NADH, to the oxidized form, NAD.
	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:0071320	cellular response to cAMP	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:0071356	cellular response to tumor necrosis factor	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and 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:0046486	glycerolipid metabolic process	The chemical reactions and pathways involving glycerolipids, any lipid with a glycerol backbone. Diacylglycerol and phosphatidate are key lipid intermediates of glycerolipid biosynthesis.
	GO:0006127	glycerophosphate shuttle	The process of transferring reducing equivalents from the cytosol into the mitochondria; NADH is used to synthesise glycerol 3-phosphate in the cytosol; this compound is then transported into the mitochondria where it is converted to dihydroxyacetone phosphate (DHAP) using FAD; DHAP then returns to the cytosol to complete the cycle.
	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:0045821	positive regulation of glycolytic process	Any process that activates or increases the frequency, rate or extent of glycolysis.
	GO:0019432	triglyceride biosynthetic process	The chemical reactions and pathways resulting in the formation of a triglyceride, any triester of glycerol.
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:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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	GPDA_HUMAN \| P21695	:	1wpq 1x0v

1wpq	CRYSTAL STRUCTURE OF HOMO SAPIENS GLYCEROL-3-PHOSPHATE DEHYDROGENASE 1 COMPLEXED WITH NAD AND HIHYDROXYACTONE
1x0v	CRYSTAL STRUCTURE OF HOMO SAPIENS GLYCEROL-3-PHOSPHATE DEHYDROGENASE 1

Description

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Ligands, Modified Residues, Ions (2, 6)

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