2A8N - JenaLib

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Title :   BIOCHEMICAL AND STRUCTURAL STUDIES OF A-TO-I EDITING BY TRNA:A34 DEAMINASES AT THE WOBBLE POSITION OF TRANSFER RNA

Authors :   Y. Elias, R. H. Huang

Date :   08 Jul 05 (Deposition) - 27 Sep 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Rna Editing, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Elias, R. H. Huang
Biochemical And Structural Studies Of A-To-I Editing By Trna:A34 Deaminases At The Wobble Position Of Transfer Rna
Biochemistry V. 44 12057 2005
PubMed-ID: 16142903 | Reference-DOI: 10.1021/BI050499F
(for further references see the PDB file header)

Molecule 1 - CYTIDINE AND DEOXYCYTIDYLATE DEAMINASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PLM1-TADA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CODA
	Organism Scientific	:	AGROBACTERIUM TUMEFACIENS
	Organism Taxid	:	358

		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	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:53 , CYS A:83 , CYS A:86 , HOH A:361	BINDING SITE FOR RESIDUE ZN A 301
2	AC2	SOFTWARE	HIS B:53 , CYS B:83 , CYS B:86 , HOH B:317	BINDING SITE FOR RESIDUE ZN B 302

(no "SS Bond" information available for 2A8N)

(no "Cis Peptide Bond" information available for 2A8N)

(no "SAP(SNP)/Variant" information available for 2A8N)

Asymmetric/Biological Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	TADA_AGRFC	2-111	1	A:2-111
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	TADA_AGRFC	53-90	2	A:53-90 B:53-90

(no "Exon" information available for 2A8N)

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
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Chain A from PDB  Type:PROTEIN  Length:130
 aligned with TADA_AGRFC | A9CK16 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:130
                                    11        21        31        41        51        61        71        81        91       101       111       121       131
           TADA_AGRFC     2 AERTHFMELALVEARSAGERDEVPIGAVLVLDGRVIARSGNRTRELNDVTAHAEIAVIRMACEALGQERLPGADLYVTLEPCTMCAAAISFARIRRLYYGAQDPKGGAVESGVRFFSQPTCHHAPDVYSG 131
               SCOP domains d2a8na1 A:2-131 Cytidine and deoxycytidylate deaminase CodA                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhh...eeeeee............hhhhh.......eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CYT_DCMP_DEAMINASES_2  PDB: A:2-111 UniProt: 2-111                                                            -------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:53-90   ----------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a8n A   2 AERTHFMELALVEARSAGERDEVPIGAVLVLDGRVIARSGNRTRELNDVTAHAEIAVIRMACEALGQERLPGADLYVTLEPCTMCAAAISFARIRRLYYGAQDPKGGAVESGVRFFSQPTCHHAPDVYSG 131
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with TADA_AGRFC | A9CK16 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:138
                                    13        23        33        43        53        63        73        83        93       103       113       123       133        
           TADA_AGRFC     4 RTHFMELALVEARSAGERDEVPIGAVLVLDGRVIARSGNRTRELNDVTAHAEIAVIRMACEALGQERLPGADLYVTLEPCTMCAAAISFARIRRLYYGAQDPKGGAVESGVRFFSQPTCHHAPDVYSGLAESESAEIL 141
               SCOP domains d2a8nb_ B: Cytidine and deoxycytidylate deaminase CodA                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee...........hhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhh...eeeeee............hhhhh.......eeee..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) CYT_DCMP_DEAMINASES_2  PDB: - UniProt: 2-111                                                                ------------------------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:53-90   --------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2a8n B   4 RTHFMELALVEARSAGERDEVPIGAVLVLDGRVIARSGNRTRELNDVTAHAEIAVIRMACEALGQERLPGADLYVTLEPCTMCAAAISFARIRRLYYGAQDPKGGAVESGVRFFSQPTCHHAPDVYSGLAESESAEIL 141
                                    13        23        33        43        53        63        73        83        93       103       113       123       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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Cytidine deaminase-like (78)

Superfamily: Cytidine deaminase-like (76)

Family: Deoxycytidylate deaminase-like (29)

Protein domain: Cytidine and deoxycytidylate deaminase CodA (1)

Agrobacterium tumefaciens [TaxId: 358] (1)

1a	d2a8na1	A:2-131
1b	d2a8nb_	B:

(no "CATH Domain" information available for 2A8N)

(no "Pfam Domain" information available for 2A8N)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TADA_AGRFC | A9CK16)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008251	tRNA-specific adenosine deaminase activity	Catalysis of the reaction: adenosine + H2O = inosine + NH3, in a tRNA molecule.
	GO:0052717	tRNA-specific adenosine-34 deaminase activity	Catalysis of the reaction: adenosine-34 + H2O = inosine-34 + NH3, in a tRNA-Ala molecule.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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:0002100	tRNA wobble adenosine to inosine editing	The process in which an adenosine in position 34 of a tRNA is post-transcriptionally converted to inosine.

Asymmetric/Biological Unit
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