1WWR - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TRNA ADENOSINE DEAMINASE TADA FROM AQUIFEX AEOLICUS

Authors :   M. Kuratani, R. Ishii, Y. Bessho, R. Fukunaga, T. Sengoku, S. Sekine, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   12 Jan 05 (Deposition) - 01 Feb 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B,C,D  (1x)

Keywords :   Homodimer, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Kuratani, R. Ishii, Y. Bessho, R. Fukunaga, T. Sengoku, M. Shirouzu, S. Sekine, S. Yokoyama
Crystal Structure Of Trna Adenosine Deaminase (Tada) From Aquifex Aeolicus
J. Biol. Chem. V. 280 16002 2005
PubMed-ID: 15677468 | Reference-DOI: 10.1074/JBC.M414541200
(for further references see the PDB file header)

Molecule 1 - TRNA ADENOSINE DEAMINASE TADA
	Chains	:	A, B, C, D
	EC Number	:	3.5.4.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21 (DE3) CODONPLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	HYPOTHETICAL PROTEIN AQ_903

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:52 , CYS A:82 , CYS A:85 , HOH A:225	BINDING SITE FOR RESIDUE ZN A 201
2	AC2	SOFTWARE	HIS B:52 , CYS B:82 , CYS B:85 , HOH B:333	BINDING SITE FOR RESIDUE ZN B 202
3	AC3	SOFTWARE	HIS C:52 , CYS C:82 , CYS C:85 , HOH C:329	BINDING SITE FOR RESIDUE ZN C 203
4	AC4	SOFTWARE	HIS D:52 , CYS D:82 , CYS D:85 , HOH D:241	BINDING SITE FOR RESIDUE ZN D 204

(no "SS Bond" information available for 1WWR)

(no "Cis Peptide Bond" information available for 1WWR)

(no "SAP(SNP)/Variant" information available for 1WWR)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	TADA_AQUAE	1-111	4	A:1-111 B:1-111 C:1-111 D:1-111
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	TADA_AQUAE	52-89	4	A:52-89 B:52-89 C:52-89 D:52-89

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_AQUAE	1-111	2	A:1-111 B:1-111 - -
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	TADA_AQUAE	52-89	2	A:52-89 B:52-89 - -

Biological Unit 2 (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_AQUAE	1-111	2	- - C:1-111 D:1-111
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	TADA_AQUAE	52-89	2	- - C:52-89 D:52-89

Biological Unit 3 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	TADA_AQUAE	1-111	4	A:1-111 B:1-111 C:1-111 D:1-111
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	TADA_AQUAE	52-89	4	A:52-89 B:52-89 C:52-89 D:52-89

(no "Exon" information available for 1WWR)

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:154
 aligned with TADA_AQUAE | O67050 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:154
                               1                                                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147    
           TADA_AQUAE     - ---MGKEYFLKVALREAKRAFEKGEVPVGAIIVKEGEIISKAHNSVEELKDPTAHAEMLAIKEACRRLNTKYLEGCELYVTLEPCIMCSYALVLSRIEKVIFSALDKKHGGVVSVFNILDEPTLNHRVKWEYYPLEEASELLSEFFKKLRNNII 151
               SCOP domains ---d1wwra1 A:1-151 tRNA adenosine deaminase TadA                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeee..............hhhhh.......eeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CYT_DCMP_DEAMINASES_2  PDB: A:1-111 UniProt: 1-111                                                             ---------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:52-89   -------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wwr A  -3 GSHMGKEYFLKVALREAKRAFEKGEVPVGAIIVKEGEIISKAHNSVEELKDPTAHAEMLAIKEACRRLNTKYLEGCELYVTLEPCIMCSYALVLSRIEKVIFSALDKKHGGVVSVFNILDEPTLNHRVKWEYYPLEEASELLSEFFKKLRNNII 151
                              ||     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147    
                             -1|                                                                                                                                                      
                               1

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with TADA_AQUAE | O67050 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:157
                                    1                                                                                                                                                    
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       
           TADA_AQUAE     - --------MGKEYFLKVALREAKRAFEKGEVPVGAIIVKEGEIISKAHNSVEELKDPTAHAEMLAIKEACRRLNTKYLEGCELYVTLEPCIMCSYALVLSRIEKVIFSALDKKHGGVVSVFNILDEPTLNHRVKWEYYPLEEASELLSEFFKKLRNN 149
               SCOP domains d1wwrb_ B: tRNA adenosine deaminase TadA                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhh..eeee..........................eeee..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------CYT_DCMP_DEAMINASES_2  PDB: B:1-111 UniProt: 1-111                                                             -------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:52-89   ------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wwr B  -8 GLVPRGSHMGKEYFLKVALREAKRAFEKGEVPVGAIIVKEGEIISKAHNSVEELKDPTAHAEMLAIKEACRRLNTKYLEGCELYVTLEPCIMCSYALVLSRIEKVIFSALDKKHGGVVSVFNILDEPTLNHRVKWEYYPLEEASELLSEFFKKLRNN 149
                                   ||2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       
                                  -1|                                                                                                                                                    
                                    1

Chain C from PDB  Type:PROTEIN  Length:160
 aligned with TADA_AQUAE | O67050 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:160
                                     1                                                                                                                                                      
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
           TADA_AQUAE     - ---------MGKEYFLKVALREAKRAFEKGEVPVGAIIVKEGEIISKAHNSVEELKDPTAHAEMLAIKEACRRLNTKYLEGCELYVTLEPCIMCSYALVLSRIEKVIFSALDKKHGGVVSVFNILDEPTLNHRVKWEYYPLEEASELLSEFFKKLRNNII 151
               SCOP domains d1wwrc_ C: tRNA adenosine deaminase TadA                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhh..eeee..........................eeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------CYT_DCMP_DEAMINASES_2  PDB: C:1-111 UniProt: 1-111                                                             ---------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: C:52-89   -------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wwr C  -9 SGLVPRGSHMGKEYFLKVALREAKRAFEKGEVPVGAIIVKEGEIISKAHNSVEELKDPTAHAEMLAIKEACRRLNTKYLEGCELYVTLEPCIMCSYALVLSRIEKVIFSALDKKHGGVVSVFNILDEPTLNHRVKWEYYPLEEASELLSEFFKKLRNNII 151
                                    |1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
                                   -1|                                                                                                                                                      
                                     1

Chain D from PDB  Type:PROTEIN  Length:151
 aligned with TADA_AQUAE | O67050 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
           TADA_AQUAE     1 MGKEYFLKVALREAKRAFEKGEVPVGAIIVKEGEIISKAHNSVEELKDPTAHAEMLAIKEACRRLNTKYLEGCELYVTLEPCIMCSYALVLSRIEKVIFSALDKKHGGVVSVFNILDEPTLNHRVKWEYYPLEEASELLSEFFKKLRNNII 151
               SCOP domains d1wwrd_ D: tRNA adenosine deaminase TadA                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..eeee..............hhhhh.......eeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CYT_DCMP_DEAMINASES_2  PDB: D:1-111 UniProt: 1-111                                                             ---------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: D:52-89   -------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wwr D   1 MGKEYFLKVALREAKRAFEKGEVPVGAIIVKEGEIISKAHNSVEELKDPTAHAEMLAIKEACRRLNTKYLEGCELYVTLEPCIMCSYALVLSRIEKVIFSALDKKHGGVVSVFNILDEPTLNHRVKWEYYPLEEASELLSEFFKKLRNNII 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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)

Aquifex aeolicus [TaxId: 63363] (1)

1a	d1wwra1	A:1-151
1b	d1wwrb_	B:
1c	d1wwrc_	C:
1d	d1wwrd_	D:

(no "CATH Domain" information available for 1WWR)

(no "Pfam Domain" information available for 1WWR)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TADA_AQUAE | O67050)

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:0019239	deaminase activity	Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3).
	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 Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wwr)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ 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 \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1wwr
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TADA_AQUAE \| O67050
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.5.4.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TADA_AQUAE \| O67050
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1WWR)

(no "Related Entries Specified in the PDB File" available for 1WWR)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File