2Z3J - JenaLib

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Title :   CRYSTAL STRUCTURE OF BLASTICIDIN S DEAMINASE (BSD) R90K MUTANT

Authors :   A. H. Teh, T. Kumasaka, M. Yamamoto, M. Furuichi, M. Nakasako, M. Kimura I. Yamaguchi, T. Ueki

Date :   04 Jun 07 (Deposition) - 23 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Hydrolase, Cytidine Deaminase Family, Tetramer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Kumasaka, M. Yamamoto, M. Furuichi, M. Nakasako, A. H. Teh, M. Kimura, I. Yamaguchi, T. Ueki
Crystal Structures Of Blasticidin S Deaminase (Bsd): Implications For Dynamic Properties Of Catalytic Zinc
J. Biol. Chem. V. 282 37103 2007
PubMed-ID: 17959604 | Reference-DOI: 10.1074/JBC.M704476200
(for further references see the PDB file header)

Molecule 1 - BLASTICIDIN-S DEAMINASE
	Chains	:	A, B, C, D
	EC Number	:	3.5.4.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-12A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ASPERGILLUS TERREUS
	Organism Taxid	:	33178
	Strain	:	S-712

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	CAC	4	Ligand/Ion	CACODYLATE ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:54 , CYS A:88 , CYS A:91 , CAC A:2501	BINDING SITE FOR RESIDUE ZN A 2001
2	AC2	SOFTWARE	CYS A:54 , GLU A:56 , LEU A:85 , SER A:86 , PRO A:87 , CYS A:88 , CYS A:91 , ZN A:2001 , HOH A:3003 , TYR B:126	BINDING SITE FOR RESIDUE CAC A 2501
3	AC3	SOFTWARE	THR A:50 , GLY A:51 , LYS A:90 , THR B:50 , GLY B:51 , LYS B:90 , THR C:50 , GLY C:51 , LYS C:90 , THR D:50 , GLY D:51 , LYS D:90	BINDING SITE FOR RESIDUE CL A 3001
4	AC4	SOFTWARE	CYS B:54 , CYS B:88 , CYS B:91 , CAC B:2502	BINDING SITE FOR RESIDUE ZN B 2002
5	AC5	SOFTWARE	TYR A:126 , CYS B:54 , GLU B:56 , LEU B:85 , SER B:86 , PRO B:87 , CYS B:88 , CYS B:91 , ZN B:2002 , HOH B:2505	BINDING SITE FOR RESIDUE CAC B 2502
6	AC6	SOFTWARE	CYS C:54 , CYS C:88 , CYS C:91 , CAC C:2503	BINDING SITE FOR RESIDUE ZN C 2003
7	AC7	SOFTWARE	CYS C:54 , GLU C:56 , LEU C:85 , SER C:86 , CYS C:88 , CYS C:91 , ZN C:2003 , HOH C:2525 , TYR D:126	BINDING SITE FOR RESIDUE CAC C 2503
8	AC8	SOFTWARE	CYS D:54 , CYS D:88 , CYS D:91 , CAC D:2504	BINDING SITE FOR RESIDUE ZN D 2004
9	AC9	SOFTWARE	TYR C:126 , CYS D:54 , GLU D:56 , LEU D:85 , SER D:86 , PRO D:87 , CYS D:88 , CYS D:91 , ZN D:2004 , HOH D:2513	BINDING SITE FOR RESIDUE CAC D 2504

(no "SS Bond" information available for 2Z3J)

(no "Cis Peptide Bond" information available for 2Z3J)

(no "SAP(SNP)/Variant" information available for 2Z3J)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	BSD_ASPTE	54-95	4	A:54-95 B:54-95 C:54-95 D:54-95

(no "Exon" information available for 2Z3J)

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
	(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:127
 aligned with BSD_ASPTE | P0C2P0 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
            BSD_ASPTE     2 PLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVW 128
               SCOP domains d2z3ja_ A: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....eee..hhhhhhhhhhhh...eeeee.....eeeee.hhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:54-95       --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z3j A   2 PLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGKCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVW 128
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with BSD_ASPTE | P0C2P0 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:128
                                    11        21        31        41        51        61        71        81        91       101       111       121        
            BSD_ASPTE     2 PLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVWE 129
               SCOP domains d2z3jb_ B: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....eee..hhhhhhhhhhhh...eeeee.....eeeeehhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:54-95       ---------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z3j B   2 PLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGKCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVWE 129
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain C from PDB  Type:PROTEIN  Length:125
 aligned with BSD_ASPTE | P0C2P0 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:125
                                    12        22        32        42        52        62        72        82        92       102       112       122     
            BSD_ASPTE     3 LSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYV 127
               SCOP domains d2z3jc_ C: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....eee..hhhhhhhhhhhh...eeeee.....eeeee.hhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: C:54-95       -------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z3j C   3 LSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGKCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYV 127
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain D from PDB  Type:PROTEIN  Length:124
 aligned with BSD_ASPTE | P0C2P0 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:124
                                    12        22        32        42        52        62        72        82        92       102       112       122    
            BSD_ASPTE     3 LSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGY 126
               SCOP domains d2z3jd_ D: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -dCMP_cyt_deam_1-2z3jD01 D:4-108                                                                          ------------------ Pfam domains (1)
           Pfam domains (2) -dCMP_cyt_deam_1-2z3jD02 D:4-108                                                                          ------------------ Pfam domains (2)
           Pfam domains (3) -dCMP_cyt_deam_1-2z3jD03 D:4-108                                                                          ------------------ Pfam domains (3)
           Pfam domains (4) -dCMP_cyt_deam_1-2z3jD04 D:4-108                                                                          ------------------ Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhh........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....eee..hhhhhhhhhhhh...eeeee.....eeeeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: D:54-95       ------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z3j D   3 LSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGKCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGY 126
                                    12        22        32        42        52        62        72        82        92       102       112       122

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: Cytidine deaminase (22)

Protein domain: automated matches (9)

Aspergillus terreus [TaxId: 33178] (6)

1a	d2z3ja_	A:
1b	d2z3jc_	C:
1c	d2z3jd_	D:
1d	d2z3jb_	B:

(no "CATH Domain" information available for 2Z3J)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CDA (39)

Family: dCMP_cyt_deam_1 (28)

Aspergillus terreus (5)

1a	dCMP_cyt_deam_1-2z3jD01	D:4-108
1b	dCMP_cyt_deam_1-2z3jD02	D:4-108
1c	dCMP_cyt_deam_1-2z3jD03	D:4-108
1d	dCMP_cyt_deam_1-2z3jD04	D:4-108

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (BSD_ASPTE | P0C2P0)

molecular function
	GO:0047711	blasticidin-S deaminase activity	Catalysis of the reaction: blasticidin S + H2O = deaminohydroxyblasticidin S + NH3.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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