3DH1 - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN TRNA-SPECIFIC ADENOSINE-34 DEAMINASE SUBUNIT ADAT2

Authors :   M. Welin, L. Tresaugues, J. Andersson, C. H. Arrowsmith, H. Berglund, R L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Ham A. Johansson, I. Johansson, T. Karlberg, T. Kotenyova, L. Lehtio, M. M M. E. Nilsson, T. Nyman, K. Olesen, C. Persson, J. Sagemark, H. Schuele A. G. Thorsell, S. Van Der Berg, M. Wisniewska, M. Wikstrom, P. Nordl Structural Genomics Consortium (Sgc)

Date :   16 Jun 08 (Deposition) - 09 Sep 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Trna-Specific Adenosine Deaminase, Zinc-Binding Protein, Translation, Trna Processing, Hydrolase, Structural Genomics, Structural Genomics Consortium, Sgc, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Welin, L. Tresaugues, J. Andersson, C. H. Arrowsmith, H. Berglund, R. Collins, L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Johansson, I. Johansson, T. Karlberg T. Kotenyova, L. Lehtio, M. Moche, M. E. Nilsson, T. Nyman, K. Olesen, C. Persson, J. Sagemark, H. Schueler, A. G. Thorsell, S. Van Der Berg M. Wisniewska, M. Wikstrom, P. Nordlund
Crystal Structure Of Human Trna-Specific Adenosine-34 Deaminase Subunit Adat2.
To Be Published
PubMed: search

Molecule 1 - TRNA-SPECIFIC ADENOSINE DEAMINASE 2
	Chains	:	A, B, C, D
	EC Number	:	3.5.4.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21(DE3) R3 PRARE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 20-185
	Gene	:	ADAT2, DEADC1
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TRNA-SPECIFIC ADENOSINE-34 DEAMINASE SUBUNIT ADAT2, DEAMINASE DOMAIN-CONTAINING PROTEIN 1

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

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:71 , GLU A:73 , CYS A:107 , CYS A:110	BINDING SITE FOR RESIDUE ZN A 201
2	AC2	SOFTWARE	HIS C:71 , GLU C:73 , CYS C:107 , CYS C:110	BINDING SITE FOR RESIDUE ZN C 201
3	AC3	SOFTWARE	HIS D:71 , GLU D:73 , CYS D:107 , CYS D:110	BINDING SITE FOR RESIDUE ZN D 201
4	AC4	SOFTWARE	HIS B:71 , GLU B:73 , CYS B:107 , CYS B:110	BINDING SITE FOR RESIDUE ZN B 201

(no "SS Bond" information available for 3DH1)

(no "Cis Peptide Bond" information available for 3DH1)

(no "SAP(SNP)/Variant" information available for 3DH1)

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.	ADAT2_HUMAN	20-145	4	A:20-145 B:20-145 C:20-145 D:20-145
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	ADAT2_HUMAN	71-114	4	A:71-114 B:71-114 C:71-114 D:71-114

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.	ADAT2_HUMAN	20-145	2	A:20-145 - - D:20-145
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	ADAT2_HUMAN	71-114	2	A:71-114 - - D:71-114

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.	ADAT2_HUMAN	20-145	2	- B:20-145 C:20-145 -
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	ADAT2_HUMAN	71-114	2	- B:71-114 C:71-114 -

(no "Exon" information available for 3DH1)

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:162
 aligned with ADAT2_HUMAN | Q7Z6V5 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:162
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171  
          ADAT2_HUMAN    12 SGACSVSAEETEKWMEEAMHMAKEALENTEVPVGCLMVYNNEVVGKGRNEVNQTKNATRHAEMVAIDQVLDWCRQSGKSPSEVFEHTVLYVTVEPCIMCAAALRLMKIPLVVYGCQNERFGGCGSVLNIASADLPNTGRPFQCIPGYRAEEAVEMLKTFYKQ 173
               SCOP domains d3dh1a_ A: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeee..hhhhhhhhhhhh..eeeeee..........................eee...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------CYT_DCMP_DEAMINASES_2  PDB: A:20-145 UniProt: 20-145                                                                          ---------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:71-114        ----------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dh1 A  12 ENLYFQSMEETEKWMEEAMHMAKEALENTEVPVGCLMVYNNEVVGKGRNEVNQTKNATRHAEMVAIDQVLDWCRQSGKSPSEVFEHTVLYVTVEPCIMCAAALRLMKIPLVVYGCQNERFGGCGSVLNIASADLPNTGRPFQCIPGYRAEEAVEMLKTFYKQ 173
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with ADAT2_HUMAN | Q7Z6V5 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:160
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
          ADAT2_HUMAN    13 GACSVSAEETEKWMEEAMHMAKEALENTEVPVGCLMVYNNEVVGKGRNEVNQTKNATRHAEMVAIDQVLDWCRQSGKSPSEVFEHTVLYVTVEPCIMCAAALRLMKIPLVVYGCQNERFGGCGSVLNIASADLPNTGRPFQCIPGYRAEEAVEMLKTFYK 172
               SCOP domains d3dh1b_ B: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeee..hhhhhhhhhhhh..eeeeee..........................eee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------CYT_DCMP_DEAMINASES_2  PDB: B:20-145 UniProt: 20-145                                                                          --------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:71-114        ---------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dh1 B  13 NLYFQSMEETEKWMEEAMHMAKEALENTEVPVGCLMVYNNEVVGKGRNEVNQTKNATRHAEMVAIDQVLDWCRQSGKSPSEVFEHTVLYVTVEPCIMCAAALRLMKIPLVVYGCQNERFGGCGSVLNIASADLPNTGRPFQCIPGYRAEEAVEMLKTFYK 172
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain C from PDB  Type:PROTEIN  Length:160
 aligned with ADAT2_HUMAN | Q7Z6V5 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:160
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
          ADAT2_HUMAN    13 GACSVSAEETEKWMEEAMHMAKEALENTEVPVGCLMVYNNEVVGKGRNEVNQTKNATRHAEMVAIDQVLDWCRQSGKSPSEVFEHTVLYVTVEPCIMCAAALRLMKIPLVVYGCQNERFGGCGSVLNIASADLPNTGRPFQCIPGYRAEEAVEMLKTFYK 172
               SCOP domains d3dh1c_ C: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhh..eeeeee..hhhhhhhhhhhh..eeeeee..........................eee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------CYT_DCMP_DEAMINASES_2  PDB: C:20-145 UniProt: 20-145                                                                          --------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: C:71-114        ---------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dh1 C  13 NLYFQSMEETEKWMEEAMHMAKEALENTEVPVGCLMVYNNEVVGKGRNEVNQTKNATRHAEMVAIDQVLDWCRQSGKSPSEVFEHTVLYVTVEPCIMCAAALRLMKIPLVVYGCQNERFGGCGSVLNIASADLPNTGRPFQCIPGYRAEEAVEMLKTFYK 172
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain D from PDB  Type:PROTEIN  Length:161
 aligned with ADAT2_HUMAN | Q7Z6V5 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:161
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 
          ADAT2_HUMAN    13 GACSVSAEETEKWMEEAMHMAKEALENTEVPVGCLMVYNNEVVGKGRNEVNQTKNATRHAEMVAIDQVLDWCRQSGKSPSEVFEHTVLYVTVEPCIMCAAALRLMKIPLVVYGCQNERFGGCGSVLNIASADLPNTGRPFQCIPGYRAEEAVEMLKTFYKQ 173
               SCOP domains d3dh1d_ D: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeee..hhhhhhhhhhhh..eeeeee..........................eee...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------CYT_DCMP_DEAMINASES_2  PDB: D:20-145 UniProt: 20-145                                                                          ---------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: D:71-114        ----------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dh1 D  13 NLYFQSMEETEKWMEEAMHMAKEALENTEVPVGCLMVYNNEVVGKGRNEVNQTKNATRHAEMVAIDQVLDWCRQSGKSPSEVFEHTVLYVTVEPCIMCAAALRLMKIPLVVYGCQNERFGGCGSVLNIASADLPNTGRPFQCIPGYRAEEAVEMLKTFYKQ 173
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Cytidine deaminase-like (78)

Superfamily: Cytidine deaminase-like (76)

Family: automated matches (11)

Protein domain: automated matches (11)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d3dh1a_	A:
1b	d3dh1b_	B:
1c	d3dh1c_	C:
1d	d3dh1d_	D:

(no "CATH Domain" information available for 3DH1)

(no "Pfam Domain" information available for 3DH1)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ADAT2_HUMAN | Q7Z6V5)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0006400	tRNA modification	The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
	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.
cellular component
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0052718	tRNA-specific adenosine-34 deaminase complex	A protein complex that possesses tRNA-specific adenosine-34 deaminase activity. In eukaryotes the complex is a heterodimer; the subunits are known as Tad2p and Tad3p in yeasts and Adat2 and Adat3 in human.

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	3dh1
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Description

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Ligands, Modified Residues, Ions (1, 4)

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