3A4T - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ATRM4 FROM M.JANNASCHII WITH SINEFUNGIN

Authors :   M. Hirano, M. Kuratani, S. Yokoyama, Riken Structural Genomics/Pro Initiative (Rsgi)

Date :   14 Jul 09 (Deposition) - 30 Jun 10 (Release) - 01 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Trna, M5C, Rossmann Fold, Structural Genomics, Rsgi, Riken Structural Genomics/Proteomics Initiative, Methyltransferase, S-Adenosyl-L- Methionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Kuratani, M. Hirano, S. Goto-Ito, Y. Itoh, Y. Hikida, M. Nishimoto, S. Sekine, Y. Bessho, T. Ito, H. Grosjean, S. Yokoyama
Crystal Structure Of Methanocaldococcus Jannaschii Trm4 Complexed With Sinefungin.
J. Mol. Biol. V. 401 323 2010
PubMed-ID: 20600111 | Reference-DOI: 10.1016/J.JMB.2010.06.046

Molecule 1 - PUTATIVE METHYLTRANSFERASE MJ0026
	Chains	:	A, B
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MJ0026
	Organism Common	:	METHANOCOCCUS JANNASCHII
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190

		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	SFG	2	Ligand/Ion	ADENOSYL-ORNITHINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SFG	1	Ligand/Ion	ADENOSYL-ORNITHINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SFG	1	Ligand/Ion	ADENOSYL-ORNITHINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:90 , CYS A:91 , ALA A:92 , ALA A:93 , PRO A:94 , GLY A:95 , GLY A:96 , LYS A:97 , GLU A:115 , ILE A:116 , ARG A:120 , ALA A:141 , ASP A:142 , MET A:143 , ASP A:163 , PRO A:165 , ASN A:169 , ARG A:189 , HOH A:295	BINDING SITE FOR RESIDUE SFG A 500
2	AC2	SOFTWARE	MET B:90 , CYS B:91 , ALA B:92 , ALA B:93 , PRO B:94 , GLY B:95 , GLY B:96 , LYS B:97 , GLU B:115 , ILE B:116 , ARG B:120 , ASP B:142 , MET B:143 , ASP B:163 , PRO B:165 , ARG B:189 , HOH B:290	BINDING SITE FOR RESIDUE SFG B 501

Asymmetric Unit

No.	Residues
1	A:166	-	A:212
2	B:166	-	B:212

Asymmetric Unit

No.	Residues
1	Ala A:93	-	Pro A:94
2	Pro A:261	-	Pro A:262
3	Ala B:93	-	Pro B:94
4	Pro B:261	-	Pro B:262

(no "SAP(SNP)/Variant" information available for 3A4T)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NOL1_NOP2_SUN	PS01153	NOL1/NOP2/sun family signature.	TRM4_METJA	157-168	2	A:157-168 B:157-168

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NOL1_NOP2_SUN	PS01153	NOL1/NOP2/sun family signature.	TRM4_METJA	157-168	1	A:157-168 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NOL1_NOP2_SUN	PS01153	NOL1/NOP2/sun family signature.	TRM4_METJA	157-168	1	- B:157-168

(no "Exon" information available for 3A4T)

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:258
 aligned with TRM4_METJA | Q60343 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:266
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268      
           TRM4_METJA     9 KMQFIRVNTLKINPEVLKKRLENKGVVLEKTFLDYAFEVKKSPFSIGSTPEYLFGYYMPQSISSMIPPIVLNPREDDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKSNINRMGVLNTIIINADMRKYKDYLLKNEIFFDKILLDAPCSGNIIKDKNRNVSEEDIKYCSLRQKELIDIGIDLLKKDGELVYSTCSMEVEENEEVIKYILQKRNDVELIIIKANEFKGINIKEGYIKGTLRVFPPNEPFFIAKLRKI 274
               SCOP domains d3a4ta_ A: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhh..eee......eeeeee.......hhhhhh..eee.hhhhhhhhhhhh.....eeee.....hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhh...eeeeeee..hhhhh--------hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee...hhhhhhhhhhhhhhhh..eeee...........eee......eee......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------NOL1_NOP2_SU---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a4t A   9 KMQFIRVNTLKINPEVLKKRLENKGVVLEKTFLDYAFEVKKSPFSIGSTPEYLFGYYMPQSISSMIPPIVLNPREDDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKSNINRMGVLNTIIINADMRKYKDYLLKNEIFFDKILLDAPCSGNI--------SEEDIKYCSLRQKELIDIGIDLLKKDGELVYSTCSMEVEENEEVIKYILQKRNDVELIIIKANEFKGINIKEGYIKGTLRVFPPNEPFFIAKLRKI 274
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168 |       -|      188       198       208       218       228       238       248       258       268      
                                                                                                                                                                                           170      179

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with TRM4_METJA | Q60343 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:265
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269     
           TRM4_METJA    10 MQFIRVNTLKINPEVLKKRLENKGVVLEKTFLDYAFEVKKSPFSIGSTPEYLFGYYMPQSISSMIPPIVLNPREDDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKSNINRMGVLNTIIINADMRKYKDYLLKNEIFFDKILLDAPCSGNIIKDKNRNVSEEDIKYCSLRQKELIDIGIDLLKKDGELVYSTCSMEVEENEEVIKYILQKRNDVELIIIKANEFKGINIKEGYIKGTLRVFPPNEPFFIAKLRKI 274
               SCOP domains d3a4tb_ B: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhh...eee......eeeeee...hhhhhhhhhh..eee..hhhhhhhhhhh.....eeee.....hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeeeeee.....------------...hhhhhhhhhhhhhhhheeeeeeeeeee.......hhhhhhhhhhhh..eeee..hhhhh....eee......eee......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------NOL1_NOP2_SU---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a4t B  10 MQFIRVNTLKINPEVLKKRLENKGVVLEKTFLDYAFEVKKSPFSIGSTPEYLFGYYMPQSISSMIPPIVLNPREDDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKSNINRMGVLNTIIINADMRKYKDYLLKNEIFFDKILLDAPCSGN------------DIKYCSLRQKELIDIGIDLLKKDGELVYSTCSMEVEENEEVIKYILQKRNDVELIIIKANEFKGINIKEGYIKGTLRVFPPNEPFFIAKLRKI 274
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         -  |    189       199       209       219       229       239       249       259       269     
                                                                                                                                                                                         169          182

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)

Methanocaldococcus jannaschii [TaxId: 2190] (2)

1a	d3a4ta_	A:
1b	d3a4tb_	B:

(no "CATH Domain" information available for 3A4T)

(no "Pfam Domain" information available for 3A4T)

Asymmetric Unit(hide GO term definitions)

Chain A,B (TRM4_METJA | Q60343)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0016428	tRNA (cytosine-5-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 5-methylcytosine.
	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:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:0030488	tRNA methylation	The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
		Ala A:93 - Pro A:94	[ RasMol ]
		Ala B:93 - Pro B:94	[ RasMol ]
		Pro A:261 - Pro A:262	[ RasMol ]
		Pro B:261 - Pro B:262	[ RasMol ]

Biological Units
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	3a4t
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(no "Related Entries Specified in the PDB File" available for 3A4T)

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

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