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Title :   HUMAN METHYLTRANSFERASE 10 DOMAIN CONTAINING PROTEIN

Authors :   J. R. Min, H. Wu, H. Zeng, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)

Date :   12 May 06 (Deposition) - 13 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Methyltransferase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Wu, J. Min, H. Zeng, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov
The Crystal Structure Of Human Methyltransferase 10 Domain Containing Protein.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - METHYLTRANSFERASE 10 DOMAIN CONTAINING PROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P28A-LIC
	Expression System Strain	:	BL21 (DE3) CODON PLUS RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 40-291
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	DTU	1	Ligand/Ion	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3	SAH	3	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DTU	1	Ligand/Ion	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DTU	-1	Ligand/Ion	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DTU	-1	Ligand/Ion	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH C:451	BINDING SITE FOR RESIDUE CL C 402
2	AC2	SOFTWARE	ASN A:8 , LEU A:38 , PRO A:40 , ARG A:45 , GLY A:73 , THR A:74 , GLY A:75 , THR A:95 , GLU A:96 , VAL A:97 , ASP A:98 , CYS A:101 , GLN A:125 , THR A:127 , LEU A:128 , ASN A:147 , PRO A:149 , PHE A:190 , ARG A:193 , HOH A:2141 , HOH A:2143 , HOH A:2150 , HOH A:2159 , HOH A:2173 , HOH A:2192	BINDING SITE FOR RESIDUE SAH A 300
3	AC3	SOFTWARE	LEU B:38 , ARG B:45 , GLY B:73 , THR B:74 , GLY B:75 , THR B:95 , GLU B:96 , VAL B:97 , ASP B:98 , THR B:127 , LEU B:128 , ASN B:147 , PRO B:149 , HOH B:402 , HOH B:403 , HOH B:412 , HOH B:418 , HOH B:427 , ASN C:8 , HOH C:420	BINDING SITE FOR RESIDUE SAH B 301
4	AC4	SOFTWARE	ASN B:8 , HOH B:413 , HOH B:432 , LEU C:38 , ARG C:45 , GLY C:73 , THR C:74 , THR C:95 , GLU C:96 , VAL C:97 , ASP C:98 , LYS C:126 , ASN C:147 , PRO C:149 , PHE C:151 , HOH C:404 , HOH C:406 , HOH C:408 , HOH C:413	BINDING SITE FOR RESIDUE SAH C 302
5	AC5	SOFTWARE	LYS A:106 , VAL A:109 , GLU A:110 , SER A:115 , ILE A:118 , VAL A:120 , HOH A:2153	BINDING SITE FOR RESIDUE DTU A 2140

(no "SS Bond" information available for 2H00)

(no "Cis Peptide Bond" information available for 2H00)

(no "SAP(SNP)/Variant" information available for 2H00)

(no "PROSITE Motif" information available for 2H00)

(no "Exon" information available for 2H00)

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:225
 aligned with MET16_HUMAN | Q86W50 from UniProtKB/Swiss-Prot  Length:562

    Alignment length:250
                                    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
          MET16_HUMAN    42 VSLNFKDPEAVRALTCTLLREDFGLSIDIPLERLIPTVPLRLNYIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQKTLLMDALKEESEIIYDFCMCNPPFFANQLEAKGVNSRNPRRPPPSSVNTGGITEIMAEGGELEFVKRIIHDSLQLKKRLRWYSCMLGKKCSLAPLKEELRIQGVPKVTYTEFCQGRTMRWALAWSFYD 291
               SCOP domains d2h00a1 A:5-254 Methyltransferase 10 domain containing protein METT10D                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh..hhhhh...eeeee.....hhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh.....eeeee....................eeee.....-------------------------....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh...eeeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h00 A   5 VSLNFKDPEAVRALTCTLLREDFGLSIDIPLERLIPTVPLRLNYIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQKTLLMDALKEESEIIYDFCMCNPPFF-------------------------GITEIMAEGGELEFVKRIIHDSLQLKKRLRWYSCMLGKKCSLAPLKEELRIQGVPKVTYTEFCQGRTMRWALAWSFYD 254
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144      |  -         -         -  |    184       194       204       214       224       234       244       254
                                                                                                                                                                            151                       177

Chain B from PDB  Type:PROTEIN  Length:210
 aligned with MET16_HUMAN | Q86W50 from UniProtKB/Swiss-Prot  Length:562

    Alignment length:246
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284      
          MET16_HUMAN    45 NFKDPEAVRALTCTLLREDFGLSIDIPLERLIPTVPLRLNYIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQKTLLMDALKEESEIIYDFCMCNPPFFANQLEAKGVNSRNPRRPPPSSVNTGGITEIMAEGGELEFVKRIIHDSLQLKKRLRWYSCMLGKKCSLAPLKEELRIQGVPKVTYTEFCQGRTMRWALAWSFY 290
               SCOP domains d2h00b_ B: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh.....eeeee.........-------..eeeeee.........-----------------------------.hhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2h00 B   8 NFKDPEAVRALTCTLLREDFGLSIDIPLERLIPTVPLRLNYIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQKTLLMD-------IIYDFCMCNPPFFANQL-----------------------------GGELEFVKRIIHDSLQLKKRLRWYSCMLGKKCSLAPLKEELRIQGVPKVTYTEFCQGRTMRWALAWSFY 253
                                    17        27        37        47        57        67        77        87        97       107       117       127   |     - |     147       | -         -         -       187       197       207       217       227       237       247      
                                                                                                                                                     131     139             155                           185

Chain C from PDB  Type:PROTEIN  Length:203
 aligned with MET16_HUMAN | Q86W50 from UniProtKB/Swiss-Prot  Length:562

    Alignment length:248
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283        
          MET16_HUMAN    44 LNFKDPEAVRALTCTLLREDFGLSIDIPLERLIPTVPLRLNYIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQKTLLMDALKEESEIIYDFCMCNPPFFANQLEAKGVNSRNPRRPPPSSVNTGGITEIMAEGGELEFVKRIIHDSLQLKKRLRWYSCMLGKKCSLAPLKEELRIQGVPKVTYTEFCQGRTMRWALAWSFYD 291
               SCOP domains d2h00c_ C: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh..-----...eeeee.....hhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhh......eeeee.........-------..eeeeee.....---------------------------------hhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h00 C   7 LNFKDPEAVRALTCTLLREDFGLSIDIPLERLIPTVPLRLNYIHWVEDLIGHQ-----TLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQKTLLMD-------IIYDFCMCNPPFF---------------------------------GGELEFVKRIIHDSLQLKKRLRWYSCMLGKKCSLAPLKEELRIQGVPKVTYTEFCQGRTMRWALAWSFYD 254
                                    16        26        36        46        56  |     66        76        86        96       106       116       126    |    -  |    146    |    -         -         -       186       196       206       216       226       236       246        
                                                                               59    65                                                               131     139         151                               185

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

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Asymmetric Unit(hide GO term definitions)

Chain A,B,C (MET16_HUMAN | Q86W50)

molecular function
	GO:0052907	23S rRNA (adenine(1618)-N(6))-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + adenine(1618) in 23S rRNA = S-adenosyl-L-homocysteine + rRNA containing N(6)-methyladenine(1618) in 23S rRNA.
	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:0070475	rRNA base methylation	The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.
cellular component
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (5, 5)

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