1MLY

Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in complex with the cis isomer of amiclenomycin

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004015	molecular_function	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
A	0004141	molecular_function	dethiobiotin synthase activity
A	0005737	cellular_component	cytoplasm
A	0008483	molecular_function	transaminase activity
A	0009102	biological_process	biotin biosynthetic process
A	0016740	molecular_function	transferase activity
A	0030170	molecular_function	pyridoxal phosphate binding
A	0042803	molecular_function	protein homodimerization activity
B	0003824	molecular_function	catalytic activity
B	0004015	molecular_function	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
B	0004141	molecular_function	dethiobiotin synthase activity
B	0005737	cellular_component	cytoplasm
B	0008483	molecular_function	transaminase activity
B	0009102	biological_process	biotin biosynthetic process
B	0016740	molecular_function	transferase activity
B	0030170	molecular_function	pyridoxal phosphate binding
B	0042803	molecular_function	protein homodimerization activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE ACZ A 731

Chain	Residue
A	TRP52
A	HOH806
B	HOH976
A	TRP53
A	TYR144
A	LYS274
A	ARG391
A	PHE393
A	PLP730
A	HOH749
A	HOH767

---

site_id	AC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE ACZ B 831

Chain	Residue
A	THR309
B	TRP52
B	TYR144
B	ALA217
B	ARG391
B	PHE393
B	TYR398
B	PLP830
B	HOH900
B	HOH914
B	HOH919
B	HOH973
B	HOH992

---

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA B 701

Chain	Residue
B	VAL96
B	THR99
B	PRO100
B	LEU103
B	HOH880

---

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA A 702

Chain	Residue
A	VAL96
A	THR99
A	PRO100
A	LEU103
A	HOH774

---

site_id	AC5
Number of Residues	17
Details	BINDING SITE FOR RESIDUE PLP A 730

Chain	Residue
A	GLY112
A	SER113
A	TYR144
A	HIS145
A	GLY146
A	GLU211
A	ASP245
A	ILE247
A	LYS274
A	ACZ731
A	HOH744
A	HOH794
A	HOH797
B	PRO308
B	THR309
B	HOH832
B	HOH847

---

site_id	AC6
Number of Residues	16
Details	BINDING SITE FOR RESIDUE PLP B 830

Chain	Residue
A	PRO308
A	THR309
A	HOH735
B	TRP53
B	GLY112
B	SER113
B	HIS145
B	GLU211
B	ASP245
B	ILE247
B	ALA248
B	LYS274
B	ACZ831
B	HOH836
B	HOH862
B	HOH875

---

Functional Information from PROSITE/UniProt

site_id	PS00600
Number of Residues	38
Details	AA_TRANSFER_CLASS_3 Aminotransferases class-III pyridoxal-phosphate attachment site. LIaDEIat.GFgRtGklfacehaeiap....DILclGKaltGG

Chain	Residue	Details
A	LEU242-GLY279

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0000269|PubMed:12218056, ECO:0007744|PDB:1MLY, ECO:0007744|PDB:1QJ3

Chain	Residue	Details
A	TRP52
A	LYS274
B	TRP52
B	LYS274

---

site_id	SWS_FT_FI2
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0000269|PubMed:12379100, ECO:0000269|PubMed:14756557, ECO:0007744|PDB:1DTY, ECO:0007744|PDB:1MGV, ECO:0007744|PDB:1QJ3, ECO:0007744|PDB:1QJ5, ECO:0007744|PDB:1S07

Chain	Residue	Details
A	GLY112
A	PRO308
B	GLY112
B	PRO308

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	BINDING: BINDING => ECO:0000305|PubMed:10452893

Chain	Residue	Details
A	TYR144
B	TYR144

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0000269|PubMed:12379100, ECO:0000269|PubMed:14756557, ECO:0007744|PDB:1MGV, ECO:0007744|PDB:1QJ3, ECO:0007744|PDB:1QJ5, ECO:0007744|PDB:1S07

Chain	Residue	Details
A	ASP245
B	ASP245

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0007744|PDB:1QJ3

Chain	Residue	Details
A	GLY307
B	GLY307

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269|PubMed:10452893, ECO:0000269|PubMed:12218056, ECO:0007744|PDB:1MLY, ECO:0007744|PDB:1MLZ, ECO:0007744|PDB:1QJ3

Chain	Residue	Details
A	ARG391
B	ARG391

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	SITE: Participates in the substrate recognition with KAPA and in a stacking interaction with the adenine ring of SAM => ECO:0000305

Chain	Residue	Details
A	TYR17
B	TYR17

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000269|PubMed:12379100, ECO:0000269|PubMed:14756557, ECO:0007744|PDB:1DTY, ECO:0007744|PDB:1MGV, ECO:0007744|PDB:1QJ3, ECO:0007744|PDB:1QJ5, ECO:0007744|PDB:1S06, ECO:0007744|PDB:1S08, ECO:0007744|PDB:1S09, ECO:0007744|PDB:1S0A

Chain	Residue	Details
A	LYS274
B	LYS274

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	4
Details	M-CSA 249

Chain	Residue	Details
A	TYR17	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
A	TYR144	hydrogen bond acceptor, steric role, van der waals interaction
A	ASP245	electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role
A	LYS274	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor

---

site_id	MCSA2
Number of Residues	4
Details	M-CSA 249

Chain	Residue	Details
B	TYR17	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
B	TYR144	hydrogen bond acceptor, steric role, van der waals interaction
B	ASP245	electrostatic stabiliser, hydrogen bond acceptor, increase basicity, steric role
B	LYS274	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor

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