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Title :   CRYSTAL STRUCTURE OF PROBABLE METHYLTRANSFERASE FROM BORDETELLA PERTUSSIS TOHAMA I

Authors :   Y. Kim, C. Tesar, L. Keigher, A. Joachimiak, Midwest Center For Stru Genomics (Mcsg)

Date :   26 Nov 09 (Deposition) - 08 Dec 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Alpha-Beta-Alpha Sandwich, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, C. Tesar, L. Keigher, A. Joachimiak
Crystal Structure Of Probable Methyltransferase Spou From Bordetella Pertussis Tohama I
To Be Published
PubMed: search

Molecule 1 - PROBABLE METHYLTRANSFERASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG19
	Expression System Strain	:	BL21 MAGIC
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	TARGET DOMAIN 1 - 170
	Gene	:	BP1901
	Organism Scientific	:	BORDETELLA PERTUSSIS
	Organism Taxid	:	520
	Strain	:	TOHAMA I

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:68 , HIS A:69 , GLU A:74 , VAL B:68 , HIS B:69 , GLU B:74	BINDING SITE FOR RESIDUE GOL B 181
2	AC2	SOFTWARE	PRO B:96 , ARG B:139 , ILE B:140	BINDING SITE FOR RESIDUE SO4 B 171
3	AC3	SOFTWARE	ARG B:90 , LEU B:129 , ILE B:134 , HOH B:212	BINDING SITE FOR RESIDUE GOL B 182
4	AC4	SOFTWARE	TYR B:149 , ARG C:26 , SER C:57	BINDING SITE FOR RESIDUE SO4 C 181

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

Asymmetric Unit

No.	Residues
1	Gly B:93	-	Pro B:94
2	Gly C:93	-	Pro C:94

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

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

(no "Exon" information available for 3KTY)

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:167
 aligned with Q7VXA3_BORPE | Q7VXA3 from UniProtKB/TrEMBL  Length:258

    Alignment length:173
                               1                                                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167   
         Q7VXA3_BORPE     - ---MTQAFSRVRFIMTQPSHPGNVGSAARAIKTMGFGELVLVAPRFPDMTAQPEAVALASGALDVLERAAVHDTLEEALAPVTLAFALTTRVRDLGPPPCDIREAAGLARRHLDDTEAGVVAIVLGTERAGLTNAQIELCHRICHIPANPQYSSLNVAQALQLAAWELRYALL 170
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.eeeeee...hhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhh.hhhhhhh.eee.hhhhhhh...eeeeee..-----...eehhhhhhhhhhhhhhh....eeeee....-..hhhhhhh..eeee..........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kty A  -2 SNAmTQAFSRVRFImTQPSHPGNVGSAARAIKTmGFGELVLVAPRFPDmTAQPEAVALASGALDVLERAAVHDTLEEALAPVTLAFALTTR-----PPPCDIREAAGLARRHLDDTEAGVVAIVLGTER-GLTNAQIELCHRICHIPANPQYSSLNVAQALQLAAWELRYALL 170
                               |     7    |   17        27   |    37        47        57        67        77        87|     | 97       107       117        |-|      137       147       157       167   
                               |         12-MSE             31-MSE         46-MSE                                    88    94                             126 |                                          
                               1-MSE                                                                                                                        128

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with Q7VXA3_BORPE | Q7VXA3 from UniProtKB/TrEMBL  Length:258

    Alignment length:173
                               1                                                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167   
         Q7VXA3_BORPE     - ---MTQAFSRVRFIMTQPSHPGNVGSAARAIKTMGFGELVLVAPRFPDMTAQPEAVALASGALDVLERAAVHDTLEEALAPVTLAFALTTRVRDLGPPPCDIREAAGLARRHLDDTEAGVVAIVLGTERAGLTNAQIELCHRICHIPANPQYSSLNVAQALQLAAWELRYALL 170
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhheeeeee...hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh..hhhhhhh.eee.hhhhhhh...eeeeee..........eehhhhhhhhhhhhhhh....eeeee.......hhhhhhhh.eeee..........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kty B  -2 SNAmTQAFSRVRFImTQPSHPGNVGSAARAIKTmGFGELVLVAPRFPDmTAQPEAVALASGALDVLERAAVHDTLEEALAPVTLAFALTTRVRDLGPPPCDIREAAGLARRHLDDTEAGVVAIVLGTERAGLTNAQIELCHRICHIPANPQYSSLNVAQALQLAAWELRYALL 170
                               |     7    |   17        27   |    37        47        57        67        77        87        97       107       117       127       137       147       157       167   
                               1-MSE     12-MSE             31-MSE         46-MSE

Chain C from PDB  Type:PROTEIN  Length:170
 aligned with Q7VXA3_BORPE | Q7VXA3 from UniProtKB/TrEMBL  Length:258

    Alignment length:170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
         Q7VXA3_BORPE     1 MTQAFSRVRFIMTQPSHPGNVGSAARAIKTMGFGELVLVAPRFPDMTAQPEAVALASGALDVLERAAVHDTLEEALAPVTLAFALTTRVRDLGPPPCDIREAAGLARRHLDDTEAGVVAIVLGTERAGLTNAQIELCHRICHIPANPQYSSLNVAQALQLAAWELRYALL 170
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------SpoU_methylase-3ktyC01 C:7-163                                                                                                                               ------- Pfam domains (1)
           Pfam domains (2) ------SpoU_methylase-3ktyC02 C:7-163                                                                                                                               ------- Pfam domains (2)
           Pfam domains (3) ------SpoU_methylase-3ktyC03 C:7-163                                                                                                                               ------- Pfam domains (3)
         Sec.struct. author ..hhhh.eeeeee...hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhh...hhhhhhhheee.hhhhhhh...eeeeee..........eehhhhhhhhhhhhhhh....eeeee.......hhhhhhhh.eeee..........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kty C   1 mTQAFSRVRFImTQPSHPGNVGSAARAIKTmGFGELVLVAPRFPDmTAQPEAVALASGALDVLERAAVHDTLEEALAPVTLAFALTTRVRDLGPPPCDIREAAGLARRHLDDTEAGVVAIVLGTERAGLTNAQIELCHRICHIPANPQYSSLNVAQALQLAAWELRYALL 170
                            |       10 |      20        30|       40     |  50        60        70        80        90       100       110       120       130       140       150       160       170
                            1-MSE     12-MSE             31-MSE         46-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 '\|'

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

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SPOUT (28)

Family: SpoU_methylase (7)

Bordetella pertussis (1)

1a	SpoU_methylase-3ktyC01	C:7-163
1b	SpoU_methylase-3ktyC02	C:7-163
1c	SpoU_methylase-3ktyC03	C:7-163

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q7VXA3_BORPE | Q7VXA3)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0008173	RNA methyltransferase activity	Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
	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:0001510	RNA methylation	Posttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor.
	GO:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.

Asymmetric Unit
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		Gly B:93 - Pro B:94	[ RasMol ]
		Gly C:93 - Pro C:94	[ RasMol ]

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