2B25 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   HUMAN PUTATIVE TRNA(1-METHYLADENOSINE)METHYLTRANSFERASE

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

Date :   16 Sep 05 (Deposition) - 27 Sep 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

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

Reference :   H. Wu, W. Tempel, A. Dong, H. Zeng, P. Loppnau, C. Arrowsmith, A. Edwards, J. Weigelt, M. Sundstrom, A. Bochkarev, A. N. Plotnikov
Human Putative Trna(1-Methyladenosine)Methyltransferase
To Be Published
PubMed: search

Molecule 1 - HYPOTHETICAL PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A-LIC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE
2	UNX	4	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE
2	UNX	2	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE
2	UNX	2	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 3 (2, 12)

No.	Name	Count	Type	Full Name
1	SAM	4	Ligand/Ion	S-ADENOSYLMETHIONINE
2	UNX	8	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:84 , THR A:87 , GLY A:111 , SER A:112 , GLY A:113 , SER A:114 , GLY A:115 , GLY A:116 , MET A:117 , GLU A:135 , VAL A:136 , ARG A:137 , HIS A:140 , ASP A:173 , ILE A:174 , ASP A:192 , MET A:193 , UNX A:701	BINDING SITE FOR RESIDUE SAM A 601
2	AC2	SOFTWARE	THR B:84 , THR B:87 , GLY B:111 , GLY B:113 , SER B:114 , GLY B:116 , MET B:117 , GLU B:135 , VAL B:136 , ARG B:137 , HIS B:140 , ASP B:173 , ILE B:174 , ASP B:192 , MET B:193 , UNX B:703	BINDING SITE FOR RESIDUE SAM B 602
3	AC3	SOFTWARE	MET A:193 , LEU A:194 , SAM A:601	BINDING SITE FOR RESIDUE UNX A 701
4	AC4	SOFTWARE	LEU B:194 , SAM B:602	BINDING SITE FOR RESIDUE UNX B 703
5	AC5	SOFTWARE	VAL B:218 , GLN B:222	BINDING SITE FOR RESIDUE UNX B 704

(no "SS Bond" information available for 2B25)

(no "Cis Peptide Bond" information available for 2B25)

(no "SAP(SNP)/Variant" information available for 2B25)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_TRM61	PS51620	tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile.	TR61B_HUMAN	154-472	2	A:11-329 B:11-329

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_TRM61	PS51620	tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile.	TR61B_HUMAN	154-472	1	A:11-329 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_TRM61	PS51620	tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile.	TR61B_HUMAN	154-472	1	- B:11-329

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_TRM61	PS51620	tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile.	TR61B_HUMAN	154-472	4	A:11-329 B:11-329

Asymmetric Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000306108	1a	ENSE00001751691	chr2:29093167-29092445	723	TR61B_HUMAN	1-233	233	2	A:6-90 (gaps) B:6-90 (gaps)	85 85
1.2	ENST00000306108	2	ENSE00001155047	chr2:29087985-29087883	103	TR61B_HUMAN	234-268	35	2	A:91-125 B:91-125	35 35
1.4b	ENST00000306108	4b	ENSE00001155042	chr2:29084174-29083984	191	TR61B_HUMAN	268-331	64	2	A:125-188 (gaps) B:125-188 (gaps)	64 64
1.5	ENST00000306108	5	ENSE00001155035	chr2:29075365-29075274	92	TR61B_HUMAN	332-362	31	2	A:189-219 B:189-219	31 31
1.6c	ENST00000306108	6c	ENSE00001155029	chr2:29074164-29073938	227	TR61B_HUMAN	362-438	77	2	A:219-254 B:219-254	36 36
1.7	ENST00000306108	7	ENSE00001757828	chr2:29073271-29073194	78	TR61B_HUMAN	438-464	27	2	A:309-321 B:309-321	13 13
1.8b	ENST00000306108	8b	ENSE00001660532	chr2:29073108-29072687	422	TR61B_HUMAN	464-477	14	2	A:321-329 B:321-329	9 9

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:254
 aligned with TR61B_HUMAN | Q9BVS5 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:324
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468    
          TR61B_HUMAN   149 RPFQAGELILAETGEGETKFKKLFRLNNFGLLNSNWGAVPFGKIVGKFPGQILRSSFGKQYMLRRPALEDYVVLMKRGTAITFPKDINMILSMMDINPGDTVLEAGSGSGGMSLFLSKAVGSQGRVISFEVRKDHHDLAKKNYKHWRDSWKLSHVEEWPDNVDFIHKDISGATEDIKSLTFDAVALDMLNPHVTLPVFYPHLKHGGVCAVYVVNITQVIELLDGIRTCELALSCEKISEVIVRDWLVCLAKQKNGILAQKVESKINTDVQLDSQEKIGVKGELFQEDDHEESHSDFPYGSFPYVARPVHWQPGHTAFLVKLRKV 472
               SCOP domains d2b25a1 A:6-3    29 Hypothetical      protein FLJ20628                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee.----...eeeee........-----.hhhhhh.....eeee.....eeeee..hhhhhhhhh.......hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhh..........eeeee......-------.eeeeee.......hhhhhh..eeeeeeeeeee.hhhhhhhhhhhhhhhh..eeeeeee......eee..------------------------------------------------------.eee.........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----SAM_TRM61  PDB: A:11-329 UniProt: 154-472                                                                                                                                                                                                                                                                                       PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:6-90 (gaps) UniProt: 1-233 [INCOMPLETE]                            Exon 1.2  PDB: A:91-125            ---------------------------------------------------------------Exon 1.5  PDB: A:189-219       ---------------------------------------------------------------------------Exon 1.7  PDB: A:309-321   -------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------Exon 1.4b  PDB: A:125-188 (gaps) UniProt: 268-331               ------------------------------Exon 1.6c  PDB: A:219-254 UniProt: 362-438 [INCOMPLETE]                      -------------------------Exon 1.8b Transcript 1 (2)
                 2b25 A   6 RPFQAGELILAET----TKFKKLFRLNNFGLLN-----VPFGKIVGKFPGQILRSSFGKQYMLRRPALEDYVVLMKRGTAITFPKDINMILSMMDINPGDTVLEAGSGSGGMSLFLSKAVGSQGRVISFEVRKDHHDLAKKNYKHWRDSWKLSHVEEWPDNVDFIHKDISGA-------TFDAVALDMLNPHVTLPVFYPHLKHGGVCAVYVVNITQVIELLDGIRTCELALSCEKISEVIVRDWLVCL------------------------------------------------------VARPVHWQPGHTAFLVKLRKV 329
                                    15  |    |25        35  |     45        55        65        75        85        95       105       115       125       135       145       155       165       175 |     185       195       205       215       225       235       245        |-         -         -         -         -         -   |   315       325    
                                       18   23             38    44                                                                                                                                  177     185                                                                  254                                                    309

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with TR61B_HUMAN | Q9BVS5 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:324
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468    
          TR61B_HUMAN   149 RPFQAGELILAETGEGETKFKKLFRLNNFGLLNSNWGAVPFGKIVGKFPGQILRSSFGKQYMLRRPALEDYVVLMKRGTAITFPKDINMILSMMDINPGDTVLEAGSGSGGMSLFLSKAVGSQGRVISFEVRKDHHDLAKKNYKHWRDSWKLSHVEEWPDNVDFIHKDISGATEDIKSLTFDAVALDMLNPHVTLPVFYPHLKHGGVCAVYVVNITQVIELLDGIRTCELALSCEKISEVIVRDWLVCLAKQKNGILAQKVESKINTDVQLDSQEKIGVKGELFQEDDHEESHSDFPYGSFPYVARPVHWQPGHTAFLVKLRKV 472
               SCOP domains d2b25b_ B: au     tomated m               atches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee.-----..eeeee..---------------........eee..----.eeee..hhhhhhh.........hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhh........eeeee......-------.eeeeee...hhhhhhhhhh..eeeeeeeeeee.hhhhhhhhhhhhhhh...eeeeeee......eee..------------------------------------------------------.eee.........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----SAM_TRM61  PDB: B:11-329 UniProt: 154-472                                                                                                                                                                                                                                                                                       PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:6-90 (gaps) UniProt: 1-233 [INCOMPLETE]                            Exon 1.2  PDB: B:91-125            ---------------------------------------------------------------Exon 1.5  PDB: B:189-219       ---------------------------------------------------------------------------Exon 1.7  PDB: B:309-321   -------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------Exon 1.4b  PDB: B:125-188 (gaps) UniProt: 268-331               ------------------------------Exon 1.6c  PDB: B:219-254 UniProt: 362-438 [INCOMPLETE]                      -------------------------Exon 1.8b Transcript 1 (2)
                 2b25 B   6 RPFQAGELILAET-----KFKKLFRLN---------------KIVGKFPGQILRS----QYMLRRPALEDYVVLMKRGTAITFPKDINMILSMMDINPGDTVLEAGSGSGGMSLFLSKAVGSQGRVISFEVRKDHHDLAKKNYKHWRDSWKLSHVEEWPDNVDFIHKDISGA-------TFDAVALDMLNPHVTLPVFYPHLKHGGVCAVYVVNITQVIELLDGIRTCELALSCEKISEVIVRDWLVCL------------------------------------------------------VARPVHWQPGHTAFLVKLRKV 329
                                    15  |     25      |  -         -  |     55    |   65        75        85        95       105       115       125       135       145       155       165       175 |     185       195       205       215       225       235       245        |-         -         -         -         -         -   |   315       325    
                                       18    24      32              48          60   65                                                                                                             177     185                                                                  254                                                    309

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 2B25)

(no "Pfam Domain" information available for 2B25)

Asymmetric Unit(hide GO term definitions)

Chain A,B (TR61B_HUMAN | Q9BVS5)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0016429	tRNA (adenine-N1-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methyladenine.
	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:0070901	mitochondrial tRNA methylation	The posttranscriptional addition of methyl groups to specific residues in a mitochondrial tRNA molecule.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	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: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: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:0031515	tRNA (m1A) methyltransferase complex	A protein complex involved in the catalysis of the formation of the modified nucleotide 1-methyladenosine (m1A) in tRNA. In yeast, it is a heterotetramer of two subunits, Gcd10p and Gcd14p, while in bacteria and archaea it is a homotetramer.

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Description

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