1Z85 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A PREDICTED RNA METHYLTRANSFERASE (TM1380) FROM THERMOTOGA MARITIMA MSB8 AT 2.12 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   29 Mar 05 (Deposition) - 12 Apr 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.12

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

Keywords :   Alpha/Beta Knot Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Tm1380) From Thermotoga Maritima At 2. 12 A Resolution
To Be Published
PubMed: search

Molecule 1 - HYPOTHETICAL PROTEIN TM1380
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TM1380
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	243274
	Strain	:	MSB8

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	CL	6	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	1	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:19 , LEU B:116	BINDING SITE FOR RESIDUE CL B 223
2	AC2	SOFTWARE	PRO B:176 , GLU B:177 , HOH B:229	BINDING SITE FOR RESIDUE CL B 224
3	AC3	SOFTWARE	GLY A:82 , PRO A:176 , GLU A:177 , HOH A:237	BINDING SITE FOR RESIDUE CL A 223
4	AC4	SOFTWARE	HOH A:263 , HOH A:267 , TRP B:84 , GLU B:85 , HOH B:266	BINDING SITE FOR RESIDUE CL B 225
5	AC5	SOFTWARE	ARG A:124 , HOH A:276	BINDING SITE FOR RESIDUE CL A 224
6	AC6	SOFTWARE	HOH A:243 , SER B:115 , LYS B:118	BINDING SITE FOR RESIDUE CL B 226
7	AC7	SOFTWARE	TYR A:6 , THR A:8 , ILE A:15 , PHE A:16 , ASP A:17 , GLU A:20 , HOH A:345	BINDING SITE FOR RESIDUE EDO A 225

(no "SS Bond" information available for 1Z85)

(no "Cis Peptide Bond" information available for 1Z85)

(no "SAP(SNP)/Variant" information available for 1Z85)

(no "PROSITE Motif" information available for 1Z85)

(no "Exon" information available for 1Z85)

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
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Chain A from PDB  Type:PROTEIN  Length:212
 aligned with Q9X1A0_THEMA | Q9X1A0 from UniProtKB/TrEMBL  Length:222

    Alignment length:221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 
         Q9X1A0_THEMA     2 PHLFYGTAQNGEVIFDEREAHHMRVVRLKEGDVIEATDGNGFSYTCILKSLKKKTAAAKIVKVEEKEKEPTEKLSVVVPIGRWERTRFLIEKCVELGVDEIFFHKFERSQHEISLDKAKIVVREAAKQCKRYLFPKVSFLEKLEFSGNVITLDLDASQNLLDANLEGSITVVVGPEGGFSEKERELLRSSTTIVSLGKKILRFETAAILTVGYIALKKQKI 222
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.eee..eeeehhhhhhhhhhh......eeeee....eeeeeeeeee....eeeeeeeeee........eeeeee..hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhh.....eeee........eeeee..---...........eeeee......hhhhhhhhhhhhee.------.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z85 A   2 PHLFYGTAQNGEVIFDEREAHHmRVVRLKEGDVIEATDGNGFSYTCILKSLKKKTAAAKIVKVEEKEKEPTEKLSVVVPIGRWERTRFLIEKCVELGVDEIFFHKFERSQHEISLDKAKIVVREAAKQCKRYLFPKVSFLEKLEFSGNVITLDL---QNLLDANLEGSITVVVGPEGGFSEKERELLRSSTTIV------LRFETAAILTVGYIALKKQKI 222
                                    11        21  |     31        41        51        61        71        81        91       101       111       121       131       141       151   |   161       171       181       191   |     -|      211       221 
                                                 24-MSE                                                                                                                            155 159                                 195    202

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with Q9X1A0_THEMA | Q9X1A0 from UniProtKB/TrEMBL  Length:222

    Alignment length:221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 
         Q9X1A0_THEMA     2 PHLFYGTAQNGEVIFDEREAHHMRVVRLKEGDVIEATDGNGFSYTCILKSLKKKTAAAKIVKVEEKEKEPTEKLSVVVPIGRWERTRFLIEKCVELGVDEIFFHKFERSQHEISLDKAKIVVREAAKQCKRYLFPKVSFLEKLEFSGNVITLDLDASQNLLDANLEGSITVVVGPEGGFSEKERELLRSSTTIVSLGKKILRFETAAILTVGYIALKKQKI 222
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------Methyltrans_RNA-1z85B01 B:14-217                                                                                                                                                                            ----- Pfam domains (1)
           Pfam domains (2) ------------Methyltrans_RNA-1z85B02 B:14-217                                                                                                                                                                            ----- Pfam domains (2)
         Sec.struct. author ..eee.eee..eeeehhhhhhhhhhh......eeeee....eeeeeeeeee....eeeeeeeeee........eeeeee..hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhh.....eeee........eeeee................eeeee......hhhhhhhhhh..eee-----..hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z85 B   2 PHLFYGTAQNGEVIFDEREAHHmRVVRLKEGDVIEATDGNGFSYTCILKSLKKKTAAAKIVKVEEKEKEPTEKLSVVVPIGRWERTRFLIEKCVELGVDEIFFHKFERSQHEISLDKAKIVVREAAKQCKRYLFPKVSFLEKLEFSGNVITLDLDASQNLLDANLEGSITVVVGPEGGFSEKERELLRSSTTIV-----ILRFETAAILTVGYIALKKQKI 222
                                    11        21  |     31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   |   201       211       221 
                                                 24-MSE                                                                                                                                                                    195   201

Legend:		→ Mismatch	(orange background)
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	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 1Z85)

(no "CATH Domain" information available for 1Z85)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SPOUT (28)

Family: Methyltrans_RNA (6)

Thermotoga maritima (1)

1a	Methyltrans_RNA-1z85B01	B:14-217
1b	Methyltrans_RNA-1z85B02	B:14-217

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9X1A0_THEMA | Q9X1A0)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0070042	rRNA (uridine-N3-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N3-methyluridine.
	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:0070475	rRNA base methylation	The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA 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.
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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Biological Units
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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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