2NOM - JenaLib

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Biological Unit 2 (Jmol Viewer)

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

Authors :   H. Luecke, J. Stagno

Date :   25 Oct 06 (Deposition) - 20 Feb 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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, A. Rosengarth, H. Luecke, R. Aphasizhev
Utp-Bound And Apo Structures Of A Minimal Rna Uridylyltransferase.
J. Mol. Biol. V. 366 882 2007
PubMed-ID: 17189640 | Reference-DOI: 10.1016/J.JMB.2006.11.065
(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	:	841358, TB11.01.7300
	Organism Scientific	:	TRYPANOSOMA BRUCEI
	Organism Taxid	:	5691

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	DUT	2	Ligand/Ion	DEOXYURIDINE-5'-TRIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	DUT	1	Ligand/Ion	DEOXYURIDINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	DUT	1	Ligand/Ion	DEOXYURIDINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:66 , ASP A:68 , MG A:402 , DUT A:501 , HOH A:556 , HOH A:590	BINDING SITE FOR RESIDUE MG A 401
2	AC2	SOFTWARE	ASP A:66 , ASP A:68 , ASP A:136 , MG A:401 , HOH A:588 , HOH A:589 , HOH A:590	BINDING SITE FOR RESIDUE MG A 402
3	AC3	SOFTWARE	PHE A:52 , GLY A:53 , SER A:54 , VAL A:57 , SER A:65 , ASP A:66 , ASP A:68 , ASN A:147 , SER A:148 , LEU A:151 , LYS A:169 , LYS A:173 , THR A:187 , SER A:188 , TYR A:189 , MG A:401 , HOH A:525 , HOH A:540 , HOH A:556 , HOH A:558 , HOH A:573 , HOH A:574 , HOH A:576 , HOH A:587 , HOH A:590	BINDING SITE FOR RESIDUE DUT A 501
4	AC4	SOFTWARE	GLY B:53 , SER B:54 , ASP B:66 , ASP B:68 , ASN B:147 , SER B:148 , LYS B:169 , LYS B:173 , THR B:187 , SER B:188 , TYR B:189 , HOH B:533	BINDING SITE FOR RESIDUE DUT B 502

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

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

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

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

(no "Exon" information available for 2NOM)

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: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 .hhhhhhhhhhhh....-----...hhhhhhhhhhhhhhhhh...eeeeehhhhhhh.......eeeeeehhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeee......eeeee.....eeeeee..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhhhhhhh...............hhhhhhhhhhhhhhhhhh......ee........hhhhhh.hhhhhh..hhhhh......ee..............hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nom A   3 PSPAVVGRSLVNSFKQF-----HTRHVDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTI 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
                                           19    25

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with Q381M1_TRYB2 | Q381M1 from UniProtKB/TrEMBL  Length:333

    Alignment length:333
                                    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   
         Q381M1_TRYB2     1 MPPSPAVVGRSLVNSFKQFVSKDLHTRHVDATYRLVLDCVAAVDPLMRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLARVIRQKHLSWNVEEVRRTRVPVVRVKGGGAVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTIV 333
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.....---------------------------.eehhhhhhh.-----.eeeee...------.....------..hhhhh----------------------------------..eeeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhh....................hhhhhhhhhhhhhhhhhh.....ee........eehhhhh.hhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nom B   1 MPPSPAVVGRSLVNSFKQFVSK---------------------------YTFGSTVVYGV-----DVDFVVLNK------KGGDA------GLQADIL----------------------------------VDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSITSYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPADEGLELGTQVLDFLHFFLHEFDSDKQVISLNRPGITTKEELDWTKSAEDFARMNGEKVHYQWCIEDPYELNLNVGRNVTPLKRDFLRRHLEKARDTALLTIV 333
                                    10        20 |       -         -        50        60     |  70   |     -|   |    - |     | -         -         -         -  |    140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   
                                                22                          50        60    66      74     81  85     92    98                                133

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 2NOM)

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

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

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 2nom)

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
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	2nom
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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 2q0c 2q0d 2q0e 2q0f 2q0g 5kal

2ikf	SAME ENZYME WITH DIFFERENT SUBSTRATE.

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

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