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	0000166	molecular_function	nucleotide binding
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	0051259	biological_process	protein complex oligomerization
A	0051291	biological_process	protein heterooligomerization
A	0061431	biological_process	cellular response to methionine
A	1904263	biological_process	positive regulation of TORC1 signaling
B	0000166	molecular_function	nucleotide binding
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	0051259	biological_process	protein complex oligomerization
B	0051291	biological_process	protein heterooligomerization
B	0061431	biological_process	cellular response to methionine
B	1904263	biological_process	positive regulation of TORC1 signaling
C	0000166	molecular_function	nucleotide binding
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	0051259	biological_process	protein complex oligomerization
C	0051291	biological_process	protein heterooligomerization
C	0061431	biological_process	cellular response to methionine
C	1904263	biological_process	positive regulation of TORC1 signaling
D	0000166	molecular_function	nucleotide binding
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	0051259	biological_process	protein complex oligomerization
D	0051291	biological_process	protein heterooligomerization
D	0061431	biological_process	cellular response to methionine
D	1904263	biological_process	positive regulation of TORC1 signaling
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	0030234	molecular_function	enzyme regulator activity
E	0048269	cellular_component	methionine adenosyltransferase complex
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	0030234	molecular_function	enzyme regulator activity
F	0048269	cellular_component	methionine adenosyltransferase complex
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	8
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"25075345","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26858410","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"4NDN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A19","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25075345","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26858410","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"4KTT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4NDN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A19","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A1G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A1I","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P0A817","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"25075345","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"4NDN","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"25075345","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	8
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"25075345","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26858410","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"4KTT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4NDN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A19","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A1G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A1I","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	12
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"25075345","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26858410","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"4KTT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4NDN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A1G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A1I","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25075345","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26858410","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"4NDN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A1I","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25075345","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"4NDN","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25075345","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26858410","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"4NDN","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	4
Details	Binding site: {"description":"in other chain","evidences":[{"source":"UniProtKB","id":"P0A817","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	3
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	12
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	24
Details	Region: {"description":"Flexible loop","evidences":[{"source":"UniProtKB","id":"P0A817","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	30
Details	Region: {"description":"Required for interaction with MAT2A","evidences":[{"source":"PubMed","id":"25075345","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	20
Details	Binding site: {"evidences":[{"source":"PDB","id":"2YDX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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)