3S82 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF A S-ADENOSYLMETHIONINE SYNTHETASE FROM MYCOBACTERIUM AVIUM

Authors :   Seattle Structural Genomics Center For Infectious Disease, Se Structural Genomics Center For Infectious Disease (Ssgcid)

Date :   27 May 11 (Deposition) - 08 Jun 11 (Release) - 22 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

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

Keywords :   Seattle Structural Genomics Center For Infectious Disease, Ssgcid, S- Adenosylmethionine Synthetase, 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
	Chains	:	A, B
	EC Number	:	2.5.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	METK, MAV_3382
	Organism Scientific	:	MYCOBACTERIUM AVIUM
	Organism Taxid	:	243243
	Strain	:	104
	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 (4, 8)

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

Biological Unit 1 (3, 4)

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

Biological Unit 2 (3, 8)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:309 , LYS A:400 , HOH A:509 , HOH A:969 , ASN B:225 , ASN B:229 , HOH B:467	BINDING SITE FOR RESIDUE EDO B 404
2	AC2	SOFTWARE	ASP A:234 , HOH A:1647 , HOH A:1651 , HOH A:1792 , GLU B:187 , GLU B:189	BINDING SITE FOR RESIDUE CA A 404
3	AC3	SOFTWARE	ASN A:394 , ASP A:397 , ASP A:398 , HOH A:696 , HOH A:741 , HOH A:848 , HOH A:1140 , HOH B:463	BINDING SITE FOR RESIDUE CA A 405
4	AC4	SOFTWARE	HOH A:1659 , ASN B:394 , ASP B:397 , ASP B:398 , HOH B:1744 , HOH B:1773 , HOH B:1774	BINDING SITE FOR RESIDUE CA B 405
5	AC5	SOFTWARE	ARG A:401 , ARG B:401 , HOH B:1803 , HOH B:1804	BINDING SITE FOR RESIDUE CA B 406
6	AC6	SOFTWARE	PHE A:188 , ASP A:191 , ARG A:314 , HOH A:477 , HOH B:1666	BINDING SITE FOR RESIDUE GOL A 408

(no "SS Bond" information available for 3S82)

(no "Cis Peptide Bond" information available for 3S82)

(no "SAP(SNP)/Variant" information available for 3S82)

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_MYCA1	131-141	2	A:133-141 B:133-141
2	ADOMET_SYNTHASE_2	PS00377	S-adenosylmethionine synthase signature 2.	METK_MYCA1	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_MYCA1	131-141	2	A:133-141 B:133-141
2	ADOMET_SYNTHASE_2	PS00377	S-adenosylmethionine synthase signature 2.	METK_MYCA1	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_MYCA1	131-141	4	A:133-141 B:133-141
2	ADOMET_SYNTHASE_2	PS00377	S-adenosylmethionine synthase signature 2.	METK_MYCA1	279-287	4	A:279-287 B:279-287

(no "Exon" information available for 3S82)

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_MYCA1 | A0QI26 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_MYCA1     5 GRLFTSESVTEGHPDKICDAISDSVLDALLAQDPRSRVAVETLVTTGQVHVVGEVTTTAKEAFADITNTVRERILDIGYDSSDKGFDGASCGVNIGIGAQSPDIAQGVDTAHETRVEGAADPLDAQGAGDQGLMFGYAINDTPERMPLPIALAHRLSRRLTEVRKNGVLPYLRPDGKTQVTIEFEDDVPVRLDTVVISTQHAADIDLENTLTPDIREKVLNTVLNDLAHDTLDTSSTRLLVNPTGKFVVGGPMGDAGLTGRKIIVDTYGGWARHGGGAFSGKDPSKVDRSAAYAMRWVAKNIVAAGLAERVEVQVAYAIGKAAPVGLFIETFGTATVDPVKIEKIVPEVFDLRPGAIIRDLDLLRPIYAQTAAYGHFGRTDVELPWEQLNKVDDLKRAI 403
               SCOP domains d3s82a1 A:5-106 automated matches                                                                     --------------------------d3s82a2 A:133-252 automated matches                                                                                     d3s82a3 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......hhhhh...........hhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ADOMET_SYNT-----------------------------------------------------------------------------------------------------------------------------------------ADOMET_SY-------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s82 A   5 GRLFTSESVTEGHPDKICDAISDSVLDALLAQDPRSRVAVETLVTTGQVHVVGEVTTTAKEAFADITNTVRERILDIGYDSSDKGFDGASCGVNIGIGAQSP--------------------------GDQGLMFGYAINDTPERMPLPIALAHRLSRRLTEVRKNGVLPYLRPDGKTQVTIEFEDDVPVRLDTVVISTQHAADIDLENTLTPDIREKVLNTVLNDLAHDTLDTSSTRLLVNPTGKFVVGGPMGDAGLTGRKIIVDTYGGWARHGGGAFSGKDPSKVDRSAAYAMRWVAKNIVAAGLAERVEVQVAYAIGKAAPVGLFIETFGTATVDPVKIEKIVPEVFDLRPGAIIRDLDLLRPIYAQTAAYGHFGRTDVELPWEQLNKVDDLKRAI 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:376
 aligned with METK_MYCA1 | A0QI26 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:402
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401  
           METK_MYCA1     2 SEKGRLFTSESVTEGHPDKICDAISDSVLDALLAQDPRSRVAVETLVTTGQVHVVGEVTTTAKEAFADITNTVRERILDIGYDSSDKGFDGASCGVNIGIGAQSPDIAQGVDTAHETRVEGAADPLDAQGAGDQGLMFGYAINDTPERMPLPIALAHRLSRRLTEVRKNGVLPYLRPDGKTQVTIEFEDDVPVRLDTVVISTQHAADIDLENTLTPDIREKVLNTVLNDLAHDTLDTSSTRLLVNPTGKFVVGGPMGDAGLTGRKIIVDTYGGWARHGGGAFSGKDPSKVDRSAAYAMRWVAKNIVAAGLAERVEVQVAYAIGKAAPVGLFIETFGTATVDPVKIEKIVPEVFDLRPGAIIRDLDLLRPIYAQTAAYGHFGRTDVELPWEQLNKVDDLKRAI 403
               SCOP domains d3s82b1 B:2-106 automated matches                                                                        --------------------------d3s82b2 B:133-252 automated matches                                                                                     d3s82b3 B:253-403 automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --S-AdoMet_synt_N-3s82B05 B:4-106                                                                        --------------------------S-AdoMet_synt_M-3s82B03 B:133-251                                                                                      -S-AdoMet_synt_C-3s82B01 B:253-392                                                                                                           ----------- Pfam domains (1)
           Pfam domains (2) --S-AdoMet_synt_N-3s82B06 B:4-106                                                                        --------------------------S-AdoMet_synt_M-3s82B04 B:133-251                                                                                      -S-AdoMet_synt_C-3s82B02 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..hhhhhhhhhh.....hhhhh...........hhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------ADOMET_SYNT-----------------------------------------------------------------------------------------------------------------------------------------ADOMET_SY-------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3s82 B   2 SEKGRLFTSESVTEGHPDKICDAISDSVLDALLAQDPRSRVAVETLVTTGQVHVVGEVTTTAKEAFADITNTVRERILDIGYDSSDKGFDGASCGVNIGIGAQSP--------------------------GDQGLMFGYAINDTPERMPLPIALAHRLSRRLTEVRKNGVLPYLRPDGKTQVTIEFEDDVPVRLDTVVISTQHAADIDLENTLTPDIREKVLNTVLNDLAHDTLDTSSTRLLVNPTGKFVVGGPMGDAGLTGRKIIVDTYGGWARHGGGAFSGKDPSKVDRSAAYAMRWVAKNIVAAGLAERVEVQVAYAIGKAAPVGLFIETFGTATVDPVKIEKIVPEVFDLRPGAIIRDLDLLRPIYAQTAAYGHFGRTDVELPWEQLNKVDDLKRAI 403
                                    11        21        31        41        51        61        71        81        91       101    |    -         -         - |     141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401  
                                                                                                                                  106                        133

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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(

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Superfamilies( (-)

)

Families(

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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 avium [TaxId: 243243] (1)

1a	d3s82a1	A:5-106
1b	d3s82a2	A:133-252
1c	d3s82a3	A:253-403
1d	d3s82b1	B:2-106
1e	d3s82b2	B:133-252
1f	d3s82b3	B:253-403

(no "CATH Domain" information available for 3S82)

Asymmetric Unit(hide GO term definitions)

Chain A,B (METK_MYCA1 | A0QI26)

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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	3s82
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Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (6, 6)

SS Bonds (0, 0)

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