2Q0G - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   TERMINAL URIDYLYL TRANSFERASE 4 FROM TRYPANOSOMA BRUCEI WITH BOUND UPU

Authors :   J. Stagno, H. Luecke

Date :   21 May 07 (Deposition) - 28 Aug 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Tutase, Trypanosoma, Nucleotidyltransferase, Utp-Binding, Rna-Editing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Stagno, I. Aphasizheva, R. Aphasizhev, H. Luecke
Dual Role Of The Rna Substrate In Selectivity And Catalysis By Terminal Uridylyl Transferases.
Proc. Natl. Acad. Sci. Usa V. 104 14634 2007
PubMed-ID: 17785418 | Reference-DOI: 10.1073/PNAS.0704259104
(for further references see the PDB file header)

Molecule 1 - RNA URIDYLYL TRANSFERASE
	Chains	:	A, B
	EC Number	:	2.7.7.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TUT4
	Organism Scientific	:	TRYPANOSOMA BRUCEI
	Organism Taxid	:	5691
	Synonym	:	RNA URIDYLYLTRANSFERASE 4

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	UPU	2	Ligand/Ion	[(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-4-HYDROXY-2-(HYDROXYMETHYL)TETRAHYDROFURAN-3-YLHYDROGEN (S)-PHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	UPU	1	Ligand/Ion	[(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-4-HYDROXY-2-(HYDROXYMETHYL)TETRAHYDROFURAN-3-YLHYDROGEN (S)-PHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	UPU	1	Ligand/Ion	[(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-4-HYDROXY-2-(HYDROXYMETHYL)TETRAHYDROFURAN-3-YLHYDROGEN (S)-PHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:66 , ASP A:68 , ASP A:136 , UPU A:501 , HOH A:552	BINDING SITE FOR RESIDUE MG A 401
2	AC2	SOFTWARE	ASP B:66 , ASP B:68 , ASP B:136 , UPU B:502	BINDING SITE FOR RESIDUE MG B 402
3	AC3	SOFTWARE	HIS A:246 , HIS A:250 , HOH A:523 , HOH A:610	BINDING SITE FOR RESIDUE CL A 403
4	AC4	SOFTWARE	HIS B:246 , HIS B:250 , HOH B:504 , HOH B:552	BINDING SITE FOR RESIDUE CL B 404
5	AC5	SOFTWARE	PHE A:52 , GLY A:53 , ASP A:68 , ARG A:121 , ARG A:126 , ASP A:136 , GLY A:144 , ASN A:147 , SER A:148 , TYR A:189 , MG A:401 , HOH A:502 , HOH A:505 , HOH A:512 , HOH A:535 , HOH A:552 , HOH A:592 , HOH A:600	BINDING SITE FOR RESIDUE UPU A 501
6	AC6	SOFTWARE	PHE B:52 , GLY B:53 , ASP B:66 , ASP B:68 , ARG B:121 , VAL B:122 , GLY B:144 , ASN B:147 , SER B:148 , TYR B:189 , MG B:402 , HOH B:503 , HOH B:517 , HOH B:532 , HOH B:535	BINDING SITE FOR RESIDUE UPU B 502

(no "SS Bond" information available for 2Q0G)

(no "Cis Peptide Bond" information available for 2Q0G)

(no "SAP(SNP)/Variant" information available for 2Q0G)

(no "PROSITE Motif" information available for 2Q0G)

(no "Exon" information available for 2Q0G)

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:325
 aligned with Q381M1_TRYB2 | Q381M1 from UniProtKB/TrEMBL  Length:333

    Alignment length:330
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
         Q381M1_TRYB2     3 PSPAVVGRSLVNSFKQFVSKDLHTRHVDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTI 332
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.....-----.hhhhhhhhhhhhhhhhh...eeeeehhhhhhh.......eeeeeehhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeee......eeeee.....eeeeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhhhhhhh...............hhhhhhhhhhhhhhhhhh.....eee.......eehhhhh.hhhhhh.............ee..............hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q0g A   3 PSPAVVGRSLVNSFKQFVS-----RHVDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTI 332
                                    12        |-    |   32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
                                             21    27

Chain B from PDB  Type:PROTEIN  Length:324
 aligned with Q381M1_TRYB2 | Q381M1 from UniProtKB/TrEMBL  Length:333

    Alignment length:330
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
         Q381M1_TRYB2     3 PSPAVVGRSLVNSFKQFVSKDLHTRHVDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTI 332
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.......------hhhhhhhhhhhhhh.....eeeeehhhhhhh.......eeeeeehhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeee......eeeee.....eeeeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhh....................hhhhhhhhhhhhhhhhhh.....ee........ee......hhhhhhhhhhh........................hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q0g B   3 PSPAVVGRSLVNSFKQFVSK------VDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTI 332
                                    12        22      | 32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
                                              22     29

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 2Q0G)

(no "CATH Domain" information available for 2Q0G)

(no "Pfam Domain" information available for 2Q0G)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q381M1_TRYB2 | Q381M1)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
cellular component
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2q0g)

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

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	2q0g
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	Q381M1_TRYB2 \| Q381M1
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	2.7.7.52
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	Q381M1_TRYB2 \| Q381M1
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UniProtKB/TrEMBL
	Q381M1_TRYB2 \| Q381M1	:	2ikf 2nom 2q0c 2q0d 2q0e 2q0f 5kal

2ikf	THE SAME PROTEIN WITH BOUND UTP SUBSTRATE.
2nom	THE SAME PROTEIN WITH BOUND DUTP SUBSTRATE.
2q0c
2q0d
2q0e
2q0f

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (5, 5)

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