3D2L - JenaLib

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Title :   CRYSTAL STRUCTURE OF SAM-DEPENDENT METHYLTRANSFERASE (ZP_00538691.1) FROM EXIGUOBACTERIUM SP. 255-15 AT 1.90 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   08 May 08 (Deposition) - 20 May 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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 :   Zp_00538691. 1, Sam-Dependent Methyltransferase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Methyltransferase Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Sam-Dependent Methyltransferase (Zp_00538691. 1) From Exiguobacterium Sp. 255-15 At 1. 90 A Resolution
To Be Published
PubMed: search

Molecule 1 - SAM-DEPENDENT METHYLTRANSFERASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Vector Type	:	PLASMID
	Gene	:	ZP_00538691.1, EXIGDRAFT_1659
	Organism Scientific	:	EXIGUOBACTERIUM SIBIRICUM 255-15
	Organism Taxid	:	262543

		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 (2, 27)

No.	Name	Count	Type	Full Name
1	MG	6	Ligand/Ion	MAGNESIUM ION
2	MSE	21	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	5	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	5	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 5)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	5	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:128 , GLU B:67	BINDING SITE FOR RESIDUE MG A 243
2	AC3	SOFTWARE	GLU A:67 , ASP B:128	BINDING SITE FOR RESIDUE MG B 243
3	AC4	SOFTWARE	ASP C:128	BINDING SITE FOR RESIDUE MG C 243
4	AC6	SOFTWARE	ASP B:226 , ASP D:114	BINDING SITE FOR RESIDUE MG D 244

(no "SS Bond" information available for 3D2L)

(no "Cis Peptide Bond" information available for 3D2L)

(no "SAP(SNP)/Variant" information available for 3D2L)

(no "PROSITE Motif" information available for 3D2L)

(no "Exon" information available for 3D2L)

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:238
 aligned with B1YKR8_EXIS2 | B1YKR8 from UniProtKB/TrEMBL  Length:242

    Alignment length:238
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234        
         B1YKR8_EXIS2     5 QFAYVYDELMQDVPYPEWVAWVLEQVEPGKRIADIGCGTGTATLLLADHYEVTGVDLSEEMLEIAQEKAMETNRHVDFWVQDMRELELPEPVDAITILCDSLNYLQTEADVKQTFDSAARLLTDGGKLLFDVHSPYKMETLFNGKTYATHAEQSSYIWFADPGEEPLSVVHELTFFIEGEDGRYDRVDETHHQRTYPPEQYITWLREAGFRVCAVTGDFKSDAPTETAERIFFVAEKI 242
               SCOP domains d3d2la_ A: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh...hhhhhhhhhhhhh....eeeee....hhhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeee.hhhhh.....eeeeee..hhhhhh.hhhhhhhhhhhhhhheeeeeeeeeeeehhhhhhh....eeeeee...eeeeeeeee.....eeeeeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh.eeeeeeee............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d2l A   5 QFAYVYDELmQDVPYPEWVAWVLEQVEPGKRIADIGCGTGTATLLLADHYEVTGVDLSEEmLEIAQEKAmETNRHVDFWVQDmRELELPEPVDAITILCDSLNYLQTEADVKQTFDSAARLLTDGGKLLFDVHSPYKmETLFNGKTYATHAEQSSYIWFADPGEEPLSVVHELTFFIEGEDGRYDRVDETHHQRTYPPEQYITWLREAGFRVCAVTGDFKSDAPTETAERIFFVAEKI 242
                                    14        24        34        44        54        64|       74        84  |     94       104       114       124       134       144       154       164       174       184       194       204       214       224       234        
                                    14-MSE                                             65-MSE   74-MSE       87-MSE                                                142-MSE

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with B1YKR8_EXIS2 | B1YKR8 from UniProtKB/TrEMBL  Length:242

    Alignment length:238
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234        
         B1YKR8_EXIS2     5 QFAYVYDELMQDVPYPEWVAWVLEQVEPGKRIADIGCGTGTATLLLADHYEVTGVDLSEEMLEIAQEKAMETNRHVDFWVQDMRELELPEPVDAITILCDSLNYLQTEADVKQTFDSAARLLTDGGKLLFDVHSPYKMETLFNGKTYATHAEQSSYIWFADPGEEPLSVVHELTFFIEGEDGRYDRVDETHHQRTYPPEQYITWLREAGFRVCAVTGDFKSDAPTETAERIFFVAEKI 242
               SCOP domains d3d2lb_ B: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh...hhhhhhhhhhhhh....eeeee....hhhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeee.hhhhh.......eeee..hhhhhh.hhhhhhhhhhhhhhhh....eeeeeeehhhhhhhh...eeeeee...eeeeeeeee.....eeeeeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh.eeeeeeee............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d2l B   5 QFAYVYDELmQDVPYPEWVAWVLEQVEPGKRIADIGCGTGTATLLLADHYEVTGVDLSEEmLEIAQEKAmETNRHVDFWVQDmRELELPEPVDAITILCDSLNYLQTEADVKQTFDSAARLLTDGGKLLFDVHSPYKmETLFNGKTYATHAEQSSYIWFADPGEEPLSVVHELTFFIEGEDGRYDRVDETHHQRTYPPEQYITWLREAGFRVCAVTGDFKSDAPTETAERIFFVAEKI 242
                                    14        24        34        44        54        64|       74        84  |     94       104       114       124       134       144       154       164       174       184       194       204       214       224       234        
                                    14-MSE                                             65-MSE   74-MSE       87-MSE                                                142-MSE

Chain C from PDB  Type:PROTEIN  Length:242
 aligned with B1YKR8_EXIS2 | B1YKR8 from UniProtKB/TrEMBL  Length:242

    Alignment length:242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
         B1YKR8_EXIS2     1 MAYEQFAYVYDELMQDVPYPEWVAWVLEQVEPGKRIADIGCGTGTATLLLADHYEVTGVDLSEEMLEIAQEKAMETNRHVDFWVQDMRELELPEPVDAITILCDSLNYLQTEADVKQTFDSAARLLTDGGKLLFDVHSPYKMETLFNGKTYATHAEQSSYIWFADPGEEPLSVVHELTFFIEGEDGRYDRVDETHHQRTYPPEQYITWLREAGFRVCAVTGDFKSDAPTETAERIFFVAEKI 242
               SCOP domains d3d2lc_ C: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh...hhhhhhhhhhhhh....eeeee....hhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eeee.hhhhh.......eeee..hhhhhh.hhhhhhhhhhhhhhhh....eeeeeeehhhhhhh....eeeeee...eeeeeeeee.....eeeeeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh.eeeeeeee............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d2l C   1 mAYEQFAYVYDELmQDVPYPEWVAWVLEQVEPGKRIADIGCGTGTATLLLADHYEVTGVDLSEEmLEIAQEKAmETNRHVDFWVQDmRELELPEPVDAITILCDSLNYLQTEADVKQTFDSAARLLTDGGKLLFDVHSPYKmETLFNGKTYATHAEQSSYIWFADPGEEPLSVVHELTFFIEGEDGRYDRVDETHHQRTYPPEQYITWLREAGFRVCAVTGDFKSDAPTETAERIFFVAEKI 242
                            |       10   |    20        30        40        50        60    |   70   |    80      | 90       100       110       120       130       140 |     150       160       170       180       190       200       210       220       230       240  
                            1-MSE       14-MSE                                             65-MSE   74-MSE       87-MSE                                                142-MSE

Chain D from PDB  Type:PROTEIN  Length:238
 aligned with B1YKR8_EXIS2 | B1YKR8 from UniProtKB/TrEMBL  Length:242

    Alignment length:238
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234        
         B1YKR8_EXIS2     5 QFAYVYDELMQDVPYPEWVAWVLEQVEPGKRIADIGCGTGTATLLLADHYEVTGVDLSEEMLEIAQEKAMETNRHVDFWVQDMRELELPEPVDAITILCDSLNYLQTEADVKQTFDSAARLLTDGGKLLFDVHSPYKMETLFNGKTYATHAEQSSYIWFADPGEEPLSVVHELTFFIEGEDGRYDRVDETHHQRTYPPEQYITWLREAGFRVCAVTGDFKSDAPTETAERIFFVAEKI 242
               SCOP domains d3d2ld_ D: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh...hhhhhhhhhhhhh....eeeee....hhhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeee.hhhhh.....eeeeee..hhhhhh.hhhhhhhhhhhhhhheeeeeeeeeeeehhhhhhh....eeeeee...eeeeeeeee.....eeeeeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh.eeeeeeee............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d2l D   5 QFAYVYDELmQDVPYPEWVAWVLEQVEPGKRIADIGCGTGTATLLLADHYEVTGVDLSEEmLEIAQEKAmETNRHVDFWVQDmRELELPEPVDAITILCDSLNYLQTEADVKQTFDSAARLLTDGGKLLFDVHSPYKmETLFNGKTYATHAEQSSYIWFADPGEEPLSVVHELTFFIEGEDGRYDRVDETHHQRTYPPEQYITWLREAGFRVCAVTGDFKSDAPTETAERIFFVAEKI 242
                                    14        24        34        44        54        64|       74        84  |     94       104       114       124       134       144       154       164       174       184       194       204       214       224       234        
                                    14-MSE                                             65-MSE   74-MSE       87-MSE                                                142-MSE

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: automated matches (94)

Protein domain: automated matches (94)

Exiguobacterium sibiricum [TaxId: 262543] (1)

1a	d3d2la_	A:
1b	d3d2lb_	B:
1c	d3d2lc_	C:
1d	d3d2ld_	D:

(no "CATH Domain" information available for 3D2L)

(no "Pfam Domain" information available for 3D2L)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (B1YKR8_EXIS2 | B1YKR8)

molecular function
	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.

Asymmetric Unit
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 27)

Sites (4, 4)

SS Bonds (0, 0)

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