2B3J | PR0180 - JenaLib

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Title :   CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS TRNA ADENOSINE DEAMINASE, TADA, IN COMPLEX WITH RNA

Authors :   H. C. Losey, A. J. Ruthenburg, G. L. Verdine

Date :   20 Sep 05 (Deposition) - 24 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Mixed Alpha-Beta, Protein-Rna Complex, Rna Stem-Loop, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. C. Losey, A. J. Ruthenburg, G. L. Verdine
Crystal Structure Of Staphylococcus Aureus Trna Adenosine Deaminase Tada In Complex With Rna.
Nat. Struct. Mol. Biol. V. 13 153 2006
PubMed-ID: 16415880 | Reference-DOI: 10.1038/NSMB1047

Molecule 1 - ANTICODON STEM-LOOP OF T-RNA-ARG2 (NUCLEOTIDES 27-42)
	Chains	:	E, F, G, H
	Engineered	:	YES
	Other Details	:	THE SEQUENCE IS DERIVED FROM S. AUREUS T-RNA-ARG2 NUCLEOTIDES 27-42
	Synthetic	:	YES

Molecule 2 - TRNA ADENOSINE DEAMINASE
	Chains	:	A, B, C, D
	EC Number	:	3.5.4.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TADA
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50
	Organism Taxid	:	158878
	Strain	:	SUBSP. AUREUS MU50
	Synonym	:	SIMILAR TO CYTOSINE DEAMINASE, TADA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	P5P	4	Mod. Nucleotide	PURINE RIBOSIDE-5'-MONOPHOSPHATE
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	P5P	2	Mod. Nucleotide	PURINE RIBOSIDE-5'-MONOPHOSPHATE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	P5P	2	Mod. Nucleotide	PURINE RIBOSIDE-5'-MONOPHOSPHATE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:53 , CYS A:83 , CYS A:86 , HOH A:2002	BINDING SITE FOR RESIDUE ZN A 2001
2	AC2	SOFTWARE	CYS A:83 , VAL A:84 , GLY A:107 , HOH A:2052 , HOH A:2059 , PHE B:122 , ASN B:123	BINDING SITE FOR RESIDUE GOL A 1001
3	AC3	SOFTWARE	HIS B:53 , GLU B:55 , CYS B:83 , CYS B:86 , HOH B:2003	BINDING SITE FOR RESIDUE ZN B 2002
4	AC4	SOFTWARE	PHE A:122 , ASN A:123 , CYS B:83 , VAL B:84 , GLY B:107 , HOH B:2041 , HOH B:2042	BINDING SITE FOR RESIDUE GOL B 1002
5	AC5	SOFTWARE	HIS C:53 , CYS C:83 , CYS C:86 , HOH C:2004	BINDING SITE FOR RESIDUE ZN C 2003
6	AC6	SOFTWARE	CYS C:83 , VAL C:84 , GLY C:107 , HOH C:2060 , PHE D:122 , ASN D:123	BINDING SITE FOR RESIDUE GOL C 1004
7	AC7	SOFTWARE	HIS D:53 , CYS D:83 , CYS D:86 , HOH D:2005	BINDING SITE FOR RESIDUE ZN D 2004
8	AC8	SOFTWARE	MET C:92 , PHE C:122 , ASN C:123 , CYS D:83 , VAL D:84 , GLY D:107 , HOH D:2037 , HOH D:2053 , HOH H:50	BINDING SITE FOR RESIDUE GOL D 1003

(no "SS Bond" information available for 2B3J)

(no "Cis Peptide Bond" information available for 2B3J)

(no "SAP(SNP)/Variant" information available for 2B3J)

Asymmetric Unit (2, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	TADA_STAAM	2-120	3	A:2-120 B:2-120 C:2-120
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	TADA_STAAM	53-90	4	A:53-90 B:53-90 C:53-90 D:53-90

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	TADA_STAAM	2-120	2	A:2-120 B:2-120 -
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	TADA_STAAM	53-90	2	A:53-90 B:53-90 - -

Biological Unit 2 (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_STAAM	2-120	1	- - C:2-120
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	TADA_STAAM	53-90	2	- - C:53-90 D:53-90

(no "Exon" information available for 2B3J)

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:151
 aligned with TADA_STAAM | Q99W51 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
           TADA_STAAM     1 MTNDIYFMTLAIEEAKKAAQLGEVPIGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWRLEGCTLYVTLEPCVMCAGTIVMSRIPRVVYGADDPKGGCSGSLMNLLQQSNFNHRAIVDKGVLKEACSTLLTTFFKNLRAN 151
               SCOP domains d2b3ja1 A:1-151 tRNA adenosine deaminase TadA                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhh...eeeeee........................eee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CYT_DCMP_DEAMINASES_2  PDB: A:2-120 UniProt: 2-120                                                                     ------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:53-90   ------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b3j A   1 MTNDIYFMTLAIEEAKKAAQLGEVPIGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWRLEGCTLYVTLEPCVMCAGTIVMSRIPRVVYGADDPKGGCSGSLMNLLQQSNFNHRAIVDKGVLKEACSTLLTTFFKNLRAN 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with TADA_STAAM | Q99W51 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
           TADA_STAAM     1 MTNDIYFMTLAIEEAKKAAQLGEVPIGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWRLEGCTLYVTLEPCVMCAGTIVMSRIPRVVYGADDPKGGCSGSLMNLLQQSNFNHRAIVDKGVLKEACSTLLTTFFKNLRAN 151
               SCOP domains d2b3jb_ B: tRNA adenosine deaminase TadA                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.....eeeeee...eeeeee.hhhhhh....hhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhh...eeeeee........................eee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CYT_DCMP_DEAMINASES_2  PDB: B:2-120 UniProt: 2-120                                                                     ------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:53-90   ------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b3j B   1 MTNDIYFMTLAIEEAKKAAQLGEVPIGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWRLEGCTLYVTLEPCVMCAGTIVMSRIPRVVYGADDPKGGCSGSLMNLLQQSNFNHRAIVDKGVLKEACSTLLTTFFKNLRAN 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:152
 aligned with TADA_STAAM | Q99W51 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
           TADA_STAAM     1 MTNDIYFMTLAIEEAKKAAQLGEVPIGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWRLEGCTLYVTLEPCVMCAGTIVMSRIPRVVYGADDPKGGCSGSLMNLLQQSNFNHRAIVDKGVLKEACSTLLTTFFKNLRANK 152
               SCOP domains d2b3jc_ C: tRNA adenosine deaminase TadA                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhh...eeeeee............hhhhh.......eeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CYT_DCMP_DEAMINASES_2  PDB: C:2-120 UniProt: 2-120                                                                     -------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: C:53-90   -------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b3j C   1 MTNDIYFMTLAIEEAKKAAQLGEVPIGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWRLEGCTLYVTLEPCVMCAGTIVMSRIPRVVYGADDPKGGCSGSLMNLLQQSNFNHRAIVDKGVLKEACSTLLTTFFKNLRANK 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain D from PDB  Type:PROTEIN  Length:150
 aligned with TADA_STAAM | Q99W51 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152
           TADA_STAAM     3 NDIYFMTLAIEEAKKAAQLGEVPIGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWRLEGCTLYVTLEPCVMCAGTIVMSRIPRVVYGADDPKGGCSGSLMNLLQQSNFNHRAIVDKGVLKEACSTLLTTFFKNLRANK 152
               SCOP domains d2b3jd_ D: tRNA adenosine deaminase TadA                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh......eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh..eeeeee............hhhhh.......eee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) CYT_DCMP_DEAMINASES_2  PDB: - UniProt: 2-120                                                                          -------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: D:53-90   -------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b3j D   3 NDIYFMTLAIEEAKKAAQLGEVPIGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIERAAKVLGSWRLEGCTLYVTLEPCVMCAGTIVMSRIPRVVYGADDPKGGCSGSLMNLLQQSNFNHRAIVDKGVLKEACSTLLTTFFKNLRANK 152
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain E from PDB  Type:RNA  Length:15
                                               
                 2b3j E  28 UUGACUaCGGAUCAA  42
                                  | 37     
                                 34-P5P

Chain F from PDB  Type:RNA  Length:15
                                               
                 2b3j F  28 UUGACUaCGGAUCAA  42
                                  | 37     
                                 34-P5P

Chain G from PDB  Type:RNA  Length:8
                                        
                 2b3j G  30 GACUaCGG  37
                                |   
                               34-P5P

Chain H from PDB  Type:RNA  Length:16
                                                
                 2b3j H  27 UUUGACUaCGGAUCAA  42
                                   |36      
                                  34-P5P

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 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: tRNA adenosine deaminase TadA (3)

Staphylococcus aureus [TaxId: 1280] (1)

1a	d2b3ja1	A:1-151
1b	d2b3jb_	B:
1c	d2b3jc_	C:
1d	d2b3jd_	D:

(no "CATH Domain" information available for 2B3J)

(no "Pfam Domain" information available for 2B3J)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TADA_STAAM | Q99W51)

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.

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