4Z0H

X-ray structure of cytoplasmic glyceraldehyde-3-phosphate dehydrogenase (GapC1) complexed with NAD

Functional Information from GO Data

Chain	GOid	namespace	contents
O	0000325	cellular_component	plant-type vacuole
O	0003677	molecular_function	DNA binding
O	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
O	0005507	molecular_function	copper ion binding
O	0005515	molecular_function	protein binding
O	0005634	cellular_component	nucleus
O	0005737	cellular_component	cytoplasm
O	0005739	cellular_component	mitochondrion
O	0005740	cellular_component	mitochondrial envelope
O	0005794	cellular_component	Golgi apparatus
O	0005829	cellular_component	cytosol
O	0005886	cellular_component	plasma membrane
O	0005975	biological_process	carbohydrate metabolic process
O	0006006	biological_process	glucose metabolic process
O	0006094	biological_process	gluconeogenesis
O	0006096	biological_process	glycolytic process
O	0006979	biological_process	response to oxidative stress
O	0008886	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity
O	0009408	biological_process	response to heat
O	0009507	cellular_component	chloroplast
O	0009744	biological_process	response to sucrose
O	0010154	biological_process	fruit development
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	0042542	biological_process	response to hydrogen peroxide
O	0045893	biological_process	positive regulation of DNA-templated transcription
O	0048046	cellular_component	apoplast
O	0048316	biological_process	seed development
O	0050661	molecular_function	NADP binding
O	0051287	molecular_function	NAD binding
O	0051775	biological_process	response to redox state
O	1901149	molecular_function	salicylic acid binding
R	0000325	cellular_component	plant-type vacuole
R	0003677	molecular_function	DNA binding
R	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
R	0005507	molecular_function	copper ion binding
R	0005515	molecular_function	protein binding
R	0005634	cellular_component	nucleus
R	0005737	cellular_component	cytoplasm
R	0005739	cellular_component	mitochondrion
R	0005740	cellular_component	mitochondrial envelope
R	0005794	cellular_component	Golgi apparatus
R	0005829	cellular_component	cytosol
R	0005886	cellular_component	plasma membrane
R	0005975	biological_process	carbohydrate metabolic process
R	0006006	biological_process	glucose metabolic process
R	0006094	biological_process	gluconeogenesis
R	0006096	biological_process	glycolytic process
R	0006979	biological_process	response to oxidative stress
R	0008886	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity
R	0009408	biological_process	response to heat
R	0009507	cellular_component	chloroplast
R	0009744	biological_process	response to sucrose
R	0010154	biological_process	fruit development
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	0042542	biological_process	response to hydrogen peroxide
R	0045893	biological_process	positive regulation of DNA-templated transcription
R	0048046	cellular_component	apoplast
R	0048316	biological_process	seed development
R	0050661	molecular_function	NADP binding
R	0051287	molecular_function	NAD binding
R	0051775	biological_process	response to redox state
R	1901149	molecular_function	salicylic acid binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	25
Details	binding site for residue NAD O 401

Chain	Residue
O	ASN6
O	PHE34
O	ILE35
O	ILE76
O	ARG77
O	SER95
O	THR96
O	GLY97
O	PHE99
O	SER119
O	ALA120
O	GLY7
O	CYS149
O	ALA180
O	ASN313
O	TYR317
O	SO4402
O	HOH520
O	PHE8
O	GLY9
O	ARG10
O	ILE11
O	ASN31
O	ASP32
O	PRO33

---

site_id	AC2
Number of Residues	4
Details	binding site for residue SO4 O 402

Chain	Residue
O	THR179
O	THR181
O	ARG231
O	NAD401

---

site_id	AC3
Number of Residues	5
Details	binding site for residue SO4 O 403

Chain	Residue
O	SER148
O	THR150
O	THR208
O	GLY209
O	HOH503

---

site_id	AC4
Number of Residues	5
Details	binding site for residue SO4 O 404

Chain	Residue
O	SER200
O	SER200
O	PRO233
R	SER200
R	PHE201

---

site_id	AC5
Number of Residues	20
Details	binding site for residue NAD R 401

Chain	Residue
R	ASN6
R	PHE8
R	GLY9
R	ARG10
R	ILE11
R	ASP32
R	PRO33
R	PHE34
R	ARG77
R	SER95
R	THR96
R	GLY97
R	SER119
R	ALA120
R	ALA180
R	ASN313
R	TYR317
R	SO4402
R	HOH514
R	HOH529

---

site_id	AC6
Number of Residues	5
Details	binding site for residue SO4 R 402

Chain	Residue
R	THR179
R	THR181
R	ARG231
R	NAD401
R	HOH531

---

site_id	AC7
Number of Residues	5
Details	binding site for residue SO4 R 403

Chain	Residue
R	SER148
R	THR150
R	THR208
R	GLY209
R	ALA210

---

site_id	AC8
Number of Residues	2
Details	binding site for residue SO4 R 404

Chain	Residue
R	ASN287
R	TRP315

---

site_id	AC9
Number of Residues	4
Details	binding site for residue SO4 R 405

Chain	Residue
R	LYS268
R	ARG288
R	HOH511
R	HOH535

---

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	ALA147-LEU154

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2015","submissionDatabase":"PDB data bank","title":"Structural determinants of sulfenic acid reactivity in the active site of cytoplasmic and photosynthetic Arabidopsis GAPDHs from Arabidopsis thaliana.","authors":["Zaffagnini M.","Fermani S.","Calvaresi M.","Marchand C.","Orru R.","Iommarini L.","Sparla F.","Bottoni F.","Falini G.","Lemaire S.D.","Trost P."]}}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	18
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P00362","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	Site: {"description":"Activates thiol group during catalysis","evidences":[{"source":"UniProtKB","id":"P00362","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	Modified residue: {"description":"S-nitrosocysteine; transient; alternate","evidences":[{"source":"UniProtKB","id":"Q9FX54","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	Modified residue: {"description":"S-nitrosocysteine; transient","evidences":[{"source":"UniProtKB","id":"Q9FX54","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---