2NYU - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN FTSJ HOMOLOG 2 (E.COLI) PROTEIN IN COMPLEX WITH S-ADENOSYLMETHIONINE

Authors :   A. Dong, 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 :   21 Nov 06 (Deposition) - 05 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.76

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

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

Reference :   H. Wu, A. Dong, H. Zeng, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov
The Crystal Structure Of Human Ftsj Homolog 2 (E. Coli) Protein In Complex With Adomet
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PUTATIVE RIBOSOMAL RNA METHYLTRANSFERASE 2
	Chains	:	A, B
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P28-LIC-THROMBIN DERIVED FROM PET28
	Expression System Strain	:	BL21 CODON PLUS RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 51-246
	Gene	:	FTSJ2, FJH1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RRNA (URIDINE-2'-O-)-METHYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

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

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:6 , GLY A:30 , ALA A:31 , ALA A:32 , PRO A:33 , GLY A:34 , ALA A:35 , TRP A:36 , ASP A:62 , LEU A:63 , LEU A:64 , ALA A:78 , ASP A:79 , VAL A:80 , ASP A:104 , MET A:105 , ALA A:106 , LYS A:144 , HOH A:205 , HOH A:225 , HOH A:232 , HOH A:235	BINDING SITE FOR RESIDUE SAM A 201
2	AC2	SOFTWARE	SER B:6 , GLY B:30 , ALA B:31 , ALA B:32 , PRO B:33 , GLY B:34 , ALA B:35 , TRP B:36 , ASP B:62 , LEU B:63 , LEU B:64 , ALA B:78 , ASP B:79 , VAL B:80 , ASP B:104 , MET B:105 , ALA B:106 , LYS B:144 , HOH B:204 , HOH B:205 , HOH B:215 , HOH B:219 , HOH B:273	BINDING SITE FOR RESIDUE SAM B 201

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

Asymmetric Unit

No.	Residues
1	Ala A:32	-	Pro A:33
2	Cys A:76	-	Pro A:77
3	Ser B:1	-	Tyr B:2
4	Ala B:32	-	Pro B:33
5	Cys B:76	-	Pro B:77
6	His B:188	-	Gly B:189

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

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

Asymmetric Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000242257	1b	ENSE00001405763	chr7:2281833-2281797	37	MRM2_HUMAN	1-3	3	0	-	-
1.3	ENST00000242257	3	ENSE00000831505	chr7:2279342-2279053	290	MRM2_HUMAN	3-100	98	2	A:1-50 B:1-50	50 50
1.6d	ENST00000242257	6d	ENSE00001860591	chr7:2275199-2273926	1274	MRM2_HUMAN	100-246	147	2	A:50-189 (gaps) B:50-189 (gaps)	140 140

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:181
 aligned with MRM2_HUMAN | Q9UI43 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:189
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
           MRM2_HUMAN    51 SYRCRSAFKLLEVNERHQILRPGLRVLDCGAAPGAWSQVAVQKVNAAGTDPSSPVGFVLGVDLLHIFPLEGATFLCPADVTDPRTSQRILEVLPGRRADVILSDMAPNATGFRDLDHDRLISLCLTLLSVTPDILQPGGTFLCKTWAGSQSRRLQRRLTEEFQNVRIIKPEASRKESSEVYFLATQYHG 239
               SCOP domains d2nyua_ A: automated matches                                                                                                                                                                  SCOP domains
               CATH domains 2nyuA00 A:1-189 Vaccinia Virus protein VP39                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh............eeeee...........eee......hhhhhhhhhhhhhhhheeeeee........hhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee..hhhhhhhhhhhhhheeeeeee..--------.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:1-50 UniProt: 3-100 [INCOMPLETE] ------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.6d  PDB: A:50-189 (gaps) UniProt: 100-246 [INCOMPLETE]                                                                                Transcript 1 (2)
                 2nyu A   1 SYRSRSAFKLLEVNERHQILRPGLRVLDCGAAPGAWSQVAVQKVNAAGTDPSSPVGFVLGVDLLHIFPLEGATFLCPADVTDPRTSQRILEVLPGRRADVILSDMAPNATGFRDLDHDRLISLCLTLLSVTPDILQPGGTFLCKTWAGSQSRRLQRRLTEEFQNVRIIKP--------EVYFLATQYHG 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
                                                                                                                                                                                                   170      179

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with MRM2_HUMAN | Q9UI43 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:189
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
           MRM2_HUMAN    51 SYRCRSAFKLLEVNERHQILRPGLRVLDCGAAPGAWSQVAVQKVNAAGTDPSSPVGFVLGVDLLHIFPLEGATFLCPADVTDPRTSQRILEVLPGRRADVILSDMAPNATGFRDLDHDRLISLCLTLLSVTPDILQPGGTFLCKTWAGSQSRRLQRRLTEEFQNVRIIKPEASRKESSEVYFLATQYHG 239
               SCOP domains d2nyub_ B: automated matches                                                                                                                                                                  SCOP domains
               CATH domains 2nyuB00 B:1-189 Vaccinia Virus protein VP39                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...........eeeee..........eeee......hhhhhhhhhhhhhhhheeeeee........hhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee...hhhhhhhhhhhheeeeeee.-------..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:1-50 UniProt: 3-100 [INCOMPLETE] ------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.6d  PDB: B:50-189 (gaps) UniProt: 100-246 [INCOMPLETE]                                                                                Transcript 1 (2)
                 2nyu B   1 SYRSRSAFKLLEVNERHQILRPGLRVLDCGAAPGAWSQVAVQKVNAAGTDPSSPVGFVLGVDLLHIFPLEGATFLCPADVTDPRTSQRILEVLPGRRADVILSDMAPNATGFRDLDHDRLISLCLTLLSVTPDILQPGGTFLCKTWAGSQSRRLQRRLTEEFQNVRIIK-------SSEVYFLATQYHG 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        |-      |180         
                                                                                                                                                                                                  169     177

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)

Human (Homo sapiens) [TaxId: 9606] (7)

1a	d2nyua_	A:
1b	d2nyub_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Human (Homo sapiens) (49)

1a	2nyuB00	B:1-189
1b	2nyuA00	A:1-189

(no "Pfam Domain" information available for 2NYU)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MRM2_HUMAN | Q9UI43)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0008650	rRNA (uridine-2'-O-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methyluridine.
	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:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0000453	enzyme-directed rRNA 2'-O-methylation	The addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis where the methylase specifies the site that becomes methylated without using a guide RNA.
	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: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:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:32 - Pro A:33	[ RasMol ]
		Ala B:32 - Pro B:33	[ RasMol ]
		Cys A:76 - Pro A:77	[ RasMol ]
		Cys B:76 - Pro B:77	[ RasMol ]
		His B:188 - Gly B:189	[ RasMol ]
		Ser B:1 - Tyr B:2	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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Exons (2, 4)

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