1U8F

Crystal Structure Of Human Placental Glyceraldehyde-3-Phosphate Dehydrogenase At 1.75 Resolution

Functional Information from GO Data

Chain	GOid	namespace	contents
O	0000226	biological_process	microtubule cytoskeleton organization
O	0001819	biological_process	positive regulation of cytokine production
O	0002376	biological_process	immune system process
O	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
O	0005515	molecular_function	protein binding
O	0005634	cellular_component	nucleus
O	0005737	cellular_component	cytoplasm
O	0005811	cellular_component	lipid droplet
O	0005829	cellular_component	cytosol
O	0005856	cellular_component	cytoskeleton
O	0005886	cellular_component	plasma membrane
O	0006006	biological_process	glucose metabolic process
O	0006096	biological_process	glycolytic process
O	0006417	biological_process	regulation of translation
O	0006915	biological_process	apoptotic process
O	0008017	molecular_function	microtubule binding
O	0010951	biological_process	negative regulation of endopeptidase activity
O	0015630	cellular_component	microtubule cytoskeleton
O	0016020	cellular_component	membrane
O	0016241	biological_process	regulation of macroautophagy
O	0016491	molecular_function	oxidoreductase activity
O	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
O	0016740	molecular_function	transferase activity
O	0017148	biological_process	negative regulation of translation
O	0019828	molecular_function	aspartic-type endopeptidase inhibitor activity
O	0031640	biological_process	killing of cells of another organism
O	0031965	cellular_component	nuclear membrane
O	0031982	cellular_component	vesicle
O	0032481	biological_process	positive regulation of type I interferon production
O	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
O	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
O	0042802	molecular_function	identical protein binding
O	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
O	0045087	biological_process	innate immune response
O	0048471	cellular_component	perinuclear region of cytoplasm
O	0050661	molecular_function	NADP binding
O	0050821	biological_process	protein stabilization
O	0050832	biological_process	defense response to fungus
O	0051287	molecular_function	NAD binding
O	0051402	biological_process	neuron apoptotic process
O	0051873	biological_process	killing by host of symbiont cells
O	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
O	0070062	cellular_component	extracellular exosome
O	0071346	biological_process	cellular response to type II interferon
O	0097452	cellular_component	GAIT complex
O	0097718	molecular_function	disordered domain specific binding
O	1990904	cellular_component	ribonucleoprotein complex
P	0000226	biological_process	microtubule cytoskeleton organization
P	0001819	biological_process	positive regulation of cytokine production
P	0002376	biological_process	immune system process
P	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
P	0005515	molecular_function	protein binding
P	0005634	cellular_component	nucleus
P	0005737	cellular_component	cytoplasm
P	0005811	cellular_component	lipid droplet
P	0005829	cellular_component	cytosol
P	0005856	cellular_component	cytoskeleton
P	0005886	cellular_component	plasma membrane
P	0006006	biological_process	glucose metabolic process
P	0006096	biological_process	glycolytic process
P	0006417	biological_process	regulation of translation
P	0006915	biological_process	apoptotic process
P	0008017	molecular_function	microtubule binding
P	0010951	biological_process	negative regulation of endopeptidase activity
P	0015630	cellular_component	microtubule cytoskeleton
P	0016020	cellular_component	membrane
P	0016241	biological_process	regulation of macroautophagy
P	0016491	molecular_function	oxidoreductase activity
P	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
P	0016740	molecular_function	transferase activity
P	0017148	biological_process	negative regulation of translation
P	0019828	molecular_function	aspartic-type endopeptidase inhibitor activity
P	0031640	biological_process	killing of cells of another organism
P	0031965	cellular_component	nuclear membrane
P	0031982	cellular_component	vesicle
P	0032481	biological_process	positive regulation of type I interferon production
P	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
P	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
P	0042802	molecular_function	identical protein binding
P	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
P	0045087	biological_process	innate immune response
P	0048471	cellular_component	perinuclear region of cytoplasm
P	0050661	molecular_function	NADP binding
P	0050821	biological_process	protein stabilization
P	0050832	biological_process	defense response to fungus
P	0051287	molecular_function	NAD binding
P	0051402	biological_process	neuron apoptotic process
P	0051873	biological_process	killing by host of symbiont cells
P	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
P	0070062	cellular_component	extracellular exosome
P	0071346	biological_process	cellular response to type II interferon
P	0097452	cellular_component	GAIT complex
P	0097718	molecular_function	disordered domain specific binding
P	1990904	cellular_component	ribonucleoprotein complex
Q	0000226	biological_process	microtubule cytoskeleton organization
Q	0001819	biological_process	positive regulation of cytokine production
Q	0002376	biological_process	immune system process
Q	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
Q	0005515	molecular_function	protein binding
Q	0005634	cellular_component	nucleus
Q	0005737	cellular_component	cytoplasm
Q	0005811	cellular_component	lipid droplet
Q	0005829	cellular_component	cytosol
Q	0005856	cellular_component	cytoskeleton
Q	0005886	cellular_component	plasma membrane
Q	0006006	biological_process	glucose metabolic process
Q	0006096	biological_process	glycolytic process
Q	0006417	biological_process	regulation of translation
Q	0006915	biological_process	apoptotic process
Q	0008017	molecular_function	microtubule binding
Q	0010951	biological_process	negative regulation of endopeptidase activity
Q	0015630	cellular_component	microtubule cytoskeleton
Q	0016020	cellular_component	membrane
Q	0016241	biological_process	regulation of macroautophagy
Q	0016491	molecular_function	oxidoreductase activity
Q	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
Q	0016740	molecular_function	transferase activity
Q	0017148	biological_process	negative regulation of translation
Q	0019828	molecular_function	aspartic-type endopeptidase inhibitor activity
Q	0031640	biological_process	killing of cells of another organism
Q	0031965	cellular_component	nuclear membrane
Q	0031982	cellular_component	vesicle
Q	0032481	biological_process	positive regulation of type I interferon production
Q	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
Q	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
Q	0042802	molecular_function	identical protein binding
Q	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
Q	0045087	biological_process	innate immune response
Q	0048471	cellular_component	perinuclear region of cytoplasm
Q	0050661	molecular_function	NADP binding
Q	0050821	biological_process	protein stabilization
Q	0050832	biological_process	defense response to fungus
Q	0051287	molecular_function	NAD binding
Q	0051402	biological_process	neuron apoptotic process
Q	0051873	biological_process	killing by host of symbiont cells
Q	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
Q	0070062	cellular_component	extracellular exosome
Q	0071346	biological_process	cellular response to type II interferon
Q	0097452	cellular_component	GAIT complex
Q	0097718	molecular_function	disordered domain specific binding
Q	1990904	cellular_component	ribonucleoprotein complex
R	0000226	biological_process	microtubule cytoskeleton organization
R	0001819	biological_process	positive regulation of cytokine production
R	0002376	biological_process	immune system process
R	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
R	0005515	molecular_function	protein binding
R	0005634	cellular_component	nucleus
R	0005737	cellular_component	cytoplasm
R	0005811	cellular_component	lipid droplet
R	0005829	cellular_component	cytosol
R	0005856	cellular_component	cytoskeleton
R	0005886	cellular_component	plasma membrane
R	0006006	biological_process	glucose metabolic process
R	0006096	biological_process	glycolytic process
R	0006417	biological_process	regulation of translation
R	0006915	biological_process	apoptotic process
R	0008017	molecular_function	microtubule binding
R	0010951	biological_process	negative regulation of endopeptidase activity
R	0015630	cellular_component	microtubule cytoskeleton
R	0016020	cellular_component	membrane
R	0016241	biological_process	regulation of macroautophagy
R	0016491	molecular_function	oxidoreductase activity
R	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
R	0016740	molecular_function	transferase activity
R	0017148	biological_process	negative regulation of translation
R	0019828	molecular_function	aspartic-type endopeptidase inhibitor activity
R	0031640	biological_process	killing of cells of another organism
R	0031965	cellular_component	nuclear membrane
R	0031982	cellular_component	vesicle
R	0032481	biological_process	positive regulation of type I interferon production
R	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
R	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
R	0042802	molecular_function	identical protein binding
R	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
R	0045087	biological_process	innate immune response
R	0048471	cellular_component	perinuclear region of cytoplasm
R	0050661	molecular_function	NADP binding
R	0050821	biological_process	protein stabilization
R	0050832	biological_process	defense response to fungus
R	0051287	molecular_function	NAD binding
R	0051402	biological_process	neuron apoptotic process
R	0051873	biological_process	killing by host of symbiont cells
R	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
R	0070062	cellular_component	extracellular exosome
R	0071346	biological_process	cellular response to type II interferon
R	0097452	cellular_component	GAIT complex
R	0097718	molecular_function	disordered domain specific binding
R	1990904	cellular_component	ribonucleoprotein complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	35
Details	BINDING SITE FOR RESIDUE NAD P 336

Chain	Residue
P	ASN9
P	GLU79
P	ARG80
P	SER98
P	THR99
P	GLY100
P	PHE102
P	SER122
P	ALA123
P	CYS152
P	ALA183
P	GLY10
P	ASN316
P	TYR320
P	HOH340
P	HOH342
P	HOH391
P	HOH444
P	HOH453
P	HOH460
P	HOH476
P	HOH478
P	PHE11
P	HOH501
P	HOH548
P	HOH576
P	HOH577
Q	PRO191
Q	HOH492
P	GLY12
P	ARG13
P	ILE14
P	ASP35
P	PRO36
P	PHE37

---

site_id	AC2
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NAD Q 336

Chain	Residue
Q	ASN9
Q	GLY10
Q	PHE11
Q	GLY12
Q	ARG13
Q	ILE14
Q	ASP35
Q	PRO36
Q	PHE37
Q	ARG80
Q	SER98
Q	THR99
Q	GLY100
Q	PHE102
Q	SER122
Q	ALA123
Q	CYS152
Q	ALA183
Q	ASN316
Q	HOH347
Q	HOH362
Q	HOH397
Q	HOH406
Q	HOH414
Q	HOH417
Q	HOH471
Q	HOH505
Q	HOH566

---

site_id	AC3
Number of Residues	26
Details	BINDING SITE FOR RESIDUE NAD R 336

Chain	Residue
O	HOH479
R	ASN9
R	GLY10
R	PHE11
R	GLY12
R	ARG13
R	ILE14
R	ASN34
R	ASP35
R	PRO36
R	PHE37
R	ILE38
R	ARG80
R	SER98
R	THR99
R	GLY100
R	SER122
R	ALA123
R	CYS152
R	ASN316
R	HOH349
R	HOH392
R	HOH407
R	HOH446
R	HOH479
R	HOH519

---

Functional Information from PROSITE/UniProt

site_id	PS00071
Number of Residues	8
Details	GAPDH Glyceraldehyde 3-phosphate dehydrogenase active site. ASCTTNcL

Chain	Residue	Details
O	ALA150-LEU157

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Nucleophile => ECO:0000269|PubMed:25086035

Chain	Residue	Details
O	THR153
P	THR153
Q	THR153
R	THR153

---

site_id	SWS_FT_FI2
Number of Residues	20
Details	BINDING: BINDING => ECO:0000269|PubMed:16239728, ECO:0000269|PubMed:16510976

Chain	Residue	Details
O	ILE14
P	GLU317
Q	ILE14
Q	PRO36
Q	ASP81
Q	ALA123
Q	GLU317
R	ILE14
R	PRO36
R	ASP81
R	ALA123
O	PRO36
R	GLU317
O	ASP81
O	ALA123
O	GLU317
P	ILE14
P	PRO36
P	ASP81
P	ALA123

---

site_id	SWS_FT_FI3
Number of Residues	16
Details	BINDING: BINDING => ECO:0000250|UniProtKB:P22513

Chain	Residue	Details
O	CYS152
Q	ALA183
Q	GLY212
Q	VAL235
R	CYS152
R	ALA183
R	GLY212
R	VAL235
O	ALA183
O	GLY212
O	VAL235
P	CYS152
P	ALA183
P	GLY212
P	VAL235
Q	CYS152

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	SITE: Activates thiol group during catalysis => ECO:0000305|PubMed:16239728, ECO:0000305|PubMed:16510976

Chain	Residue	Details
O	ALA180
P	ALA180
Q	ALA180
R	ALA180

---

site_id	SWS_FT_FI5
Number of Residues	20
Details	MOD_RES: N6,N6-dimethyllysine => ECO:0000269|PubMed:18183946

Chain	Residue	Details
O	VAL6
P	GLU335
Q	VAL6
Q	LEU67
Q	VAL261
Q	GLN264
Q	GLU335
R	VAL6
R	LEU67
R	VAL261
R	GLN264
O	LEU67
R	GLU335
O	VAL261
O	GLN264
O	GLU335
P	VAL6
P	LEU67
P	VAL261
P	GLN264

---

site_id	SWS_FT_FI6
Number of Residues	28
Details	MOD_RES: Deamidated asparagine => ECO:0000269|PubMed:18183946

Chain	Residue	Details
O	GLY10
P	GLY71
P	ALA150
P	CYS156
P	GLY226
P	GLU317
Q	GLY10
Q	GLY65
Q	GLY71
Q	ALA150
Q	CYS156
O	GLY65
Q	GLY226
Q	GLU317
R	GLY10
R	GLY65
R	GLY71
R	ALA150
R	CYS156
R	GLY226
R	GLU317
O	GLY71
O	ALA150
O	CYS156
O	GLY226
O	GLU317
P	GLY10
P	GLY65

---

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:15592455

Chain	Residue	Details
O	MET43
P	MET43
Q	MET43
R	MET43

---

site_id	SWS_FT_FI8
Number of Residues	4
Details	MOD_RES: Methionine sulfoxide; in vitro => ECO:0000305|PubMed:25086035

Chain	Residue	Details
O	PHE47
P	PHE47
Q	PHE47
R	PHE47

---

site_id	SWS_FT_FI9
Number of Residues	12
Details	MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861

Chain	Residue	Details
O	ALA62
R	ALA62
R	VAL220
R	TYR255
O	VAL220
O	TYR255
P	ALA62
P	VAL220
P	TYR255
Q	ALA62
Q	VAL220
Q	TYR255

---

site_id	SWS_FT_FI10
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000269|PubMed:18183946, ECO:0007744|PubMed:20068231

Chain	Residue	Details
O	ILE76
P	ILE76
Q	ILE76
R	ILE76

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163

Chain	Residue	Details
O	LYS84
P	LYS84
Q	LYS84
R	LYS84

---

site_id	SWS_FT_FI12
Number of Residues	8
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:18183946

Chain	Residue	Details
O	ALA123
O	ASN149
P	ALA123
P	ASN149
Q	ALA123
Q	ASN149
R	ALA123
R	ASN149

---

site_id	SWS_FT_FI13
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:23186163

Chain	Residue	Details
O	CYS152
P	CYS152
Q	CYS152
R	CYS152

---

site_id	SWS_FT_FI14
Number of Residues	4
Details	MOD_RES: S-nitrosocysteine; in reversibly inhibited form => ECO:0000250|UniProtKB:P04797

Chain	Residue	Details
O	THR153
P	THR153
Q	THR153
R	THR153

---

site_id	SWS_FT_FI15
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
O	THR154
P	THR154
Q	THR154
R	THR154

---

site_id	SWS_FT_FI16
Number of Residues	8
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:24275569

Chain	Residue	Details
O	VAL178
O	ALA183
P	VAL178
P	ALA183
Q	VAL178
Q	ALA183
R	VAL178
R	ALA183

---

site_id	SWS_FT_FI17
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:24275569

Chain	Residue	Details
O	GLN185
P	GLN185
Q	GLN185
R	GLN185

---

site_id	SWS_FT_FI18
Number of Residues	8
Details	MOD_RES: N6-malonyllysine; alternate => ECO:0000269|PubMed:21908771

Chain	Residue	Details
O	LEU195
O	ALA216
P	LEU195
P	ALA216
Q	LEU195
Q	ALA216
R	LEU195
R	ALA216

---

site_id	SWS_FT_FI19
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332

Chain	Residue	Details
O	GLY212
P	GLY212
Q	GLY212
R	GLY212

---

site_id	SWS_FT_FI20
Number of Residues	4
Details	MOD_RES: N6-acetyllysine; alternate => ECO:0007744|PubMed:19608861

Chain	Residue	Details
O	LEU228
P	LEU228
Q	LEU228
R	LEU228

---

site_id	SWS_FT_FI21
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000269|PubMed:18183946, ECO:0007744|PubMed:23186163

Chain	Residue	Details
O	GLY230
P	GLY230
Q	GLY230
R	GLY230

---

site_id	SWS_FT_FI22
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000269|PubMed:18183946

Chain	Residue	Details
O	ALA238
P	ALA238
Q	ALA238
R	ALA238

---

site_id	SWS_FT_FI23
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569

Chain	Residue	Details
O	VAL242
P	VAL242
Q	VAL242
R	VAL242

---

site_id	SWS_FT_FI24
Number of Residues	4
Details	MOD_RES: S-nitrosocysteine => ECO:0000269|PubMed:22771119, ECO:0000269|PubMed:25417112

Chain	Residue	Details
O	ARG248
P	ARG248
Q	ARG248
R	ARG248

---

site_id	SWS_FT_FI25
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:18183946, ECO:0007744|PubMed:19690332

Chain	Residue	Details
O	TRP313
P	TRP313
Q	TRP313
R	TRP313

---

site_id	SWS_FT_FI26
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
O	LYS334
P	LYS334
Q	LYS334
R	LYS334

---

site_id	SWS_FT_FI27
Number of Residues	8
Details	CARBOHYD: (Microbial infection) N-beta-linked (GlcNAc) arginine => ECO:0000269|PubMed:28522607

Chain	Residue	Details
O	ASP198
O	GLY201
P	ASP198
P	GLY201
Q	ASP198
Q	GLY201
R	ASP198
R	GLY201

---

site_id	SWS_FT_FI28
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733

Chain	Residue	Details
O	THR187
P	THR187
Q	THR187
R	THR187

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1szj

Chain	Residue	Details
O	HIS179
O	CYS152

---

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1szj

Chain	Residue	Details
P	HIS179
P	CYS152

---

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 1szj

Chain	Residue	Details
Q	HIS179
Q	CYS152

---

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 1szj

Chain	Residue	Details
R	HIS179
R	CYS152

---