2D1P - JenaLib

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Title :   CRYSTAL STRUCTURE OF HETEROHEXAMERIC TUSBCD PROTEINS, WHICH ARE CRUCIAL FOR THE TRNA MODIFICATION

Authors :   T. Numata, S. Fukai, Y. Ikeuchi, T. Suzuki, O. Nureki

Date :   30 Aug 05 (Deposition) - 28 Feb 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I
Biol. Unit 1: A,B,C  (2x)
Biol. Unit 2: D,E,F,G,H,I  (1x)

Keywords :   Trna Modification, Sulfur Transfer, Structural Genomics, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Numata, S. Fukai, Y. Ikeuchi, T. Suzuki, O. Nureki
Structural Basis For Sulfur Relay To Rna Mediated By Heterohexameric Tusbcd Complex
Structure V. 14 357 2006
PubMed-ID: 16472754 | Reference-DOI: 10.1016/J.STR.2005.11.009
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL UPF0163 PROTEIN YHEN
	Chains	:	A, D, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE80L
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YHEN
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	TUSD

Molecule 2 - HYPOTHETICAL UPF0116 PROTEIN YHEM
	Chains	:	B, E, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE80L
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YHEM
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	TUSC

Molecule 3 - HYPOTHETICAL PROTEIN YHEL
	Chains	:	C, F, I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE80L
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YHEL
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	TUSB

		1	2	3	4	5	6	7	8	9
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I
Biological Unit 1 (2x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F	G	H	I

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG H:107 , ARG H:108 , HOH H:321	BINDING SITE FOR RESIDUE SO4 H 301

(no "SS Bond" information available for 2D1P)

(no "Cis Peptide Bond" information available for 2D1P)

(no "SAP(SNP)/Variant" information available for 2D1P)

(no "PROSITE Motif" information available for 2D1P)

(no "Exon" information available for 2D1P)

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:130
 aligned with TUSD_ECOLI | P45532 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:130
                              1                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128
           TUSD_ECOLI     - --MRFAIVVTGPAYGTQQASSAFQFAQALIADGHELSSVFFYREGVYNANQLTSPASDEFDLVRAWQQLNAQHGVALNICVAAALRRGVVDETEAGRLGLASSNLQQGFTLSGLGALAEASLTCDRVVQF 128
               SCOP domains --d2d1pa1 A:1-128 tRNA 2-thiouridine synthesizing protein D, TusD                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......hhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhh..........hhhhhhhhhhhhhh.eeeeehhhhhhh...hhhhhhhhh.........eeee.hhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1p A  -1 GSMRFAIVVTGPAYGTQQASSAFQFAQALIADGHELSSVFFYREGVYNANQLTSPASDEFDLVRAWQQLNAQHGVALNICVAAALRRGVVDETEAGRLGLASSNLQQGFTLSGLGALAEASLTCDRVVQF 128
                                     8        18        28        38        48        58        68        78        88        98       108       118       128

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with TUSC_ECOLI | P45531 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
           TUSC_ECOLI     1 MKRIAFVFSTAPHGTAAGREGLDALLATSALTDDLAVFFIADGVFQLLPGQKPDAVLARDYIATFKLLGLYDIEQCWVCAASLRERGLDPQTPFVVEATPLEADALRRELANYDVILRF 119
               SCOP domains d2d1pb1 B:1-119 tRNA 2-thiouridine synthesizing protein C, TusC                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......hhhhhhhhhhhhhhh....eeeee.hhhhhhhh...hhhhhh...hhhhhhhhhhh....eeeehhhhhhh............eeehhhhhhhhhh...eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1p B   1 MKRIAFVFSTAPHGTAAGREGLDALLATSALTDDLAVFFIADGVFQLLPGQKPDAVLARDYIATFKLLGLYDIEQCWVCAASLRERGLDPQTPFVVEATPLEADALRRELANYDVILRF 119
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:95
 aligned with TUSB_ECOLI | P45530 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:95
                                    10        20        30        40        50        60        70        80        90     
           TUSB_ECOLI     1 MLHTLHRSPWLTDFAALLRLLSEGDELLLLQDGVTAAVDGNRYLESLRNAPIKVYALNEDLIARGLTGQISNDIILIDYTDFVRLTVKHPSQMAW  95
               SCOP domains d2d1pc1 C:1-95 tRNA 2-thiouridine synthesizing protein B, TusB                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhh.....eeee.hhhhhhhh....hhhhhhh...eeeeehhhhhhh..........eeehhhhhhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 2d1p C   1 MLHTLHRSPWLTDFAALLRLLSEGDELLLLQDGVTAAVDGNRYLESLRNAPIKVYALNEDLIARGLTGQISNDIILIDYTDFVRLTVKHPSQMAW  95
                                    10        20        30        40        50        60        70        80        90

Chain D from PDB  Type:PROTEIN  Length:130
 aligned with TUSD_ECOLI | P45532 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:130
                              1                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128
           TUSD_ECOLI     - --MRFAIVVTGPAYGTQQASSAFQFAQALIADGHELSSVFFYREGVYNANQLTSPASDEFDLVRAWQQLNAQHGVALNICVAAALRRGVVDETEAGRLGLASSNLQQGFTLSGLGALAEASLTCDRVVQF 128
               SCOP domains d2d1pd_ D: tRNA 2-thiouridine synthesizing protein D, TusD                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......hhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhh..........hhhhhhhhhhhhhh.eeeeehhhhhhh...hhhhhhhhh.........eeee.hhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1p D  -1 GSMRFAIVVTGPAYGTQQASSAFQFAQALIADGHELSSVFFYREGVYNANQLTSPASDEFDLVRAWQQLNAQHGVALNICVAAALRRGVVDETEAGRLGLASSNLQQGFTLSGLGALAEASLTCDRVVQF 128
                                     8        18        28        38        48        58        68        78        88        98       108       118       128

Chain E from PDB  Type:PROTEIN  Length:118
 aligned with TUSC_ECOLI | P45531 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:118
                                    11        21        31        41        51        61        71        81        91       101       111        
           TUSC_ECOLI     2 KRIAFVFSTAPHGTAAGREGLDALLATSALTDDLAVFFIADGVFQLLPGQKPDAVLARDYIATFKLLGLYDIEQCWVCAASLRERGLDPQTPFVVEATPLEADALRRELANYDVILRF 119
               SCOP domains d2d1pe_ E: tRNA 2-thiouridine synthesizing protein C, TusC                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhhhhhhh....eeeee.hhhhhhhh...hhhhhh...hhhhhhhhhhh....eeeehhhhhhh............eeehhhhhhhhhh...eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1p E   2 KRIAFVFSTAPHGTAAGREGLDALLATSALTDDLAVFFIADGVFQLLPGQKPDAVLARDYIATFKLLGLYDIEQCWVCAASLRERGLDPQTPFVVEATPLEADALRRELANYDVILRF 119
                                    11        21        31        41        51        61        71        81        91       101       111

Chain F from PDB  Type:PROTEIN  Length:95
 aligned with TUSB_ECOLI | P45530 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:95
                                    10        20        30        40        50        60        70        80        90     
           TUSB_ECOLI     1 MLHTLHRSPWLTDFAALLRLLSEGDELLLLQDGVTAAVDGNRYLESLRNAPIKVYALNEDLIARGLTGQISNDIILIDYTDFVRLTVKHPSQMAW  95
               SCOP domains d2d1pf_ F: tRNA 2-thiouridine synthesizing protein B, TusB                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhh.....eeee.hhhhhhhh....hhhhhhh...eeeeehhhhhhh.hhhhh....eeehhhhhhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 2d1p F   1 MLHTLHRSPWLTDFAALLRLLSEGDELLLLQDGVTAAVDGNRYLESLRNAPIKVYALNEDLIARGLTGQISNDIILIDYTDFVRLTVKHPSQMAW  95
                                    10        20        30        40        50        60        70        80        90

Chain G from PDB  Type:PROTEIN  Length:130
 aligned with TUSD_ECOLI | P45532 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:130
                              1                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128
           TUSD_ECOLI     - --MRFAIVVTGPAYGTQQASSAFQFAQALIADGHELSSVFFYREGVYNANQLTSPASDEFDLVRAWQQLNAQHGVALNICVAAALRRGVVDETEAGRLGLASSNLQQGFTLSGLGALAEASLTCDRVVQF 128
               SCOP domains d2d1pg_ G: tRNA 2-thiouridine synthesizing protein D, TusD                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......hhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhh..........hhhhhhhhhhhhhh.eeeeehhhhhhh...hhhhhhhhh.........eeee.hhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1p G  -1 GSMRFAIVVTGPAYGTQQASSAFQFAQALIADGHELSSVFFYREGVYNANQLTSPASDEFDLVRAWQQLNAQHGVALNICVAAALRRGVVDETEAGRLGLASSNLQQGFTLSGLGALAEASLTCDRVVQF 128
                                     8        18        28        38        48        58        68        78        88        98       108       118       128

Chain H from PDB  Type:PROTEIN  Length:118
 aligned with TUSC_ECOLI | P45531 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:118
                                    11        21        31        41        51        61        71        81        91       101       111        
           TUSC_ECOLI     2 KRIAFVFSTAPHGTAAGREGLDALLATSALTDDLAVFFIADGVFQLLPGQKPDAVLARDYIATFKLLGLYDIEQCWVCAASLRERGLDPQTPFVVEATPLEADALRRELANYDVILRF 119
               SCOP domains d2d1ph_ H: tRNA 2-thiouridine synthesizing protein C, TusC                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhhhhhhhhhh....eeeee.hhhhhhhh...hhhhhh...hhhhhhhhhhh....eeeehhhhhhh............eeehhhhhhhhhh...eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1p H   2 KRIAFVFSTAPHGTAAGREGLDALLATSALTDDLAVFFIADGVFQLLPGQKPDAVLARDYIATFKLLGLYDIEQCWVCAASLRERGLDPQTPFVVEATPLEADALRRELANYDVILRF 119
                                    11        21        31        41        51        61        71        81        91       101       111

Chain I from PDB  Type:PROTEIN  Length:95
 aligned with TUSB_ECOLI | P45530 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:95
                                    10        20        30        40        50        60        70        80        90     
           TUSB_ECOLI     1 MLHTLHRSPWLTDFAALLRLLSEGDELLLLQDGVTAAVDGNRYLESLRNAPIKVYALNEDLIARGLTGQISNDIILIDYTDFVRLTVKHPSQMAW  95
               SCOP domains d2d1pi_ I: tRNA 2-thiouridine synthesizing protein B, TusB                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhh.....eeee.hhhhhhhh....hhhhhhh...eeeeehhhhhhh..........eeehhhhhhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 2d1p I   1 MLHTLHRSPWLTDFAALLRLLSEGDELLLLQDGVTAAVDGNRYLESLRNAPIKVYALNEDLIARGLTGQISNDIILIDYTDFVRLTVKHPSQMAW  95
                                    10        20        30        40        50        60        70        80        90

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 2D1P)

(no "Pfam Domain" information available for 2D1P)

Asymmetric Unit(hide GO term definitions)

Chain A,D,G (TUSD_ECOLI | P45532)

molecular function
	GO:0097163	sulfur carrier activity	Enables the directed movement of sulfur into, out of or within a cell, or between cells.
	GO:0016783	sulfurtransferase activity	Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor).
	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:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B,E,H (TUSC_ECOLI | P45531)

biological process
	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.

Chain C,F,I (TUSB_ECOLI | P45530)

biological process
	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.
	GO:0002143	tRNA wobble position uridine thiolation	The process in which a uridine residue at position 34 in the anticodon of a tRNA is post-transcriptionally thiolated at the C2 position. This process involves transfer of a sulfur from cysteine to position C2 by several steps.
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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	2d1p
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Ligands, Modified Residues, Ions (1, 1)

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