1IVH

STRUCTURE OF HUMAN ISOVALERYL-COA DEHYDROGENASE AT 2.6 ANGSTROMS RESOLUTION: STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003995	molecular_function	acyl-CoA dehydrogenase activity
A	0004085	molecular_function	butyryl-CoA dehydrogenase activity
A	0005515	molecular_function	protein binding
A	0005654	cellular_component	nucleoplasm
A	0005739	cellular_component	mitochondrion
A	0005759	cellular_component	mitochondrial matrix
A	0006552	biological_process	L-leucine catabolic process
A	0006631	biological_process	fatty acid metabolic process
A	0008470	molecular_function	isovaleryl-CoA dehydrogenase activity
A	0009083	biological_process	branched-chain amino acid catabolic process
A	0016491	molecular_function	oxidoreductase activity
A	0016627	molecular_function	oxidoreductase activity, acting on the CH-CH group of donors
A	0016937	molecular_function	short-chain fatty acyl-CoA dehydrogenase activity
A	0033539	biological_process	fatty acid beta-oxidation using acyl-CoA dehydrogenase
A	0042802	molecular_function	identical protein binding
A	0050660	molecular_function	flavin adenine dinucleotide binding
B	0003995	molecular_function	acyl-CoA dehydrogenase activity
B	0004085	molecular_function	butyryl-CoA dehydrogenase activity
B	0005515	molecular_function	protein binding
B	0005654	cellular_component	nucleoplasm
B	0005739	cellular_component	mitochondrion
B	0005759	cellular_component	mitochondrial matrix
B	0006552	biological_process	L-leucine catabolic process
B	0006631	biological_process	fatty acid metabolic process
B	0008470	molecular_function	isovaleryl-CoA dehydrogenase activity
B	0009083	biological_process	branched-chain amino acid catabolic process
B	0016491	molecular_function	oxidoreductase activity
B	0016627	molecular_function	oxidoreductase activity, acting on the CH-CH group of donors
B	0016937	molecular_function	short-chain fatty acyl-CoA dehydrogenase activity
B	0033539	biological_process	fatty acid beta-oxidation using acyl-CoA dehydrogenase
B	0042802	molecular_function	identical protein binding
B	0050660	molecular_function	flavin adenine dinucleotide binding
C	0003995	molecular_function	acyl-CoA dehydrogenase activity
C	0004085	molecular_function	butyryl-CoA dehydrogenase activity
C	0005515	molecular_function	protein binding
C	0005654	cellular_component	nucleoplasm
C	0005739	cellular_component	mitochondrion
C	0005759	cellular_component	mitochondrial matrix
C	0006552	biological_process	L-leucine catabolic process
C	0006631	biological_process	fatty acid metabolic process
C	0008470	molecular_function	isovaleryl-CoA dehydrogenase activity
C	0009083	biological_process	branched-chain amino acid catabolic process
C	0016491	molecular_function	oxidoreductase activity
C	0016627	molecular_function	oxidoreductase activity, acting on the CH-CH group of donors
C	0016937	molecular_function	short-chain fatty acyl-CoA dehydrogenase activity
C	0033539	biological_process	fatty acid beta-oxidation using acyl-CoA dehydrogenase
C	0042802	molecular_function	identical protein binding
C	0050660	molecular_function	flavin adenine dinucleotide binding
D	0003995	molecular_function	acyl-CoA dehydrogenase activity
D	0004085	molecular_function	butyryl-CoA dehydrogenase activity
D	0005515	molecular_function	protein binding
D	0005654	cellular_component	nucleoplasm
D	0005739	cellular_component	mitochondrion
D	0005759	cellular_component	mitochondrial matrix
D	0006552	biological_process	L-leucine catabolic process
D	0006631	biological_process	fatty acid metabolic process
D	0008470	molecular_function	isovaleryl-CoA dehydrogenase activity
D	0009083	biological_process	branched-chain amino acid catabolic process
D	0016491	molecular_function	oxidoreductase activity
D	0016627	molecular_function	oxidoreductase activity, acting on the CH-CH group of donors
D	0016937	molecular_function	short-chain fatty acyl-CoA dehydrogenase activity
D	0033539	biological_process	fatty acid beta-oxidation using acyl-CoA dehydrogenase
D	0042802	molecular_function	identical protein binding
D	0050660	molecular_function	flavin adenine dinucleotide binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	23
Details	BINDING SITE FOR RESIDUE FAD A 399

Chain	Residue
A	LEU133
A	GLU379
A	LEU383
A	COS400
A	HOH512
A	HOH589
B	ARG280
B	PHE283
B	ILE287
B	PHE290
B	MET293
A	MET135
B	GLN348
B	CYS349
B	GLY352
D	GLN291
A	SER136
A	GLY141
A	SER142
A	TRP166
A	THR168
A	ILE373
A	THR377

---

site_id	AC2
Number of Residues	18
Details	BINDING SITE FOR RESIDUE COS A 400

Chain	Residue
A	GLY141
A	SER142
A	VAL144
A	SER190
A	ARG191
A	VAL244
A	TYR245
A	MET248
A	ASP252
A	GLU254
A	ARG255
A	ALA375
A	GLY376
A	VAL380
A	VAL384
A	ARG387
A	FAD399
B	PHE283

---

site_id	AC3
Number of Residues	24
Details	BINDING SITE FOR RESIDUE FAD B 399

Chain	Residue
A	ARG280
A	PHE283
A	PHE290
A	MET293
A	GLN348
A	CYS349
A	GLY352
B	LEU133
B	MET135
B	SER136
B	GLY141
B	SER142
B	TRP166
B	ILE167
B	THR168
B	LEU370
B	ILE373
B	THR377
B	GLU379
B	COS400
B	HOH525
B	HOH531
B	HOH591
C	GLN291

---

site_id	AC4
Number of Residues	21
Details	BINDING SITE FOR RESIDUE COS B 400

Chain	Residue
A	PHE283
B	GLY141
B	SER142
B	VAL144
B	VAL145
B	SER190
B	ARG191
B	VAL244
B	TYR245
B	MET248
B	LEU251
B	ASP252
B	GLU254
B	ARG255
B	GLY374
B	ALA375
B	GLY376
B	VAL380
B	ARG387
B	FAD399
B	HOH545

---

site_id	AC5
Number of Residues	28
Details	BINDING SITE FOR RESIDUE FAD C 399

Chain	Residue
C	LEU383
C	COS400
C	HOH500
C	HOH505
C	HOH517
C	HOH547
C	HOH587
D	ARG280
D	PHE283
D	ILE287
D	PHE290
D	MET293
D	GLN348
D	CYS349
D	GLY352
B	GLN291
C	LEU133
C	MET135
C	SER136
C	GLY141
C	SER142
C	TRP166
C	ILE167
C	THR168
C	LEU370
C	ILE373
C	THR377
C	GLU379

---

site_id	AC6
Number of Residues	21
Details	BINDING SITE FOR RESIDUE COS C 400

Chain	Residue
C	MET135
C	GLY141
C	SER142
C	VAL144
C	VAL145
C	SER190
C	ARG191
C	VAL244
C	TYR245
C	MET248
C	LEU251
C	GLU254
C	ARG255
C	ALA375
C	GLY376
C	VAL380
C	ARG387
C	FAD399
C	HOH587
C	HOH686
D	PHE283

---

site_id	AC7
Number of Residues	26
Details	BINDING SITE FOR RESIDUE FAD D 399

Chain	Residue
A	GLN291
C	ARG280
C	ILE287
C	PHE290
C	MET293
C	GLN348
C	CYS349
C	GLY352
C	HOH529
D	LEU133
D	MET135
D	SER136
D	GLY141
D	SER142
D	TRP166
D	ILE167
D	THR168
D	LYS213
D	LEU370
D	ILE373
D	THR377
D	GLU379
D	COS400
D	HOH564
D	HOH605
D	HOH655

---

site_id	AC8
Number of Residues	17
Details	BINDING SITE FOR RESIDUE COS D 400

Chain	Residue
C	PHE283
D	MET135
D	GLY141
D	SER142
D	SER190
D	VAL244
D	MET248
D	LEU251
D	GLU254
D	ARG255
D	GLY374
D	ALA375
D	GLY376
D	VAL380
D	VAL384
D	ARG387
D	FAD399

---

Functional Information from PROSITE/UniProt

site_id	PS00072
Number of Residues	13
Details	ACYL_COA_DH_1 Acyl-CoA dehydrogenases signature 1. AMSEpnAGSDvvS

Chain	Residue	Details
A	ALA134-SER146

---

site_id	PS00073
Number of Residues	20
Details	ACYL_COA_DH_2 Acyl-CoA dehydrogenases signature 2. QcFGGnGYinDfpmgRflrD

Chain	Residue	Details
A	GLN348-ASP367

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Proton acceptor => ECO:0000269|PubMed:7640268, ECO:0007744|PDB:1IVH

Chain	Residue	Details
A	VAL257
B	VAL257
C	VAL257
D	VAL257

---

site_id	SWS_FT_FI2
Number of Residues	44
Details	BINDING: BINDING => ECO:0000269|PubMed:9214289, ECO:0007744|PDB:1IVH

Chain	Residue	Details
A	SER136
A	SER378
A	VAL380
B	SER136
B	VAL145
B	ASN169
B	ILE193
B	MET248
B	ARG255
B	PHE283
B	GLN294
A	VAL145
B	GLY351
B	SER378
B	VAL380
C	SER136
C	VAL145
C	ASN169
C	ILE193
C	MET248
C	ARG255
C	PHE283
A	ASN169
C	GLN294
C	GLY351
C	SER378
C	VAL380
D	SER136
D	VAL145
D	ASN169
D	ILE193
D	MET248
D	ARG255
A	ILE193
D	PHE283
D	GLN294
D	GLY351
D	SER378
D	VAL380
A	MET248
A	ARG255
A	PHE283
A	GLN294
A	GLY351

---

site_id	SWS_FT_FI3
Number of Residues	16
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q9JHI5

Chain	Residue	Details
A	GLN29
C	GLU38
C	ARG49
C	ALA233
D	GLN29
D	GLU38
D	ARG49
D	ALA233
A	GLU38
A	ARG49
A	ALA233
B	GLN29
B	GLU38
B	ARG49
B	ALA233
C	GLN29

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q9JHI5

Chain	Residue	Details
A	ASP212
B	ASP212
C	ASP212
D	ASP212

---

site_id	SWS_FT_FI5
Number of Residues	4
Details	MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:Q9JHI5

Chain	Residue	Details
A	HIS289
B	HIS289
C	HIS289
D	HIS289

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	1
Details	a catalytic site defined by CSA, PubMed 14728676, 9214289

Chain	Residue	Details
A	GLU254

---

site_id	MCSA1
Number of Residues	4
Details	M-CSA 68

Chain	Residue	Details
A	MET135	electrostatic stabiliser, hydrogen bond donor
A	SER136	electrostatic stabiliser, hydrogen bond donor
A	GLU254	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, steric role
A	ARG387	electrostatic stabiliser

---

site_id	MCSA2
Number of Residues	4
Details	M-CSA 68

Chain	Residue	Details
B	MET135	electrostatic stabiliser, hydrogen bond donor
B	SER136	electrostatic stabiliser, hydrogen bond donor
B	GLU254	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, steric role
B	ARG387	electrostatic stabiliser

---

site_id	MCSA3
Number of Residues	4
Details	M-CSA 68

Chain	Residue	Details
C	MET135	electrostatic stabiliser, hydrogen bond donor
C	SER136	electrostatic stabiliser, hydrogen bond donor
C	GLU254	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, steric role
C	ARG387	electrostatic stabiliser

---

site_id	MCSA4
Number of Residues	4
Details	M-CSA 68

Chain	Residue	Details
D	MET135	electrostatic stabiliser, hydrogen bond donor
D	SER136	electrostatic stabiliser, hydrogen bond donor
D	GLU254	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, steric role
D	ARG387	electrostatic stabiliser

---