3RV2 - JenaLib

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Title :   CRYSTAL STRUCTURE OF S-ADENOSYLMETHIONINE SYNTHETASE FROM MYCOBACTERIUM MARINUM

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   05 May 11 (Deposition) - 18 May 11 (Release) - 22 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Sam, S-Adenosylmethionine, Adomet, Adomet Synthase, Methyl Donor, Methylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812 | Reference-DOI: 10.1016/J.TUBE.2014.12.003

Molecule 1 - S-ADENOSYLMETHIONINE SYNTHASE
	Atcc	:	BAA-535
	Chains	:	A, B
	EC Number	:	2.5.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PAVA0421
	Gene	:	METK, MMAR_2205
	Organism Scientific	:	MYCOBACTERIUM MARINUM M
	Organism Taxid	:	216594
	Strain	:	M
	Synonym	:	ADOMET SYNTHASE, MAT, METHIONINE ADENOSYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	4	Ligand/Ion	GLYCEROL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:259 , HOH A:447 , HOH A:448 , HOH A:482 , HOH A:506 , HOH A:601	BINDING SITE FOR RESIDUE CA A 404
2	AC2	SOFTWARE	ASP A:394 , ASP A:397 , ASP A:398 , HOH A:454 , HOH A:455 , HOH A:478	BINDING SITE FOR RESIDUE CA A 405
3	AC3	SOFTWARE	HIS A:158 , ARG A:162 , GLY A:382 , ARG A:383 , THR A:384 , ASP A:385 , HOH A:464	BINDING SITE FOR RESIDUE EDO A 406
4	AC4	SOFTWARE	ARG A:41 , ALA A:43 , GLU A:58 , VAL A:59 , THR A:60 , LYS A:290	BINDING SITE FOR RESIDUE GOL A 407
5	AC5	SOFTWARE	ASP B:259 , HOH B:442 , HOH B:466 , HOH B:490 , HOH B:545 , HOH B:604 , HOH B:611	BINDING SITE FOR RESIDUE CA B 404
6	AC6	SOFTWARE	HIS B:158 , ARG B:162 , GLY B:382 , ARG B:383 , THR B:384 , ASP B:385 , HOH B:535	BINDING SITE FOR RESIDUE EDO B 405
7	AC7	SOFTWARE	ARG A:363 , ASP A:364 , ASP B:364 , ASP B:394 , LYS B:395	BINDING SITE FOR RESIDUE EDO B 406
8	AC8	SOFTWARE	ASP A:364 , ASP A:394 , LYS A:395 , ARG B:363 , ASP B:364	BINDING SITE FOR RESIDUE EDO B 407
9	AC9	SOFTWARE	ARG B:41 , VAL B:42 , ALA B:43 , GLU B:58 , VAL B:59 , THR B:60 , LYS B:290 , HOH B:485	BINDING SITE FOR RESIDUE GOL B 408

(no "SS Bond" information available for 3RV2)

(no "Cis Peptide Bond" information available for 3RV2)

(no "SAP(SNP)/Variant" information available for 3RV2)

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.	METK_MYCMM	131-141	2	A:133-141 B:133-141
2	ADOMET_SYNTHASE_2	PS00377	S-adenosylmethionine synthase signature 2.	METK_MYCMM	279-287	2	A:279-287 B:279-287

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADOMET_SYNTHASE_1	PS00376	S-adenosylmethionine synthase signature 1.	METK_MYCMM	131-141	2	A:133-141 B:133-141
2	ADOMET_SYNTHASE_2	PS00377	S-adenosylmethionine synthase signature 2.	METK_MYCMM	279-287	2	A:279-287 B:279-287

Biological Unit 2 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADOMET_SYNTHASE_1	PS00376	S-adenosylmethionine synthase signature 1.	METK_MYCMM	131-141	4	A:133-141 B:133-141
2	ADOMET_SYNTHASE_2	PS00377	S-adenosylmethionine synthase signature 2.	METK_MYCMM	279-287	4	A:279-287 B:279-287

(no "Exon" information available for 3RV2)

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:373
 aligned with METK_MYCMM | B2HP50 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:399
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394         
           METK_MYCMM     5 GRLFTSESVTEGHPDKICDAVSDSVLDALLAADPRSRVAVETLVTTGQVHVVGEVTTTAKEAFADITNIVRERILDIGYDSSDKGFDGASCGVNIGIGAQSPDIAQGVDTAHEARVEGAADPLDAQGAGDQGLMFGYAINDTPELMPLPIALAHRLSRRLTEVRKNGVLPYLRPDGKTQVTIAYEDRVPVRLDTVVISTQHADDIDLVKTLDPDIREQVLKTVLDDLAHDTLDASAVRVLVNPTGKFVLGGPMGDAGLTGRKIIVDTYGGWARHGGGAFSGKDPSKVDRSAAYAMRWVAKNVVAAGLAERVEVQVAYAIGKAAPVGLFVETFGSEAVDPVKIEKAIGEVFDLRPGAIIRDLNLLRPIYAPTAAYGHFGRTDVDLPWERLDKVDDLKRAI 403
               SCOP domains d3rv2a1 A:5-106 automated matches                                                                     --------------------------d3rv2a2 A:133-252 automated matches                                                                                     d3rv2a3 A:253-403 automated matches                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhhhhhhh.eehhhhee....eeeeeeeee..--------------------------...eeeeeeee.......hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeeee..eeeeeeeeeeeeee........hhhhhhhhhhhhhhhhhhh.........eeee..............eee...........................hhhhhhhhhhhhhhhhhhhh....eeeeeeee........eeeee.......hhhhhhhhhhhhh..hhhhhhhhh......hhhhhh..........hhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ADOMET_SYNT-----------------------------------------------------------------------------------------------------------------------------------------ADOMET_SY-------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rv2 A   5 GRLFTSESVTEGHPDKICDAVSDSVLDALLAADPRSRVAVETLVTTGQVHVVGEVTTTAKEAFADITNIVRERILDIGYDSSDKGFDGASCGVNIGIGAQSP--------------------------GDQGLMFGYAINDTPELMPLPIALAHRLSRRLTEVRKNGVLPYLRPDGKTQVTIAYEDRVPVRLDTVVISTQHADDIDLVKTLDPDIREQVLKTVLDDLAHDTLDASAVRVLVNPTGKFVLGGPMGDAGLTGRKIIVDTYGGWARHGGGAFSGKDPSKVDRSAAYAMRWVAKNVVAAGLAERVEVQVAYAIGKAAPVGLFVETFGSEAVDPVKIEKAIGEVFDLRPGAIIRDLNLLRPIYAPTAAYGHFGRTDVDLPWERLDKVDDLKRAI 403
                                    14        24        34        44        54        64        74        84        94       104 |       -         -       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394         
                                                                                                                               106                        133

Chain B from PDB  Type:PROTEIN  Length:373
 aligned with METK_MYCMM | B2HP50 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:399
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394         
           METK_MYCMM     5 GRLFTSESVTEGHPDKICDAVSDSVLDALLAADPRSRVAVETLVTTGQVHVVGEVTTTAKEAFADITNIVRERILDIGYDSSDKGFDGASCGVNIGIGAQSPDIAQGVDTAHEARVEGAADPLDAQGAGDQGLMFGYAINDTPELMPLPIALAHRLSRRLTEVRKNGVLPYLRPDGKTQVTIAYEDRVPVRLDTVVISTQHADDIDLVKTLDPDIREQVLKTVLDDLAHDTLDASAVRVLVNPTGKFVLGGPMGDAGLTGRKIIVDTYGGWARHGGGAFSGKDPSKVDRSAAYAMRWVAKNVVAAGLAERVEVQVAYAIGKAAPVGLFVETFGSEAVDPVKIEKAIGEVFDLRPGAIIRDLNLLRPIYAPTAAYGHFGRTDVDLPWERLDKVDDLKRAI 403
               SCOP domains d3rv2b1 B:5-106 automated matches                                                                     --------------------------d3rv2b2 B:133-252 automated matches                                                                                     d3rv2b3 B:253-403 automated matches                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) S-AdoMet_synt_N-3rv2B05 B:5-106                                                                       --------------------------S-AdoMet_synt_M-3rv2B03 B:133-251                                                                                      -S-AdoMet_synt_C-3rv2B01 B:253-392                                                                                                           ----------- Pfam domains (1)
           Pfam domains (2) S-AdoMet_synt_N-3rv2B06 B:5-106                                                                       --------------------------S-AdoMet_synt_M-3rv2B04 B:133-251                                                                                      -S-AdoMet_synt_C-3rv2B02 B:253-392                                                                                                           ----------- Pfam domains (2)
         Sec.struct. author .eeeeeeee...hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhhhhhhh.eehhhhee....eeeeeeeee..--------------------------...eeeeeeee.......hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeeee..eeeeeeeeeeeeee........hhhhhhhhhhhhhhhhhhh.........eeee..............eee...........................hhhhhhhhhhhhhhhhhhhh....eeeeeeee........eeeee.......hhhhhhhhhhhhh..hhhhhhhhh......hhhhhh..........hhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ADOMET_SYNT-----------------------------------------------------------------------------------------------------------------------------------------ADOMET_SY-------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rv2 B   5 GRLFTSESVTEGHPDKICDAVSDSVLDALLAADPRSRVAVETLVTTGQVHVVGEVTTTAKEAFADITNIVRERILDIGYDSSDKGFDGASCGVNIGIGAQSP--------------------------GDQGLMFGYAINDTPELMPLPIALAHRLSRRLTEVRKNGVLPYLRPDGKTQVTIAYEDRVPVRLDTVVISTQHADDIDLVKTLDPDIREQVLKTVLDDLAHDTLDASAVRVLVNPTGKFVLGGPMGDAGLTGRKIIVDTYGGWARHGGGAFSGKDPSKVDRSAAYAMRWVAKNVVAAGLAERVEVQVAYAIGKAAPVGLFVETFGSEAVDPVKIEKAIGEVFDLRPGAIIRDLNLLRPIYAPTAAYGHFGRTDVDLPWERLDKVDDLKRAI 403
                                    14        24        34        44        54        64        74        84        94       104 |       -         -       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394         
                                                                                                                               106                        133

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	-	→ Gap	(green background, '-', border residues have a numbering label)
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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: automated matches (8)

Protein domain: automated matches (8)

Mycobacterium marinum [TaxId: 216594] (1)

1a	d3rv2a1	A:5-106
1b	d3rv2a2	A:133-252
1c	d3rv2a3	A:253-403
1d	d3rv2b1	B:5-106
1e	d3rv2b2	B:133-252
1f	d3rv2b3	B:253-403

(no "CATH Domain" information available for 3RV2)

Asymmetric Unit(hide GO term definitions)

Chain A,B (METK_MYCMM | B2HP50)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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(no "Cis Peptide Bonds" information available for 3rv2)

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3iml	BURKHOLDERIA PSEUDOMALLEI S-ADENOSYLMETHIONINE SYNTHETASE RELATED ID: MYMAA.01625.A RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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