1ZQ9 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN DIMETHYLADENOSINE TRANSFERASE

Authors :   A. Dong, H. Wu, H. Zeng, P. Loppnau, M. Sundstrom, C. Arrowsmith, A. Edwards, A. Bochkarev, A. Plotnikov, Structural Genomics Consortium (Sgc)

Date :   18 May 05 (Deposition) - 31 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B

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

Reference :   H. Wu, A. Dong, H. Zeng, P. Loppnau, M. Sundstrom, C. Arrowsmith, A. Edwards, A. Bochkarev, A. Plotnikov
Crystal Structure Of Human Dimethyladenosine Transferase With Sam
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROBABLE DIMETHYLADENOSINE TRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	S- ADENOSYLMETHIONINE-6-N',N'-ADENOSYLRRNA, DIMETHYLTRANSFERASE, 18S RRNA DIMETHYLASE, HUSSY-05

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:36 , HIS A:37 , ILE A:38 , GLY A:64 , GLY A:66 , CYS A:84 , GLU A:85 , LEU A:86 , LEU A:90 , GLY A:112 , ASP A:113 , VAL A:114 , ASN A:128 , LEU A:129 , PRO A:130 , MET A:154 , PHE A:196 , SER A:204 , HOH A:4166 , HOH A:4236 , HOH A:4282 , HOH A:4329	BINDING SITE FOR RESIDUE SAM A 4000
2	AC2	SOFTWARE	HIS B:37 , GLY B:64 , GLY B:66 , CYS B:84 , GLU B:85 , LEU B:86 , LEU B:90 , GLY B:112 , ASP B:113 , VAL B:114 , ASN B:128 , LEU B:129 , PRO B:130 , TYR B:131 , ILE B:133 , PHE B:196 , HOH B:4125 , HOH B:4166 , HOH B:4189 , HOH B:4208 , HOH B:4394	BINDING SITE FOR RESIDUE SAM B 4001

(no "SS Bond" information available for 1ZQ9)

Asymmetric/Biological Unit

No.	Residues
1	Arg A:145	-	Pro A:146
2	Arg A:197	-	Pro A:198
3	Asn A:213	-	Pro A:214
4	Arg B:145	-	Pro B:146
5	Arg B:197	-	Pro B:198
6	Asn B:213	-	Pro B:214

(no "SAP(SNP)/Variant" information available for 1ZQ9)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRNA_A_DIMETH	PS01131	Ribosomal RNA adenine dimethylases signature.	DIM1_HUMAN	60-87	2	A:60-87 B:60-87

Asymmetric/Biological Unit (11, 22)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000199320	1b	ENSE00000837034	chr5:61699760-61699521	240	DIM1_HUMAN	1-27	27	0	-	-
1.2	ENST00000199320	2	ENSE00000748423	chr5:61699173-61699100	74	DIM1_HUMAN	27-51	25	2	A:36-51 B:36-51	16 16
1.3	ENST00000199320	3	ENSE00000748421	chr5:61697949-61697863	87	DIM1_HUMAN	52-80	29	2	A:52-80 B:52-80	29 29
1.4	ENST00000199320	4	ENSE00000837030	chr5:61694708-61694647	62	DIM1_HUMAN	81-101	21	2	A:81-101 B:81-101	21 21
1.5	ENST00000199320	5	ENSE00000549149	chr5:61694566-61694473	94	DIM1_HUMAN	101-132	32	2	A:101-132 B:101-132	32 32
1.6a	ENST00000199320	6a	ENSE00000837028	chr5:61694387-61694338	50	DIM1_HUMAN	133-149	17	2	A:133-149 B:133-149	17 17
1.7	ENST00000199320	7	ENSE00000837027	chr5:61690434-61690311	124	DIM1_HUMAN	149-190	42	2	A:149-190 B:149-190	42 42
1.8	ENST00000199320	8	ENSE00000837026	chr5:61689874-61689782	93	DIM1_HUMAN	191-221	31	2	A:191-221 B:191-221	31 31
1.9a	ENST00000199320	9a	ENSE00000837025	chr5:61688817-61688753	65	DIM1_HUMAN	222-243	22	2	A:222-243 B:222-243	22 22
1.10b	ENST00000199320	10b	ENSE00000837024	chr5:61688061-61687998	64	DIM1_HUMAN	243-264	22	2	A:243-264 B:243-264	22 22
1.12b	ENST00000199320	12b	ENSE00001746643	chr5:61686809-61686703	107	DIM1_HUMAN	265-300	36	2	A:265-300 B:265-300	36 36
1.13b	ENST00000199320	13b	ENSE00000837020	chr5:61684879-61683081	1799	DIM1_HUMAN	300-313	14	2	A:300-313 B:300-313	14 14

Asymmetric/Biological 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:278
 aligned with DIM1_HUMAN | Q9UNQ2 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:278
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305        
           DIM1_HUMAN    36 QHILKNPLIINSIIDKAALRPTDVVLEVGPGTGNMTVKLLEKAKKVVACELDPRLVAELHKRVQGTPVASKLQVLVGDVLKTDLPFFDTCVANLPYQISSPFVFKLLLHRPFFRCAILMFQREFALRLVAKPGDKLYCRLSINTQLLARVDHLMKVGKNNFRPPPKVESSVVRIEPKNPPPPINFQEWDGLVRITFVRKNKTLSAAFKSSAVQQLLEKNYRIHCSVHNIIIPEDFSIADKIQQILTSTGFSDKRARSMDIDDFIRLLHGFNAEGIHFS 313
               SCOP domains d1zq9a1 A:36-313 Probable dimethyladenosine transferase                                                                                                                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhh......eeeee......hhhhhhhhh.eeeeee.hhhhhhhhhhhhh...hhh.eeeee............eeeee.hhhhhhhhhhhhhhh.....eeeeeeehhhhhhhhh.......hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.......hhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------RRNA_A_DIMETH  PDB: A:60-87 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2        Exon 1.3  PDB: A:52-80       Exon 1.4             -------------------------------Exon 1.6a        -----------------------------------------Exon 1.8  PDB: A:191-221       ---------------------Exon 1.10b            Exon 1.12b  PDB: A:265-300          ------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.5  PDB: A:101-132        ----------------Exon 1.7  PDB: A:149-190 UniProt: 149-190 -------------------------------Exon 1.9a             --------------------------------------------------------Exon 1.13b     Transcript 1 (2)
                 1zq9 A  36 QHILKNPLIINSIIDKAALRPTDVVLEVGPGTGNMTVKLLEKAKKVVACELDPRLVAELHKRVQGTPVASKLQVLVGDVLKTDLPFFDTCVANLPYQISSPFVFKLLLHRPFFRCAILMFQREFALRLVAKPGDKLYCRLSINTQLLARVDHLMKVGKNNFRPPPKVESSVVRIEPKNPPPPINFQEWDGLVRITFVRKNKTLSAAFKSSAVQQLLEKNYRIHCSVHNIIIPEDFSIADKIQQILTSTGFSDKRARSMDIDDFIRLLHGFNAEGIHFS 313
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305

Chain B from PDB  Type:PROTEIN  Length:278
 aligned with DIM1_HUMAN | Q9UNQ2 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:278
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305        
           DIM1_HUMAN    36 QHILKNPLIINSIIDKAALRPTDVVLEVGPGTGNMTVKLLEKAKKVVACELDPRLVAELHKRVQGTPVASKLQVLVGDVLKTDLPFFDTCVANLPYQISSPFVFKLLLHRPFFRCAILMFQREFALRLVAKPGDKLYCRLSINTQLLARVDHLMKVGKNNFRPPPKVESSVVRIEPKNPPPPINFQEWDGLVRITFVRKNKTLSAAFKSSAVQQLLEKNYRIHCSVHNIIIPEDFSIADKIQQILTSTGFSDKRARSMDIDDFIRLLHGFNAEGIHFS 313
               SCOP domains d1zq9b_ B: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhh......eeeee......hhhhhhh...eeeeee.hhhhhhhhhhhhh...hhh.eeeee.hhhhh......eeeee.hhhhhhhhhhhhhhh.....eeeeeeehhhhhhhhh.......hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.......hhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------RRNA_A_DIMETH  PDB: B:60-87 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2        Exon 1.3  PDB: B:52-80       Exon 1.4             -------------------------------Exon 1.6a        -----------------------------------------Exon 1.8  PDB: B:191-221       ---------------------Exon 1.10b            Exon 1.12b  PDB: B:265-300          ------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.5  PDB: B:101-132        ----------------Exon 1.7  PDB: B:149-190 UniProt: 149-190 -------------------------------Exon 1.9a             --------------------------------------------------------Exon 1.13b     Transcript 1 (2)
                 1zq9 B  36 QHILKNPLIINSIIDKAALRPTDVVLEVGPGTGNMTVKLLEKAKKVVACELDPRLVAELHKRVQGTPVASKLQVLVGDVLKTDLPFFDTCVANLPYQISSPFVFKLLLHRPFFRCAILMFQREFALRLVAKPGDKLYCRLSINTQLLARVDHLMKVGKNNFRPPPKVESSVVRIEPKNPPPPINFQEWDGLVRITFVRKNKTLSAAFKSSAVQQLLEKNYRIHCSVHNIIIPEDFSIADKIQQILTSTGFSDKRARSMDIDDFIRLLHGFNAEGIHFS 313
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305

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 "CATH Domain" information available for 1ZQ9)

(no "Pfam Domain" information available for 1ZQ9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DIM1_HUMAN | Q9UNQ2)

molecular function
	GO:0052909	18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity	Catalysis of the reaction: 4 S-adenosyl-L-methionine + adenine(1779)/adenine(1780) in 18S rRNA = 4 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(1779)/N(6)-dimethyladenine(1780) in 18S rRNA.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0000179	rRNA (adenine-N6,N6-)-dimethyltransferase activity	Catalysis of the dimethylation two adjacent A residues in the loop closing the 3'-terminal stem of the 18S rRNA, using S-adenosyl-L-methionine as a methyl donor.
	GO:0008649	rRNA methyltransferase activity	Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA 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:0031167	rRNA methylation	The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
	GO:0000154	rRNA modification	The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Arg A:145 - Pro A:146	[ RasMol ]
		Arg A:197 - Pro A:198	[ RasMol ]
		Arg B:145 - Pro B:146	[ RasMol ]
		Arg B:197 - Pro B:198	[ RasMol ]
		Asn A:213 - Pro A:214	[ RasMol ]
		Asn B:213 - Pro B:214	[ RasMol ]

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	1zq9
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

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Exons (11, 22)

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