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Title :   CRYSTAL STRUCTURE OF N-METHYLTRANSFERASE NODS FROM BRADYRHIZOBIUM JAPONICUM WM9 IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE (SAH)

Authors :   O. Cakici, M. Sikorski, T. Stepkowski, G. Bujacz, M. Jaskolski

Date :   15 Aug 10 (Deposition) - 27 Oct 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Nods, N-Methyltransferase, Sah, Sam, Nod Factor, Nodulation, Nitrogen Fixation, Symbiosis, Alpha/Beta Structure, Variant Of Rossmann Fold, Sam-Dependent N-Methyltransferase, S-Adenosyl-L-Methionine (Sam), Lipochitooligosaccharide, Methylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Cakici, M. Sikorski, T. Stepkowski, G. Bujacz, M. Jaskolski
Crystal Structures Of Nods N-Methyltransferase From Bradyrhizobium Japonicum In Ligand-Free Form And As Sah Complex.
J. Mol. Biol. V. 404 874 2010
PubMed-ID: 20970431 | Reference-DOI: 10.1016/J.JMB.2010.10.016
(for further references see the PDB file header)

Molecule 1 - NODULATION PROTEIN S
	Chains	:	A, B, C, D
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET151/D-TOPO
	Expression System Strain	:	BL21 CODONPLUS(DE3)RIPL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	NODS
	Organism Scientific	:	BRADYRHIZOBIUM SP.
	Organism Taxid	:	133505
	Strain	:	WM9

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SAH	4	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:10 , LEU A:22 , ARG A:31 , HIS A:32 , GLY A:52 , CYS A:53 , ALA A:54 , ASP A:73 , VAL A:74 , MET A:75 , ASP A:98 , ILE A:99 , ALA A:114 , GLU A:115 , VAL A:116 , TYR A:119 , HOH A:215 , HOH A:216 , HOH A:235 , HOH A:268	BINDING SITE FOR RESIDUE SAH A 217
2	AC2	SOFTWARE	LEU B:10 , LEU B:22 , ARG B:31 , HIS B:32 , GLY B:52 , ALA B:54 , ASP B:73 , VAL B:74 , MET B:75 , ASP B:98 , ILE B:99 , ALA B:114 , GLU B:115 , VAL B:116 , LEU B:120 , HOH B:210 , HOH B:212 , HOH B:219 , HOH B:220	BINDING SITE FOR RESIDUE SAH B 217
3	AC3	SOFTWARE	TRP C:20 , LEU C:22 , ARG C:31 , HIS C:32 , GLY C:52 , ALA C:54 , ASP C:73 , VAL C:74 , MET C:75 , ASP C:98 , ILE C:99 , ALA C:114 , GLU C:115 , VAL C:116 , TYR C:119 , LEU C:120 , HOH C:212 , HOH C:214 , HOH C:229 , HOH C:278	BINDING SITE FOR RESIDUE SAH C 217
4	AC4	SOFTWARE	ARG C:200 , ARG D:31 , HIS D:32 , GLY D:52 , ALA D:54 , ASP D:73 , VAL D:74 , MET D:75 , THR D:97 , ASP D:98 , ILE D:99 , ALA D:114 , GLU D:115 , VAL D:116 , HOH D:211 , HOH D:223 , HOH D:230 , HOH D:298 , HOH D:770	BINDING SITE FOR RESIDUE SAH D 217

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

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

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

(no "PROSITE Motif" information available for 3OFK)

(no "Exon" information available for 3OFK)

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:204
 aligned with Q9AQ22_BRASW | Q9AQ22 from UniProtKB/TrEMBL  Length:209

    Alignment length:204
                                 1                                                                                                                                                                                                      
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195    
         Q9AQ22_BRASW     - -----MSVDNTYQSLERELANDDPWRLDDNPFERERHTQLLRLSLSSGAVSNGLEIGCAAGAFTEKLAPHCKRLTVIDVMPRAIGRACQRTKRWSHISWAATDILQFSTAELFDLIVVAEVLYYLEDMTQMRTAIDNMVKMLAPGGHLVFGSARDATCRRWGHVAGAETVITILTEALTEVERVQCQGQSADEDCLLARFRNPE 199
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhh..eeeeeeee.hhhhhhhhhhhh.....eeeee...........eeeeeee.hhhhh.hhhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhh....hhhhhhhhhhhhheeeeeeeee......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ofk A  -4 DPFTMVSVDNTYQSLERELANDDPWRLDDNPFERERHTQLLRLSLSSGAVSNGLEIGCAAGAFTEKLAPHCKRLTVIDVMPRAIGRACQRTKRWSHISWAATDILQFSTAELFDLIVVAEVLYYLEDMTQMRTAIDNMVKMLAPGGHLVFGSARDATCRRWGHVAGAETVITILTEALTEVERVQCQGQSADEDCLLARFRNPE 199
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195

Chain B from PDB  Type:PROTEIN  Length:196
 aligned with Q9AQ22_BRASW | Q9AQ22 from UniProtKB/TrEMBL  Length:209

    Alignment length:196
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193      
         Q9AQ22_BRASW     4 DNTYQSLERELANDDPWRLDDNPFERERHTQLLRLSLSSGAVSNGLEIGCAAGAFTEKLAPHCKRLTVIDVMPRAIGRACQRTKRWSHISWAATDILQFSTAELFDLIVVAEVLYYLEDMTQMRTAIDNMVKMLAPGGHLVFGSARDATCRRWGHVAGAETVITILTEALTEVERVQCQGQSADEDCLLARFRNPE 199
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhh..eeee..hhhhhhhhhhhh.....eeee............eeeeeee.hhhhh.hhhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhh....hhhhhhhhhhhhheeeeeeeee......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ofk B   4 DNTYQSLERELANDDPWRLDDNPFERERHTQLLRLSLSSGAVSNGLEIGCAAGAFTEKLAPHCKRLTVIDVMPRAIGRACQRTKRWSHISWAATDILQFSTAELFDLIVVAEVLYYLEDMTQMRTAIDNMVKMLAPGGHLVFGSARDATCRRWGHVAGAETVITILTEALTEVERVQCQGQSADEDCLLARFRNPE 199
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193

Chain C from PDB  Type:PROTEIN  Length:202
 aligned with Q9AQ22_BRASW | Q9AQ22 from UniProtKB/TrEMBL  Length:209

    Alignment length:202
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203  
         Q9AQ22_BRASW     4 DNTYQSLERELANDDPWRLDDNPFERERHTQLLRLSLSSGAVSNGLEIGCAAGAFTEKLAPHCKRLTVIDVMPRAIGRACQRTKRWSHISWAATDILQFSTAELFDLIVVAEVLYYLEDMTQMRTAIDNMVKMLAPGGHLVFGSARDATCRRWGHVAGAETVITILTEALTEVERVQCQGQSADEDCLLARFRNPERSSIRP 205
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhh..eeee..hhhhhhhhhhhh.....eeee..hhhhh.....eeeeeee.hhhhh.hhhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhh....hhhhhhhhhhhhheeeeeeeee......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ofk C   4 DNTYQSLERELANDDPWRLDDNPFERERHTQLLRLSLSSGAVSNGLEIGCAAGAFTEKLAPHCKRLTVIDVMPRAIGRACQRTKRWSHISWAATDILQFSTAELFDLIVVAEVLYYLEDMTQMRTAIDNMVKMLAPGGHLVFGSARDATCRRWGHVAGAETVITILTEALTEVERVQCQGQSADEDCLLARFRNPERSSIRP 205
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Chain D from PDB  Type:PROTEIN  Length:181
 aligned with Q9AQ22_BRASW | Q9AQ22 from UniProtKB/TrEMBL  Length:209

    Alignment length:181
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 
         Q9AQ22_BRASW    23 DDNPFERERHTQLLRLSLSSGAVSNGLEIGCAAGAFTEKLAPHCKRLTVIDVMPRAIGRACQRTKRWSHISWAATDILQFSTAELFDLIVVAEVLYYLEDMTQMRTAIDNMVKMLAPGGHLVFGSARDATCRRWGHVAGAETVITILTEALTEVERVQCQGQSADEDCLLARFRNPERSSI 203
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) NodS-3ofkD01 D:23-202                                                                                                                                                               - Pfam domains (1)
           Pfam domains (2) NodS-3ofkD02 D:23-202                                                                                                                                                               - Pfam domains (2)
           Pfam domains (3) NodS-3ofkD03 D:23-202                                                                                                                                                               - Pfam domains (3)
           Pfam domains (4) NodS-3ofkD04 D:23-202                                                                                                                                                               - Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhh..eeeeeeee.hhhhhhhhhhhh.....eeeee...........eeeeeee.hhhhh.hhhhhhhhhhhhhhheeeeeeeeeeeehhhhhhhh....hhhhhhhhhhhhheeeeeeeee......eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ofk D  23 DDNPFERERHTQLLRLSLSSGAVSNGLEIGCAAGAFTEKLAPHCKRLTVIDVMPRAIGRACQRTKRWSHISWAATDILQFSTAELFDLIVVAEVLYYLEDMTQMRTAIDNMVKMLAPGGHLVFGSARDATCRRWGHVAGAETVITILTEALTEVERVQCQGQSADEDCLLARFRNPERSSI 203
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

(no "SCOP Domain" information available for 3OFK)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: NodS (2)

Bradyrhizobium sp. (strain WM9) (2)

1a	NodS-3ofkD01	D:23-202
1b	NodS-3ofkD02	D:23-202
1c	NodS-3ofkD03	D:23-202
1d	NodS-3ofkD04	D:23-202

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q9AQ22_BRASW | Q9AQ22)

molecular function
	GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0009877	nodulation	The formation of nitrogen-fixing root nodules on plant roots.
	GO:0009312	oligosaccharide biosynthetic process	The chemical reactions and pathways resulting in the formation of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.

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