2ZZN - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE COMPLEX STRUCTURE OF ATRM5 AND TRNACYS

Authors :   S. Goto-Ito, T. Ito, S. Yokoyama

Date :   19 Feb 09 (Deposition) - 15 Sep 09 (Release) - 03 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

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

Keywords :   Protein-Rna Complex, Transferase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Goto-Ito, T. Ito, M. Kuratani, Y. Bessho, S. Yokoyama
Tertiary Structure Checkpoint At Anticodon Loop Modification In Trna Functional Maturation.
Nat. Struct. Mol. Biol. V. 16 1109 2009
PubMed-ID: 19749755 | Reference-DOI: 10.1038/NSMB.1653
(for further references see the PDB file header)

Molecule 1 - UNCHARACTERIZED PROTEIN MJ0883
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET26B
	Expression System Strain	:	ROSETTA2(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	METHANOCOCCUS JANNASCHII
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190

Molecule 2 - RNA (71-MER)
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	SYNTHESIZED IN VITRO WITH THE RECOMBINANT RNA POLYMERASE OF T7 PHAGE
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	MG	7	Ligand/Ion	MAGNESIUM ION
2	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:143 , PHE A:144 , TYR A:177 , PHE A:178 , ARG A:186 , MET A:202 , PHE A:203 , GLY A:205 , PRO A:208 , PHE A:209 , ASP A:223 , ILE A:224 , ASN A:225 , SER A:250 , ASP A:251 , VAL A:252 , ASN A:265 , PHE A:273 , G C:37 , U D:46	BINDING SITE FOR RESIDUE SAM A 401
2	AC2	SOFTWARE	GLU B:143 , PHE B:144 , TYR B:177 , PHE B:178 , SER B:179 , ARG B:186 , PHE B:203 , PRO B:208 , PHE B:209 , ASP B:223 , ILE B:224 , ASN B:225 , ASP B:251 , VAL B:252 , ASN B:265 , PHE B:273 , G D:37	BINDING SITE FOR RESIDUE SAM B 402
3	AC3	SOFTWARE	G C:23 , G C:24	BINDING SITE FOR RESIDUE MG C 102
4	AC4	SOFTWARE	G C:29	BINDING SITE FOR RESIDUE MG C 103
5	AC5	SOFTWARE	U C:50	BINDING SITE FOR RESIDUE MG C 104
6	AC6	SOFTWARE	U C:8 , A C:14	BINDING SITE FOR RESIDUE MG C 105
7	AC7	SOFTWARE	G C:7 , G C:49	BINDING SITE FOR RESIDUE MG C 106
8	AC8	SOFTWARE	A D:26 , G D:27 , HOH D:801	BINDING SITE FOR RESIDUE MG D 201

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

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

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

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

(no "Exon" information available for 2ZZN)

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

    Alignment length:336
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330      
          TRM5B_METJA     1 MPLCLKINKKHGEQTRRILIENNLLNKDYKITSEGNYLYLPIKDVDEDILKSILNIEFELVDKELEEKKIIKKPSFREIISKKYRKEIDEGLISLSYDVVGDLVILQISDEVDEKIRKEIGELAYKLIPCKGVFRRKSEVKGEFRVRELEHLAGENRTLTIHKENGYRLWVDIAKVYFSPRLGGERARIMKKVSLNDVVVDMFAGVGPFSIACKNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDVKGNRVIMNLPKFAHKFIDKALDIVEEGGVIHYYTIGKDFDKAIKLFEKKCDCEVLEKRIVKSYAPREYILALDFKINKK 336
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhh.........eee..eeee.....hhhhhhhhh.....eee............hhhhhhhhhhhhhhh...eeeeeeee..eeeeee....hhhhhhhhhhhhhhhh...eeee...............eeee....eeeeee..eeeeee......hhhhhhhhhhhhhhh.....eee.....hhhhhhh.....eeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhh...eeeeee....hhhhhhhhhhhheeeeeeeeeeeee..hhhhhhhhhh...eeeeeeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------SAM_MT_TRM5_TYW2  PDB: A:97-335 UniProt: 97-335                                                                                                                                                                                                - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zzn A   1 MPLCLKINKKHGEQTRRILIENNLLNKDYKITSEGNYLYLPIKDVDEDILKSILNIEFELVDKELEEKKIIKKPSFREIISKKYRKEIDEGLISLSYDVVGDLVILQISDEVDEKIRKEIGELAYKLIPCKGVFRRKSEVKGEFRVRELEHLAGENRTLTIHKENGYRLWVDIAKVYFSPRLGGERARIMKKVSLNDVVVDMFAGVGPFSIACKNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDVKGNRVIMNLPKFAHKFIDKALDIVEEGGVIHYYTIGKDFDKAIKLFEKKCDCEVLEKRIVKSYAPREYILALDFKINKK 336
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330

Chain B from PDB  Type:PROTEIN  Length:335
 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....hhhhhhhhh....eeee............hhhhhhhhhhhhhhhh.......eee..eeee......hhhhhhhhhhhhhhhh...eeeee............eeeeee....eeeeee..eeeeee......hhhhhhhhh..........eeee........hhhhh...eeee...hhhhhhhhhhhhhhh.....eee...hhhhh...eeeeee.....hhhhhhhhhhheeeeeeeeeeeee..hhhhhhhhhhh.eeeeeeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------SAM_MT_TRM5_TYW2  PDB: B:97-335 UniProt: 97-335                                                                                                                                                                                                - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zzn B   2 PLCLKINKKHGEQTRRILIENNLLNKDYKITSEGNYLYLPIKDVDEDILKSILNIEFELVDKELEEKKIIKKPSFREIISKKYRKEIDEGLISLSYDVVGDLVILQISDEVDEKIRKEIGELAYKLIPCKGVFRRKSEVKGEFRVRELEHLAGENRTLTIHKENGYRLWVDIAKVYFSPRLGGERARIMKKVSLNDVVVDMFAGVGPFSIACKNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDVKGNRVIMNLPKFAHKFIDKALDIVEEGGVIHYYTIGKDFDKAIKLFEKKCDCEVLEKRIVKSYAPREYILALDFKINKK 336
                                    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

Chain C from PDB  Type:RNA  Length:71
                                                                                                       
                 2zzn C   1 GCCGGGGUAGUCUAGGGGCUAGGCAGCGGACUGCAGAUCCGCCUUACGUGGGUUCAAAUCCCACCCCCGGC  72
                                    10     || 21        31        41        51        61        71 
                                          16|                                                      
                                           18

Chain D from PDB  Type:RNA  Length:71
                                                                                                       
                 2zzn D   1 GCCGGGGUAGUCUAGGGGCUAGGCAGCGGACUGCAGAUCCGCCUUACGUGGGUUCAAAUCCCACCCCCGGC  72
                                    10     || 21        31        41        51        61        71 
                                          16|                                                      
                                           18

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 2ZZN)

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

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

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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2zzn)

Biological Units
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	2zzn
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	TRM5B_METJA \| Q58293	:	2yx1 2zzm 3ay0

(no "Related Entries Specified in the PDB File" available for 2ZZN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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