3KNU - JenaLib

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Title :   CRYSTAL STRUCTURE OF TRNA (GUANINE-N1)-METHYLTRANSFERASE FROM ANAPLASMA PHAGOCYTOPHILUM

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   12 Nov 09 (Deposition) - 24 Nov 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Niaid, Ssgcid, Seattle Structural Genomics Center For Infectious Disease, Trna Methyl Transferase, Protein Knot, Trefoil Knot, Rna- Binding Protein, Methyltransferase, S-Adenosyl-L-Methionine, Transferase, Trna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. E. Edwards, J. Abendroth, G. Stahl, B. Sankaran, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Trna (Guanine-N1)-Methyltransferase From Anaplasma Phagocytophilum
To Be Published
PubMed: search

Molecule 1 - TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE
	Chains	:	A, B, C, D
	EC Number	:	2.1.1.31
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	AVA0421
	Gene	:	TRMD, APH_1267
	Organism Scientific	:	ANAPLASMA PHAGOCYTOPHILUM
	Organism Taxid	:	212042
	Strain	:	HZ
	Synonym	:	M1G-METHYLTRANSFERASE, TRNA [GM37] METHYLTRANSFERASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3KNU)

(no "Site" information available for 3KNU)

(no "SS Bond" information available for 3KNU)

Asymmetric Unit

No.	Residues
1	Phe A:13	-	Pro A:14
2	Arg A:181	-	Pro A:182
3	Phe B:13	-	Pro B:14
4	Arg B:181	-	Pro B:182
5	Phe C:13	-	Pro C:14
6	Arg C:181	-	Pro C:182
7	Phe D:13	-	Pro D:14
8	Arg D:181	-	Pro D:182

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

(no "PROSITE Motif" information available for 3KNU)

(no "Exon" information available for 3KNU)

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:192
 aligned with TRMD_ANAPZ | Q2GIL5 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:212
                             1                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209  
           TRMD_ANAPZ     - -MIFNVLTIFPQMFPGPLGVSNLGSALKKGLWTLNVFDIRAFANNKHNTVDDTPYGGGPGMLLRADVLGRCIDEVLSLHPNTKLMFTSPRGVSFTQDIARQTMNFDNITLLCGRFEGIDERVVDFYKLQEVSIGDYVLSGGELAAMVIIDTCVRMVPGVIGNAESLKQESMEGSLEYPQYTRPASWKGMEVPEVLLTGNHGEIEKWRRNASL 211
               SCOP domains d3knua_ A: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh-----..ee.........eehhhhhhhhhhhhhhhh...eeeee....ee.hhhhhhhhhh..eeeeee......hhhhhhhhh.eeee........hhhhhhhhhhhhhh......---------------.........ee..ee.hhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knu A   0 SMIFNVLTIFPQMFPGPLGVSNLGSALKKGLWTLNVFDIRAFA-----TVDDTPYGGGPGMLLRADVLGRCIDEVLSLHPNTKLMFTSPRGVSFTQDIARQTMNFDNITLLCGRFEGIDERVVDFYKLQEVSIGDYVLSGGELAAMVIIDTCVRMVPGVI---------------EYPQYTRPASWKGMEVPEVLLTGNHGEIEKWRRNASL 211
                                     9        19        29        39  |     49        59        69        79        89        99       109       119       129       139       149       159         -     | 179       189       199       209  
                                                                     42    48                                                                                                            159             175

Chain B from PDB  Type:PROTEIN  Length:197
 aligned with TRMD_ANAPZ | Q2GIL5 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:212
                             1                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209  
           TRMD_ANAPZ     - -MIFNVLTIFPQMFPGPLGVSNLGSALKKGLWTLNVFDIRAFANNKHNTVDDTPYGGGPGMLLRADVLGRCIDEVLSLHPNTKLMFTSPRGVSFTQDIARQTMNFDNITLLCGRFEGIDERVVDFYKLQEVSIGDYVLSGGELAAMVIIDTCVRMVPGVIGNAESLKQESMEGSLEYPQYTRPASWKGMEVPEVLLTGNHGEIEKWRRNASL 211
               SCOP domains d3knub_ B: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh.hhhhh.ee.........eehhhhhhhhhhhhhhhh...eeeee....ee.hhhhhhhhh...eeeee.......hhhhhhhhh.eeee........hhhhhhhhhhhhhh......---------------.........ee..ee.hhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knu B   0 SMIFNVLTIFPQMFPGPLGVSNLGSALKKGLWTLNVFDIRAFANNKHNTVDDTPYGGGPGMLLRADVLGRCIDEVLSLHPNTKLMFTSPRGVSFTQDIARQTMNFDNITLLCGRFEGIDERVVDFYKLQEVSIGDYVLSGGELAAMVIIDTCVRMVPGVI---------------EYPQYTRPASWKGMEVPEVLLTGNHGEIEKWRRNASL 211
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159         -     | 179       189       199       209  
                                                                                                                                                                                         159             175

Chain C from PDB  Type:PROTEIN  Length:199
 aligned with TRMD_ANAPZ | Q2GIL5 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:211
                             1                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 
           TRMD_ANAPZ     - -MIFNVLTIFPQMFPGPLGVSNLGSALKKGLWTLNVFDIRAFANNKHNTVDDTPYGGGPGMLLRADVLGRCIDEVLSLHPNTKLMFTSPRGVSFTQDIARQTMNFDNITLLCGRFEGIDERVVDFYKLQEVSIGDYVLSGGELAAMVIIDTCVRMVPGVIGNAESLKQESMEGSLEYPQYTRPASWKGMEVPEVLLTGNHGEIEKWRRNAS 210
               SCOP domains d3knuc_ C: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh.hhhhh.ee.........eehhhhhhhhhhhhhhhh...eeeee....ee.hhhhhhhhh...eeeeee......hhhhhhhhh.eeee........hhhhhhhhhhhhhh........------------..........ee..ee.hhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knu C   0 SMIFNVLTIFPQMFPGPLGVSNLGSALKKGLWTLNVFDIRAFANNKHNTVDDTPYGGGPGMLLRADVLGRCIDEVLSLHPNTKLMFTSPRGVSFTQDIARQTMNFDNITLLCGRFEGIDERVVDFYKLQEVSIGDYVLSGGELAAMVIIDTCVRMVPGVIGN------------LEYPQYTRPASWKGMEVPEVLLTGNHGEIEKWRRNAS 210
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 |       -    |  179       189       199       209 
                                                                                                                                                                                           161          174

Chain D from PDB  Type:PROTEIN  Length:197
 aligned with TRMD_ANAPZ | Q2GIL5 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           TRMD_ANAPZ     1 MIFNVLTIFPQMFPGPLGVSNLGSALKKGLWTLNVFDIRAFANNKHNTVDDTPYGGGPGMLLRADVLGRCIDEVLSLHPNTKLMFTSPRGVSFTQDIARQTMNFDNITLLCGRFEGIDERVVDFYKLQEVSIGDYVLSGGELAAMVIIDTCVRMVPGVIGNAESLKQESMEGSLEYPQYTRPASWKGMEVPEVLLTGNHGEIEKWRRNASLS 212
               SCOP domains d3knud_ D: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------tRNA_m1G_MT-3knuD01 D:2 2-212                                                                                                                                                                   Pfam domains (1)
           Pfam domains (2) ---------------------tRNA_m1G_MT-3knuD02 D:2 2-212                                                                                                                                                                   Pfam domains (2)
           Pfam domains (3) ---------------------tRNA_m1G_MT-3knuD03 D:2 2-212                                                                                                                                                                   Pfam domains (3)
           Pfam domains (4) ---------------------tRNA_m1G_MT-3knuD04 D:2 2-212                                                                                                                                                                   Pfam domains (4)
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhh..-....ee.........eehhhhhhhhhhhhhhhh...eeeee....ee.hhhhhhhhhh..eeeeee......hhhhhhhhh.eeee........hhhhhhhhhhhhhh......--------------..........ee..ee.hhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knu D   1 MIFNVLTIFPQMFPGPLGVSNLGSALKKGLWTLNVFDIRAFANN-HNTVDDTPYGGGPGMLLRADVLGRCIDEVLSLHPNTKLMFTSPRGVSFTQDIARQTMNFDNITLLCGRFEGIDERVVDFYKLQEVSIGDYVLSGGELAAMVIIDTCVRMVPGVI--------------LEYPQYTRPASWKGMEVPEVLLTGNHGEIEKWRRNASLS 212
                                    10        20        30        40   | |  50        60        70        80        90       100       110       120       130       140       150        |-         -   |   180       190       200       210  
                                                                      44 |                                                                                                              159            174                                      
                                                                        46

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: alpha/beta knot (57)

Superfamily: alpha/beta knot (57)

Family: automated matches (17)

Protein domain: automated matches (17)

Anaplasma phagocytophilum [TaxId: 212042] (2)

1a	d3knua_	A:
1b	d3knub_	B:
1c	d3knuc_	C:
1d	d3knud_	D:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SPOUT (28)

Family: tRNA_m1G_MT (9)

Anaplasma phagocytophilum (strain HZ) (1)

1a	tRNA_m1G_MT-3knuD01	D:22-212
1b	tRNA_m1G_MT-3knuD02	D:22-212
1c	tRNA_m1G_MT-3knuD03	D:22-212
1d	tRNA_m1G_MT-3knuD04	D:22-212

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TRMD_ANAPZ | Q2GIL5)

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:0006400	tRNA modification	The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
	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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3knu)

	Sites
(no "Sites" information available for 3knu)

	Cis Peptide Bonds
		Arg A:181 - Pro A:182	[ RasMol ]
		Arg B:181 - Pro B:182	[ RasMol ]
		Arg C:181 - Pro C:182	[ RasMol ]
		Arg D:181 - Pro D:182	[ RasMol ]
		Phe A:13 - Pro A:14	[ RasMol ]
		Phe B:13 - Pro B:14	[ RasMol ]
		Phe C:13 - Pro C:14	[ RasMol ]
		Phe D:13 - Pro D:14	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2.1.1.31
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	TRMD_ANAPZ \| Q2GIL5	:	4ig6

3e5y	TRNA METHYL TRANSFERASE FROM BURKHOLDERIA PSEUDOMALLEI
3ief	TRNA METHYL TRANSFERASE FROM BARTONELLA HENSELAE RELATED ID: ANPHA.00316.A RELATED DB: TARGETDB

Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 4)

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Pfam Domains (1, 4)

Gene Ontology (9, 9)

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