1QM4 - JenaLib

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Title :   METHIONINE ADENOSYLTRANSFERASE COMPLEXED WITH A L-METHIONINE ANALOGOUS

Authors :   B. Gonzalez, M. A. Pajares, J. A. Hermoso, J. Sanz-Aparicio

Date :   20 Sep 99 (Deposition) - 21 Sep 00 (Release) - 12 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.66

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Transferase, Adenosyltransferase, Methionine Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Gonzalez, M. A. Pajares, J. A. Hermoso, L. Alvarez, F. Garrido, J. R. Sufrin, J. Sanz-Aparicio
The Crystal Structure Of Tetrameric Methionine Adenosyltransferase From Rat Liver Reveals The Methionine-Binding Site
J. Mol. Biol. V. 300 363 2000
PubMed-ID: 10873471 | Reference-DOI: 10.1006/JMBI.2000.3858
(for further references see the PDB file header)

Molecule 1 - METHIONINE ADENOSYLTRANSFERASE, ALPHA FORM
	Chains	:	A, B
	EC Number	:	2.5.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSSRL-T7N
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organ	:	LIVER
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	ADOMET SYNTHETASE, MAT-I, S-ADENOSYLMETHIONINE SYNTHETASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	AMB	1	Ligand/Ion	L-2-AMINO-4-METHOXY-CIS-BUT-3-ENOIC ACID
2	K	3	Ligand/Ion	POTASSIUM ION
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	AMB	2	Ligand/Ion	L-2-AMINO-4-METHOXY-CIS-BUT-3-ENOIC ACID
2	K	-1	Ligand/Ion	POTASSIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:265 , LYS A:266 , GLY B:280 , GLY B:281 , ALA B:282 , LYS B:286 , K B:402 , HOH B:507	BINDING SITE FOR RESIDUE SO4 C 398
2	AC2	SOFTWARE	LYS A:182 , GLN A:184 , ASP B:135 , GLN B:136 , MG A:405	BINDING SITE FOR RESIDUE SO4 C 399
3	AC3	SOFTWARE	GLY A:280 , GLY A:281 , ALA A:282 , LYS A:286 , ARG B:265 , LYS B:266 , K A:407	BINDING SITE FOR RESIDUE SO4 C 400
4	AC4	SOFTWARE	PRO A:31 , ASP A:180 , AMB A:401	BINDING SITE FOR RESIDUE MG C 401
5	AC5	SOFTWARE	SER A:248 , ASP B:135 , SO4 A:402	BINDING SITE FOR RESIDUE MG C 402
6	AC6	SOFTWARE	GLY A:264 , ARG B:265	BINDING SITE FOR RESIDUE K C 403
7	AC7	SOFTWARE	SO4 B:401	BINDING SITE FOR RESIDUE K C 404
8	AC8	SOFTWARE	SO4 A:403	BINDING SITE FOR RESIDUE K C 405
9	AC9	SOFTWARE	ASP A:180 , PHE A:251 , MG A:404	BINDING SITE FOR RESIDUE AMB C 397

(no "SS Bond" information available for 1QM4)

(no "Cis Peptide Bond" information available for 1QM4)

(no "SAP(SNP)/Variant" information available for 1QM4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADOMET_SYNTHASE_1	PS00376	S-adenosylmethionine synthase signature 1.	METK1_RAT	132-142	2	A:132-142 B:132-142
2	ADOMET_SYNTHASE_2	PS00377	S-adenosylmethionine synthase signature 2.	METK1_RAT	279-287	2	A:279-287 B:279-287

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADOMET_SYNTHASE_1	PS00376	S-adenosylmethionine synthase signature 1.	METK1_RAT	132-142	4	A:132-142 B:132-142
2	ADOMET_SYNTHASE_2	PS00377	S-adenosylmethionine synthase signature 2.	METK1_RAT	279-287	4	A:279-287 B:279-287

(no "Exon" information available for 1QM4)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:368
 aligned with METK1_RAT | P13444 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:381
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396 
            METK1_RAT    17 GAFMFTSESVGEGHPDKICDQISDAVLDAHLKQDPNAKVACETVCKTGMVLLCGEITSMAMIDYQRVVRDTIKHIGYDDSAKGFDFKTCNVLVALEQQSPDIAQCVHLDRNEEDVGAGDQGLMFGYATDETEECMPLTIVLAHKLNTRMADLRRSGVLPWLRPDSKTQVTVQYVQDNGAVIPVRVHTIVISVQHNEDITLEAMREALKEQVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKAGLCRRVLVQVSYAIGVAEPLSISIFTYGTSKKTERDELLEVVNKNFDLRPGVIVRDLDLKKPIYQKTACYGHFGRSEFPWEVPKKLVF 397
               SCOP domains d1qm4a1 A:17-116 S-adenosylmethionine synthetase                                                    ------------d1qm4a2 A:129-252 S-adenosylmethionine synthetase                                                                           d1qm4a3 A:253-396 S-adenosylmethionine synthetase                                                                                                 SCOP domains
               CATH domains 1qm4A03  1qm4A02 A:26-129,A:254-290  [code=3.30.300.10, no name defined]                                         1qm4A01                1qm4A03 A:17-25,A:153-253  [code=3.30.300.10, no name defined]                                       1qm4A02 A:26-129,A:254-290           1qm4A01 A:130-152,A:291-395  [code=3.30.300.10, no nam e defined]                                         - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...hhhhhhhhhhhhhhhhhhh.....eeeeeeee...eeeeeeeee.....hhhhhhhhhhhhhh.............eeee.......------------........eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..........eeeeeeeee......hhhhhhhhhhhh...............eeee............................................hhhhhhhhhhhhhhhhhhhh....eeeeeeee.........eeeee.........-hhhhhhhhhh..hhhhhhhhh.....hhhhhh.........hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ADOMET_SYNT----------------------------------------------------------------------------------------------------------------------------------------ADOMET_SY-------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qm4 A  17 GAFMFTSESVGEGHPDKICDQISDAVLDAHLKQDPNAKVACETVCKTGMVLLCGEITSMAMIDYQRVVRDTIKHIGYDDSAKGFDFKTCNVLVALEQQSP------------EDVGAGDQGLMFGYATDETEECMPLTIVLAHKLNTRMADLRRSGVLPWLRPDSKTQVTVQYVQDNGAVIPVRVHTIVISVQHNEDITLEAMREALKEQVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKAGLCRRVLVQVSYAIGVAEPLSISIFTYGTSKKTER-ELLEVVNKNFDLRPGVIVRDLDLKKPIYQKTACYGHFGRSEFPWEVPKKLVF 396
                                    26        36        46        56        66        76        86        96       106       116         -  |    136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       345       355       365       375       385       395 
                                                                                                                             116          129                                                                                                                                                                                                                    344 |                                                   
                                                                                                                                                                                                                                                                                                                                                                   345

Chain B from PDB  Type:PROTEIN  Length:368
 aligned with METK1_RAT | P13444 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:381
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396 
            METK1_RAT    17 GAFMFTSESVGEGHPDKICDQISDAVLDAHLKQDPNAKVACETVCKTGMVLLCGEITSMAMIDYQRVVRDTIKHIGYDDSAKGFDFKTCNVLVALEQQSPDIAQCVHLDRNEEDVGAGDQGLMFGYATDETEECMPLTIVLAHKLNTRMADLRRSGVLPWLRPDSKTQVTVQYVQDNGAVIPVRVHTIVISVQHNEDITLEAMREALKEQVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKAGLCRRVLVQVSYAIGVAEPLSISIFTYGTSKKTERDELLEVVNKNFDLRPGVIVRDLDLKKPIYQKTACYGHFGRSEFPWEVPKKLVF 397
               SCOP domains d1qm4b1 B:17-116 S-adenosylmethionine synthetase                                                    ------------d1qm4b2 B:129-252 S-adenosylmethionine synthetase                                                                           d1qm4b3 B:253-396 S-adenosylmethionine synthetase                                                                                                 SCOP domains
               CATH domains 1qm4B03  1qm4B02 B:26-129,B:254-290  [code=3.30.300.10, no name defined]                                         1qm4B01                1qm4B03 B:17-25,B:153-253  [code=3.30.300.10, no name defined]                                       1qm4B02 B:26-129,B:254-290           1qm4B01 B:130-152,B:291-395  [code=3.30.300.10, no nam e defined]                                         - CATH domains
           Pfam domains (1) S-AdoMet_synt_N-1qm4B05 B:17-116                                                                    ------------S-AdoMet_synt_M-1qm4B03 B:129-251                                                                                          -S-AdoMet_synt_C-1qm4B01 B:253-390                                                           -                                              ------ Pfam domains (1)
           Pfam domains (2) S-AdoMet_synt_N-1qm4B06 B:17-116                                                                    ------------S-AdoMet_synt_M-1qm4B04 B:129-251                                                                                          -S-AdoMet_synt_C-1qm4B02 B:253-390                                                           -                                              ------ Pfam domains (2)
         Sec.struct. author ..eeeeeeee...hhhhhhhhhhhhhhhhhhh.....eeeeeeee...eeeeeeeee.....hhhhhhhhhhhhhh.............eeee.......------------........eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..........eeeeeeeee......hhhhhhhhhhhh...............eeee............................................hhhhhhhhhhhhhhhhhhhh....eeeeeeee.........eeeee.........-hhhhhhhhhh..hhhhhhhhh.....hhhhhh.........hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ADOMET_SYNT----------------------------------------------------------------------------------------------------------------------------------------ADOMET_SY-------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qm4 B  17 GAFMFTSESVGEGHPDKICDQISDAVLDAHLKQDPNAKVACETVCKTGMVLLCGEITSMAMIDYQRVVRDTIKHIGYDDSAKGFDFKTCNVLVALEQQSP------------EDVGAGDQGLMFGYATDETEECMPLTIVLAHKLNTRMADLRRSGVLPWLRPDSKTQVTVQYVQDNGAVIPVRVHTIVISVQHNEDITLEAMREALKEQVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAKSLVKAGLCRRVLVQVSYAIGVAEPLSISIFTYGTSKKTER-ELLEVVNKNFDLRPGVIVRDLDLKKPIYQKTACYGHFGRSEFPWEVPKKLVF 396
                                    26        36        46        56        66        76        86        96       106       116         -  |    136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       345       355       365       375       385       395 
                                                                                                                             116          129                                                                                                                                                                                                                    344 |                                                   
                                                                                                                                                                                                                                                                                                                                                                   345

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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: S-adenosylmethionine synthetase (23)

Superfamily: S-adenosylmethionine synthetase (23)

Family: S-adenosylmethionine synthetase (15)

Protein domain: S-adenosylmethionine synthetase (15)

Norway rat (Rattus norvegicus) [TaxId: 10116] (5)

1a	d1qm4a1	A:17-116
1b	d1qm4a2	A:129-252
1c	d1qm4a3	A:253-396
1d	d1qm4b1	B:17-116
1e	d1qm4b2	B:129-252
1f	d1qm4b3	B:253-396

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: GMP Synthetase; Chain A, domain 3 (192)

Homologous Superfamily: [code=3.30.300.10, no name defined] (22)

Rat (Rattus norvegicus) (5)

1a	1qm4A01	A:130-152,A:291-395
1b	1qm4B01	B:130-152,B:291-395
1c	1qm4A03	A:17-25,A:153-253
1d	1qm4B03	B:17-25,B:153-253
1e	1qm4A02	A:26-129,A:254-290
1f	1qm4B02	B:26-129,B:254-290

Asymmetric Unit(hide GO term definitions)

Chain A,B (METK1_RAT | P13444)

molecular function
	GO:0043531	ADP binding	Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004478	methionine adenosyltransferase activity	Catalysis of the reaction: ATP + L-methionine + H2O = phosphate + diphosphate + S-adenosyl-L-methionine.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006556	S-adenosylmethionine biosynthetic process	The chemical reactions and pathways resulting in the formation of S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0051262	protein tetramerization	The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016363	nuclear matrix	The dense fibrillar network lying on the inner side of the nuclear membrane.

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1mxa	S-ADENOSYLMETHIONINE SYNTHETASE WITH PPI (ESCHERICHIA COLI)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

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