Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4NDN

Structural insights of MAT enzymes: MATa2b complexed with SAM and PPNP

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004478	molecular_function	methionine adenosyltransferase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005829	cellular_component	cytosol
A	0006556	biological_process	S-adenosylmethionine biosynthetic process
A	0006730	biological_process	one-carbon metabolic process
A	0016740	molecular_function	transferase activity
A	0034214	biological_process	protein hexamerization
A	0036094	molecular_function	small molecule binding
A	0042802	molecular_function	identical protein binding
A	0046872	molecular_function	metal ion binding
A	0048269	cellular_component	methionine adenosyltransferase complex
A	0051291	biological_process	protein heterooligomerization
A	0061431	biological_process	cellular response to methionine
A	1904263	biological_process	positive regulation of TORC1 signaling
A	1990830	biological_process	cellular response to leukemia inhibitory factor
B	0004478	molecular_function	methionine adenosyltransferase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005829	cellular_component	cytosol
B	0006556	biological_process	S-adenosylmethionine biosynthetic process
B	0006730	biological_process	one-carbon metabolic process
B	0016740	molecular_function	transferase activity
B	0034214	biological_process	protein hexamerization
B	0036094	molecular_function	small molecule binding
B	0042802	molecular_function	identical protein binding
B	0046872	molecular_function	metal ion binding
B	0048269	cellular_component	methionine adenosyltransferase complex
B	0051291	biological_process	protein heterooligomerization
B	0061431	biological_process	cellular response to methionine
B	1904263	biological_process	positive regulation of TORC1 signaling
B	1990830	biological_process	cellular response to leukemia inhibitory factor
C	0004478	molecular_function	methionine adenosyltransferase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005829	cellular_component	cytosol
C	0006556	biological_process	S-adenosylmethionine biosynthetic process
C	0006730	biological_process	one-carbon metabolic process
C	0016740	molecular_function	transferase activity
C	0034214	biological_process	protein hexamerization
C	0036094	molecular_function	small molecule binding
C	0042802	molecular_function	identical protein binding
C	0046872	molecular_function	metal ion binding
C	0048269	cellular_component	methionine adenosyltransferase complex
C	0051291	biological_process	protein heterooligomerization
C	0061431	biological_process	cellular response to methionine
C	1904263	biological_process	positive regulation of TORC1 signaling
C	1990830	biological_process	cellular response to leukemia inhibitory factor
D	0004478	molecular_function	methionine adenosyltransferase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005829	cellular_component	cytosol
D	0006556	biological_process	S-adenosylmethionine biosynthetic process
D	0006730	biological_process	one-carbon metabolic process
D	0016740	molecular_function	transferase activity
D	0034214	biological_process	protein hexamerization
D	0036094	molecular_function	small molecule binding
D	0042802	molecular_function	identical protein binding
D	0046872	molecular_function	metal ion binding
D	0048269	cellular_component	methionine adenosyltransferase complex
D	0051291	biological_process	protein heterooligomerization
D	0061431	biological_process	cellular response to methionine
D	1904263	biological_process	positive regulation of TORC1 signaling
D	1990830	biological_process	cellular response to leukemia inhibitory factor
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005829	cellular_component	cytosol
E	0006556	biological_process	S-adenosylmethionine biosynthetic process
E	0006730	biological_process	one-carbon metabolic process
E	0019899	molecular_function	enzyme binding
E	0048269	cellular_component	methionine adenosyltransferase complex
E	0048270	molecular_function	methionine adenosyltransferase regulator activity
E	0070062	cellular_component	extracellular exosome
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005829	cellular_component	cytosol
F	0006556	biological_process	S-adenosylmethionine biosynthetic process
F	0006730	biological_process	one-carbon metabolic process
F	0019899	molecular_function	enzyme binding
F	0048269	cellular_component	methionine adenosyltransferase complex
F	0048270	molecular_function	methionine adenosyltransferase regulator activity
F	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 401

Chain	Residue
A	ASP31
A	LYS265
A	MG402
A	PPK406
A	HOH529
A	HOH600

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 402

Chain	Residue
B	HOH595
A	MG401
A	PPK406
B	LYS285

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 403

Chain	Residue
A	ALA162
A	ALA165
A	GLU166
A	ARG169

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 404

Chain	Residue
A	GLN36
A	GLN372
A	ARG373
A	ARG382
A	HOH531

site_id	AC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO A 405

Chain	Residue
A	GLY69
A	GLU70
A	ALA109
A	GLU111
B	LYS61
B	THR62
B	GLY257
B	ASP258
B	ALA259

site_id	AC6
Number of Residues	16
Details	BINDING SITE FOR RESIDUE PPK A 406

Chain	Residue
A	GLU23
A	HIS29
A	ASP31
A	LYS181
A	ARG264
A	LYS265
A	MG401
A	MG402
A	SAM407
A	HOH600
B	ASP134
B	GLY280
B	ALA281
B	LYS285
B	ASP291
B	HOH585

site_id	AC7
Number of Residues	20
Details	BINDING SITE FOR RESIDUE SAM A 407

Chain	Residue
A	HIS29
A	PRO30
A	ASP179
A	LYS181
A	SER247
A	ARG249
A	PHE250
A	ASP258
A	PPK406
A	HOH503
A	HOH505
B	ALA55
B	GLU70
B	GLN113
B	ASP116
B	ILE117
B	ASP134
B	LYS289
B	HOH504
B	HOH509

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 401

Chain	Residue
A	LYS61
A	GLN256
B	GLU111
B	GLN112
B	PRO115

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO B 402

Chain	Residue
D	HOH523

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 403

Chain	Residue
B	ASP191
B	ARG192
B	ARG312
B	THR337

site_id	BC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO B 404

Chain	Residue
B	HIS326
B	ASP354

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO B 405

Chain	Residue
A	THR17
B	SER331
B	ILE332
B	ARG343
B	LEU346
B	HOH529
B	HOH549

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 401

Chain	Residue
C	ASP31
C	ARG264
C	PPK404
C	HOH507
C	HOH552
D	MG401

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 402

Chain	Residue
C	PHE139
C	THR270
C	HIS277
C	GLY278

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 403

Chain	Residue
C	LEU328
C	SER329
C	ILE330
C	HOH534
C	HOH591

site_id	BC7
Number of Residues	18
Details	BINDING SITE FOR RESIDUE PPK C 404

Chain	Residue
C	HIS29
C	ASP31
C	LYS181
C	ARG264
C	LYS265
C	MG401
C	SAM405
C	HOH502
C	HOH552
C	HOH567
C	HOH579
D	ASP134
D	GLY280
D	ALA281
D	LYS285
D	ASP291
D	MG401
C	GLU23

site_id	BC8
Number of Residues	20
Details	BINDING SITE FOR RESIDUE SAM C 405

Chain	Residue
C	HIS29
C	PRO30
C	ASP179
C	LYS181
C	SER247
C	ARG249
C	PHE250
C	ASP258
C	PPK404
C	HOH504
C	HOH558
D	ALA55
D	GLU70
D	GLN113
D	ASP116
D	ILE117
D	ASP134
D	LYS289
D	HOH528
D	HOH574

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG D 401

Chain	Residue
C	MG401
C	PPK404
C	HOH567

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 402

Chain	Residue
D	TYR242
D	HIS243
D	LEU244

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 403

Chain	Residue
D	GLN36
D	HIS89
D	GLN372
D	ARG373
D	HOH564

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO D 404

Chain	Residue
B	ASP78
B	GLN80
D	ILE71
D	TYR79
D	LEU110

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 405

Chain	Residue
D	VAL82
D	GLU85
D	ALA86
D	GLN372

site_id	CC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 406

Chain	Residue
D	ARG192
D	ARG312
D	GLY336
D	THR337

site_id	CC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 407

Chain	Residue
D	LYS228
D	ALA229
D	PRO232

site_id	CC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO E 401

Chain	Residue
E	GLY241
E	ASN242
E	GLN283
E	LEU284
E	ARG297
E	HOH508
E	HOH533

Functional Information from PROSITE/UniProt

site_id	PS00376
Number of Residues	11
Details	ADOMET_SYNTHASE_1 S-adenosylmethionine synthase signature 1. GAGDQGlmfGY

Chain	Residue	Details
A	GLY131-TYR141

site_id	PS00377
Number of Residues	9
Details	ADOMET_SYNTHASE_2 S-adenosylmethionine synthase signature 2. GGGAFSgKD

Chain	Residue	Details
A	GLY278-ASP286

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	14
Details	BINDING: BINDING => ECO:0007744\|PDB:2YDX

Chain	Residue	Details
E	THR26
F	ASN60
F	CYS82
F	ARG86
F	TYR148
F	LEU174
E	PHE49
E	ASN60
E	CYS82
E	ARG86
E	TYR148
E	LEU174
F	THR26
F	PHE49

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
E	THR298
F	THR298
C	ASP31
D	ASP31

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P0A817

Chain	Residue	Details
A	GLU57
B	GLU57
C	GLU57
D	GLU57

site_id	SWS_FT_FI4
Number of Residues	4
Details	BINDING: in other chain => ECO:0000305\|PubMed:25075345, ECO:0007744\|PDB:4NDN

Chain	Residue	Details
A	GLU70
B	GLU70
C	GLU70
D	GLU70

site_id	SWS_FT_FI5
Number of Residues	4
Details	BINDING: in other chain => ECO:0000305\|PubMed:25075345

Chain	Residue	Details
A	GLN113
B	GLN113
C	GLN113
D	GLN113

site_id	SWS_FT_FI6
Number of Residues	4
Details	BINDING: in other chain => ECO:0000305\|PubMed:25075345, ECO:0000305\|PubMed:26858410, ECO:0007744\|PDB:4KTT, ECO:0007744\|PDB:4NDN, ECO:0007744\|PDB:5A19, ECO:0007744\|PDB:5A1G, ECO:0007744\|PDB:5A1I

Chain	Residue	Details
A	ASP179
B	ASP179
C	ASP179
D	ASP179

site_id	SWS_FT_FI7
Number of Residues	4
Details	BINDING: in other chain => ECO:0000305\|PubMed:25075345, ECO:0000305\|PubMed:26858410, ECO:0007744\|PDB:4KTT, ECO:0007744\|PDB:4NDN, ECO:0007744\|PDB:5A1G, ECO:0007744\|PDB:5A1I

Chain	Residue	Details
A	SER247
B	SER247
C	SER247
D	SER247

site_id	SWS_FT_FI8
Number of Residues	4
Details	BINDING: BINDING => ECO:0000305\|PubMed:25075345, ECO:0000305\|PubMed:26858410, ECO:0007744\|PDB:4NDN, ECO:0007744\|PDB:5A1I

Chain	Residue	Details
A	ASP258
B	ASP258
C	ASP258
D	ASP258

site_id	SWS_FT_FI9
Number of Residues	4
Details	BINDING: BINDING => ECO:0000305\|PubMed:25075345, ECO:0007744\|PDB:4NDN

Chain	Residue	Details
A	ALA281
B	ALA281
C	ALA281
D	ALA281

site_id	SWS_FT_FI10
Number of Residues	8
Details	BINDING: BINDING => ECO:0000305\|PubMed:25075345, ECO:0000305\|PubMed:26858410, ECO:0007744\|PDB:4NDN

Chain	Residue	Details
A	LYS285
A	ASP291
B	LYS285
B	ASP291
C	LYS285
C	ASP291
D	LYS285
D	ASP291

site_id	SWS_FT_FI11
Number of Residues	4
Details	BINDING: in other chain => ECO:0000250\|UniProtKB:P0A817

Chain	Residue	Details
A	LYS289
B	LYS289
C	LYS289
D	LYS289

site_id	SWS_FT_FI12
Number of Residues	4
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
A	LYS81
B	LYS81
C	LYS81
D	LYS81

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

Chain	Residue	Details
A	SER114
B	SER114
C	SER114
D	SER114

site_id	SWS_FT_FI14
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	SER384
B	SER384
C	SER384
D	SER384

site_id	SWS_FT_FI15
Number of Residues	12
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744\|PubMed:28112733

Chain	Residue	Details
A	LYS228
D	LYS228
D	LYS234
A	LYS234
B	LYS228
B	LYS234
C	LYS228
C	LYS234

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	14
Details	M-CSA 9

Chain	Residue	Details
A	HIS29	proton acceptor, proton donor
A	ARG264	electrostatic stabiliser
A	LYS265	electrostatic stabiliser
A	LYS285	electrostatic stabiliser
A	LYS289	electrostatic stabiliser
A	ASP291	electrostatic stabiliser
A	ASP31	electrostatic stabiliser, metal ligand
A	LYS32	electrostatic stabiliser
A	GLU57	metal ligand
A	GLU70	electrostatic stabiliser, steric role
A	LYS181	electrostatic stabiliser
A	PHE250	steric role
A	ASP258	electrostatic stabiliser, metal ligand, steric role
A	ALA259	metal ligand

site_id	MCSA2
Number of Residues	14
Details	M-CSA 9

Chain	Residue	Details
B	HIS29	proton acceptor, proton donor
B	ARG264	electrostatic stabiliser
B	LYS265	electrostatic stabiliser
B	LYS285	electrostatic stabiliser
B	LYS289	electrostatic stabiliser
B	ASP291	electrostatic stabiliser
B	ASP31	electrostatic stabiliser, metal ligand
B	LYS32	electrostatic stabiliser
B	GLU57	metal ligand
B	GLU70	electrostatic stabiliser, steric role
B	LYS181	electrostatic stabiliser
B	PHE250	steric role
B	ASP258	electrostatic stabiliser, metal ligand, steric role
B	ALA259	metal ligand

site_id	MCSA3
Number of Residues	14
Details	M-CSA 9

Chain	Residue	Details
C	HIS29	proton acceptor, proton donor
C	ARG264	electrostatic stabiliser
C	LYS265	electrostatic stabiliser
C	LYS285	electrostatic stabiliser
C	LYS289	electrostatic stabiliser
C	ASP291	electrostatic stabiliser
C	ASP31	electrostatic stabiliser, metal ligand
C	LYS32	electrostatic stabiliser
C	GLU57	metal ligand
C	GLU70	electrostatic stabiliser, steric role
C	LYS181	electrostatic stabiliser
C	PHE250	steric role
C	ASP258	electrostatic stabiliser, metal ligand, steric role
C	ALA259	metal ligand

site_id	MCSA4
Number of Residues	14
Details	M-CSA 9

Chain	Residue	Details
D	HIS29	proton acceptor, proton donor
D	ARG264	electrostatic stabiliser
D	LYS265	electrostatic stabiliser
D	LYS285	electrostatic stabiliser
D	LYS289	electrostatic stabiliser
D	ASP291	electrostatic stabiliser
D	ASP31	electrostatic stabiliser, metal ligand
D	LYS32	electrostatic stabiliser
D	GLU57	metal ligand
D	GLU70	electrostatic stabiliser, steric role
D	LYS181	electrostatic stabiliser
D	PHE250	steric role
D	ASP258	electrostatic stabiliser, metal ligand, steric role
D	ALA259	metal ligand

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)