1V6Z - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TT1573 FROM THERMUS THERMOPHILUS

Authors :   K. Murayama, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   05 Dec 03 (Deposition) - 14 Dec 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Murayama, M. Shirouzu, S. Yokoyama
Crystal Structure Of Tt1573 From Thermus Thermophilus
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL PROTEIN TTHA0657
	Chains	:	A, B
	Organism Scientific	:	THERMUS THERMOPHILUS HB8
	Organism Taxid	:	300852
	Strain	:	HB8 / ATCC 27634 / DSM 579
	Synonym	:	METHYLTRANSFERASE TT1573

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1V6Z)

(no "SS Bond" information available for 1V6Z)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:52	-	Pro A:53
2	Pro A:53	-	Pro A:54
3	Gly B:52	-	Pro B:53
4	Pro B:53	-	Pro B:54

(no "SAP(SNP)/Variant" information available for 1V6Z)

(no "PROSITE Motif" information available for 1V6Z)

(no "Exon" information available for 1V6Z)

Asymmetric/Biological 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:227
 aligned with Q5SKI6_THET8 | Q5SKI6 from UniProtKB/TrEMBL  Length:228

    Alignment length:227
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       
         Q5SKI6_THET8     2 RPHRAFSPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGEREALAEVVDLGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEMGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
               SCOP domains --d1v6za1 A:4-66 Hypothetical protein TTHA0657 (TT1575)          d1v6za2 A:67-228 Hypothetical protein TTHA0657 (TT1575)                                                                                                            SCOP domains
               CATH domains 1v6zA01 A:2-66 Hypothetical PUA domain-like; domain 1            1v6zA02 A:67-228  [code=3.40.1280.10, no name defined]                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhh...hhhhhhhhhh........eeeee....eeeeeeee.....eeeeeeee.........eeeeee....hhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhh......ee...ee.hhh.....eeee......hhhhhh.....eeeee......hhhhhhhhhhhheeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v6z A   2 RPHRAFSPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGEREALAEVVDLGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEmGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
                                    11        21        31        41        51        61        71        81        91       101       111 |     121       131       141       151       161       171       181       191       201       211       221       
                                                                                                                                         113-MSE

Chain A from PDB  Type:PROTEIN  Length:227
 aligned with Q72K73_THET2 | Q72K73 from UniProtKB/TrEMBL  Length:228

    Alignment length:227
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       
         Q72K73_THET2     2 RPHRAFSPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGEREALAEVVDLGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEMGEGKLRRLRAVALEAAKQSGRVRVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
               SCOP domains --d1v6za1 A:4-66 Hypothetical protein TTHA0657 (TT1575)          d1v6za2 A:67-228 Hypothetical protein TTHA0657 (TT1575)                                                                                                            SCOP domains
               CATH domains 1v6zA01 A:2-66 Hypothetical PUA domain-like; domain 1            1v6zA02 A:67-228  [code=3.40.1280.10, no name defined]                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhh...hhhhhhhhhh........eeeee....eeeeeeee.....eeeeeeee.........eeeeee....hhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhh......ee...ee.hhh.....eeee......hhhhhh.....eeeee......hhhhhhhhhhhheeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v6z A   2 RPHRAFSPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGEREALAEVVDLGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEmGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
                                    11        21        31        41        51        61        71        81        91       101       111 |     121       131       141       151       161       171       181       191       201       211       221       
                                                                                                                                         113-MSE

Chain B from PDB  Type:PROTEIN  Length:225
 aligned with Q5SKI6_THET8 | Q5SKI6 from UniProtKB/TrEMBL  Length:228

    Alignment length:225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
         Q5SKI6_THET8     4 HRAFSPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGEREALAEVVDLGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEMGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
               SCOP domains d1v6zb1 B:4-66 Hypothetical protein TTHA0657 (TT1575)          d1v6zb2 B:67-228 Hypothetical protein TTHA0657 (TT1575)                                                                                                            SCOP domains
               CATH domains 1v6zB01 B:4-67 Hypothetical PUA domain-like; domain 1           1v6zB02 B:68-228  [code=3.40.1280.10, no name defined]                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........hhhhhhhhhh........eeeee....eeeeeeee.....eeeeeee..........eeeeee....hhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhh......ee...ee.hhh.....eeee......hhhhhh.....eeeee......hhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v6z B   4 HRAFSPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGEREALAEVVDLGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEmGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
                                                                                                                                       113-MSE

Chain B from PDB  Type:PROTEIN  Length:225
 aligned with Q72K73_THET2 | Q72K73 from UniProtKB/TrEMBL  Length:228

    Alignment length:225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
         Q72K73_THET2     4 HRAFSPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGEREALAEVVDLGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEMGEGKLRRLRAVALEAAKQSGRVRVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
               SCOP domains d1v6zb1 B:4-66 Hypothetical protein TTHA0657 (TT1575)          d1v6zb2 B:67-228 Hypothetical protein TTHA0657 (TT1575)                                                                                                            SCOP domains
               CATH domains 1v6zB01 B:4-67 Hypothetical PUA domain-like; domain 1           1v6zB02 B:68-228  [code=3.40.1280.10, no name defined]                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........hhhhhhhhhh........eeeee....eeeeeeee.....eeeeeee..........eeeeee....hhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhh......ee...ee.hhh.....eeee......hhhhhh.....eeeee......hhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v6z B   4 HRAFSPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGEREALAEVVDLGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEmGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR 228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
                                                                                                                                       113-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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PUA domain-like (96)

Superfamily: PUA domain-like (96)

Family: YggJ N-terminal domain-like (6)

Protein domain: Hypothetical protein TTHA0657 (TT1575) (3)

Thermus thermophilus [TaxId: 274] (3)

1a	d1v6za1	A:4-66
1b	d1v6zb1	B:4-66

Class: Alpha and beta proteins (a/b) (23833)

Fold: alpha/beta knot (57)

Superfamily: alpha/beta knot (57)

Family: YggJ C-terminal domain-like (7)

Protein domain: Hypothetical protein TTHA0657 (TT1575) (3)

Thermus thermophilus [TaxId: 274] (3)

2a	d1v6za2	A:67-228
2b	d1v6zb2	B:67-228

(no "Pfam Domain" information available for 1V6Z)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q5SKI6_THET8 | Q5SKI6)

molecular function
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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: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.

Chain A,B (Q72K73_THET2 | Q72K73)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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: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.

Asymmetric/Biological Unit
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	Sites
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	Cis Peptide Bonds
		Gly A:52 - Pro A:53	[ RasMol ]
		Gly B:52 - Pro B:53	[ RasMol ]
		Pro A:53 - Pro A:54	[ RasMol ]
		Pro B:53 - Pro B:54	[ RasMol ]

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	Q5SKI6_THET8 \| Q5SKI6	:	2cx8 2z0y

(no "Related Entries Specified in the PDB File" available for 1V6Z)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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