2YX1 - JenaLib

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Title :   CRYSTAL STRUCTURE OF M.JANNASCHII TRNA M1G37 METHYLTRANSFERASE

Authors :   S. Goto-Ito, T. Ito, R. Ishii, Y. Bessho, S. Yokoyama

Date :   23 Apr 07 (Deposition) - 22 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Methyl Transferase, Trna Modification Enzyme, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Goto-Ito, T. Ito, R. Ishii, Y. Muto, Y. Bessho, S. Yokoyama
Crystal Structure Of Archaeal Trna(M(1)G37)Methyltransferas Atrm5.
Proteins V. 72 1274 2008
PubMed-ID: 18384044 | Reference-DOI: 10.1002/PROT.22019

Molecule 1 - HYPOTHETICAL PROTEIN MJ0883
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28C
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	2.1.1.31
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	METHYL TRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 18)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	SFG	2	Ligand/Ion	SINEFUNGIN
3	ZN	10	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	SFG	1	Ligand/Ion	SINEFUNGIN
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	SFG	1	Ligand/Ion	SINEFUNGIN
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MSE	-1	Mod. Amino Acid	SELENOMETHIONINE
2	SFG	-1	Ligand/Ion	SINEFUNGIN
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:227 , GLU A:230 , HOH A:632	BINDING SITE FOR RESIDUE ZN A 501
2	AC2	SOFTWARE	HIS A:243 , HOH A:505 , HOH A:625	BINDING SITE FOR RESIDUE ZN A 502
3	AC3	SOFTWARE	PHE A:303 , CYS A:307 , CYS A:309	BINDING SITE FOR RESIDUE ZN A 503
4	AC4	SOFTWARE	TYR A:177	BINDING SITE FOR RESIDUE ZN A 504
5	AC5	SOFTWARE	LYS B:175 , HIS B:227 , GLU B:230	BINDING SITE FOR RESIDUE ZN B 506
6	AC6	SOFTWARE	PHE B:303 , GLU B:304 , CYS B:307 , CYS B:309	BINDING SITE FOR RESIDUE ZN B 507
7	AC7	SOFTWARE	HIS B:271 , LYS B:272	BINDING SITE FOR RESIDUE ZN B 509
8	AC8	SOFTWARE	TYR A:177 , ARG A:186 , PHE A:203 , ALA A:204 , PRO A:208 , PHE A:209 , ASP A:223 , ILE A:224 , SER A:250 , ASP A:251 , ASN A:265 , LEU A:266 , HOH A:517 , HOH A:531 , HOH A:537 , HOH A:581 , HOH A:597	BINDING SITE FOR RESIDUE SFG A 401
9	AC9	SOFTWARE	ARG B:186 , PHE B:203 , ALA B:204 , GLY B:205 , PRO B:208 , PHE B:209 , ASP B:223 , ILE B:224 , ASN B:225 , SER B:250 , ASP B:251 , ASN B:265 , LEU B:266 , HOH B:515 , HOH B:519 , HOH B:529 , HOH B:561 , HOH B:603	BINDING SITE FOR RESIDUE SFG B 402

(no "SS Bond" information available for 2YX1)

(no "Cis Peptide Bond" information available for 2YX1)

(no "SAP(SNP)/Variant" information available for 2YX1)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_TRM5_TYW2	PS51684	SAM-dependent methyltransferase TRM5/TYW2-type domain profile.	TRM5B_METJA	97-335	2	A:97-335 B:97-335

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_TRM5_TYW2	PS51684	SAM-dependent methyltransferase TRM5/TYW2-type domain profile.	TRM5B_METJA	97-335	1	A:97-335 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_TRM5_TYW2	PS51684	SAM-dependent methyltransferase TRM5/TYW2-type domain profile.	TRM5B_METJA	97-335	1	- B:97-335

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_TRM5_TYW2	PS51684	SAM-dependent methyltransferase TRM5/TYW2-type domain profile.	TRM5B_METJA	97-335	2	A:97-335 B:97-335

(no "Exon" information available for 2YX1)

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:323
 aligned with TRM5B_METJA | Q58293 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:335
                                    11        21        31        41        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       301       311       321       331     
          TRM5B_METJA     2 PLCLKINKKHGEQTRRILIENNLLNKDYKITSEGNYLYLPIKDVDEDILKSILNIEFELVDKELEEKKIIKKPSFREIISKKYRKEIDEGLISLSYDVVGDLVILQISDEVDEKIRKEIGELAYKLIPCKGVFRRKSEVKGEFRVRELEHLAGENRTLTIHKENGYRLWVDIAKVYFSPRLGGERARIMKKVSLNDVVVDMFAGVGPFSIACKNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDVKGNRVIMNLPKFAHKFIDKALDIVEEGGVIHYYTIGKDFDKAIKLFEKKCDCEVLEKRIVKSYAPREYILALDFKINKK 336
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhh.........eee..eeeee....hhhhhh.......eeee......-----..hhhhhhhhhhhhhh........eee..eeee......hhhhhhhhhhhhhhhh...eeeee.-------....eeeeee....eeeeee..eeeeee......hhhhhhhhhhhhhhh....eeee.....hhhhhhh....eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhh...eeeeee....hhhhhhhhhhhheeeeeeeeeeeee..hhhhhhhhhhhheeeeeeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------SAM_MT_TRM5_TYW2  PDB: A:97-335 UniProt: 97-335                                                                                                                                                                                                - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yx1 A   2 PLCLKINKKHGEQTRRILIENNLLNKDYKITSEGNYLYLPIKDVDEDILKSILNIEFELVDKELEEK-----PSFREIISKKYRKEIDEGLISLSYDVVGDLVILQISDEVDEKIRKEIGELAYKLIPCKGVFRRK-------RVRELEHLAGENRTLTIHKENGYRLWVDIAKVYFSPRLGGERARImKKVSLNDVVVDmFAGVGPFSIACKNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDVKGNRVImNLPKFAHKFIDKALDIVEEGGVIHYYTIGKDFDKAIKLFEKKCDCEVLEKRIVKSYAPREYILALDFKINKK 336
                                    11        21        31        41        51        61      |  -  |     81        91       101       111       121       131     |   -   |   151       161       171       181       191       201|      211       221       231       241       251       261  |    271       281       291       301       311       321       331     
                                                                                             68    74                                                            137     145                                          190-MSE     202-MSE                                                       264-MSE

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with TRM5B_METJA | Q58293 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:335
                                    11        21        31        41        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       301       311       321       331     
          TRM5B_METJA     2 PLCLKINKKHGEQTRRILIENNLLNKDYKITSEGNYLYLPIKDVDEDILKSILNIEFELVDKELEEKKIIKKPSFREIISKKYRKEIDEGLISLSYDVVGDLVILQISDEVDEKIRKEIGELAYKLIPCKGVFRRKSEVKGEFRVRELEHLAGENRTLTIHKENGYRLWVDIAKVYFSPRLGGERARIMKKVSLNDVVVDMFAGVGPFSIACKNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDVKGNRVIMNLPKFAHKFIDKALDIVEEGGVIHYYTIGKDFDKAIKLFEKKCDCEVLEKRIVKSYAPREYILALDFKINKK 336
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------       -----          ----Met_10-2yx1B01 B:95-289                                                                                                                                                                            ----------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------       -----          ----Met_10-2yx1B02 B:95-289                                                                                                                                                                            ----------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee..hhhhhhhhhhhh.........eee..eeeee....hhhhhhhhh....eeee......-------.....----------.......eee..eeee..........hhhhhhhhhhhh...eeeee.--------...eeeeee....eeeeee..eeeeee......hhhhhhhhhhhhh......eeee.....hhhhhhh....eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhh...eeeeee....hhhhhhhhhhhheeeeeeeeeeeee..hhhhhhhhhhhheeeeeeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------SAM_MT_TRM5_TYW2  PDB: B:97-335 UniProt: 97-335                                                                                                                                                                                                - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yx1 B   2 PLCLKINKKHGEQTRRILIENNLLNKDYKITSEGNYLYLPIKDVDEDILKSILNIEFELVDKELEEK-------FREII----------GLISLSYDVVGDLVILQISDEVDEKIRKEIGELAYKLIPCKGVFRRK--------VRELEHLAGENRTLTIHKENGYRLWVDIAKVYFSPRLGGERARImKKVSLNDVVVDmFAGVGPFSIACKNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDVKGNRVImNLPKFAHKFIDKALDIVEEGGVIHYYTIGKDFDKAIKLFEKKCDCEVLEKRIVKSYAPREYILALDFKINKK 336
                                    11        21        31        41        51        61      |  -    |   |-        91       101       111       121       131     |   -    |  151       161       171       181       191       201|      211       221       231       241       251       261  |    271       281       291       301       311       321       331     
                                                                                             68      76  80         91                                           137      146                                         190-MSE     202-MSE                                                       264-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 2YX1)

(no "CATH Domain" information available for 2YX1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Met_10 (2)

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth (2)

1a	Met_10-2yx1B01	B:95-289
1b	Met_10-2yx1B02	B:95-289

Asymmetric Unit(hide GO term definitions)

Chain A,B (TRM5B_METJA | Q58293)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0052906	tRNA (guanine(37)-N(1))-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + guanine(37) in tRNA = N(1)-methylguanine(37) in tRNA + S-adenosyl-L-homocysteine.
	GO:0009019	tRNA (guanine-N1-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine.
	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: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
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	2yx1
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	TRM5B_METJA \| Q58293
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	TRM5B_METJA \| Q58293	:	2zzm 2zzn 3ay0

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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