2Z3I - JenaLib

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Title :   CRYSTAL STRUCTURE OF BLASTICIDIN S DEAMINASE (BSD) MUTANT E56Q COMPLEXED WITH SUBSTRATE

Authors :   T. Kumasaka, M. Yamamoto, M. Furuichi, M. Nakasako, M. Kimura, I. Yamag T. Ueki

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

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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, 12)

No.	Name	Count	Type	Full Name
1	BLS	4	Ligand/Ion	BLASTICIDIN S
2	CAC	4	Ligand/Ion	CACODYLATE ION
3	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:25 , ASP A:26 , SER A:28 , VAL A:29 , ASN A:45 , TYR A:47 , CYS A:54 , ALA A:55 , GLN A:56 , ARG A:82 , SER A:86 , PRO A:87 , CYS A:88 , HOH A:3002 , HOH A:3091 , HOH A:3093 , HOH A:3138 , TYR B:126 , TRP B:128 , HOH B:3028 , TRP D:128 , GLY D:130	BINDING SITE FOR RESIDUE BLS A 2500
02	AC2	SOFTWARE	TYR A:126 , TRP A:128 , GLU B:25 , ASP B:26 , SER B:28 , VAL B:29 , ASN B:45 , TYR B:47 , CYS B:54 , ALA B:55 , GLN B:56 , ARG B:82 , SER B:86 , PRO B:87 , CYS B:88 , HOH B:3015 , HOH B:3088 , HOH B:3113 , HOH B:3137 , TRP C:128	BINDING SITE FOR RESIDUE BLS B 2501
03	AC3	SOFTWARE	GLY B:130 , GLU C:25 , ASP C:26 , SER C:28 , VAL C:29 , ASN C:45 , TYR C:47 , CYS C:54 , ALA C:55 , GLN C:56 , ARG C:82 , SER C:86 , PRO C:87 , CYS C:88 , HOH C:3028 , HOH C:3078 , HOH C:3098 , HOH C:3105 , HOH C:3133 , HOH C:3149 , TYR D:126 , TRP D:128	BINDING SITE FOR RESIDUE BLS C 2502
04	AC4	SOFTWARE	TRP A:128 , GLU A:129 , TYR C:126 , TRP C:128 , GLU C:129 , GLU D:25 , ASP D:26 , SER D:28 , VAL D:29 , ASN D:45 , TYR D:47 , CYS D:54 , ALA D:55 , GLN D:56 , ARG D:82 , SER D:86 , PRO D:87 , CYS D:88 , HOH D:3089 , HOH D:3093 , HOH D:3132 , HOH D:3139	BINDING SITE FOR RESIDUE BLS D 2503
05	AC5	SOFTWARE	CYS A:54 , CYS A:88 , CYS A:91 , HOH A:3063 , HOH A:3138	BINDING SITE FOR RESIDUE ZN A 2001
06	AC6	SOFTWARE	SER A:4 , GLU A:7 , CYS A:73 , ALA A:115	BINDING SITE FOR RESIDUE CAC A 3001
07	AC7	SOFTWARE	CYS B:54 , CYS B:88 , CYS B:91 , HOH B:3047 , HOH B:3141	BINDING SITE FOR RESIDUE ZN B 2002
08	AC8	SOFTWARE	SER B:4 , GLU B:7 , THR B:72 , CYS B:73 , LYS B:103 , ALA B:115 , HOH B:3021	BINDING SITE FOR RESIDUE CAC B 3002
09	AC9	SOFTWARE	CYS C:54 , CYS C:88 , CYS C:91 , HOH C:3063 , HOH C:3149	BINDING SITE FOR RESIDUE ZN C 2003
10	BC1	SOFTWARE	GLU C:7 , CYS C:73 , ILE C:105 , ALA C:115	BINDING SITE FOR RESIDUE CAC C 3003
11	BC2	SOFTWARE	CYS D:54 , CYS D:88 , CYS D:91 , HOH D:3049 , HOH D:3139	BINDING SITE FOR RESIDUE ZN D 2004
12	BC3	SOFTWARE	GLU D:6 , GLU D:7 , CYS D:73 , LYS D:103 , ALA D:115	BINDING SITE FOR RESIDUE CAC D 3004

(no "SS Bond" information available for 2Z3I)

(no "Cis Peptide Bond" information available for 2Z3I)

(no "SAP(SNP)/Variant" information available for 2Z3I)

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 2Z3I)

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:129
 aligned with BSD_ASPTE | P0C2P0 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
            BSD_ASPTE     2 PLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVWEG 130
               SCOP domains d2z3ia_ A: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.......eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....eee..hhhhhhhhhhhh...eeeee.....eeeeehhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:54-95       ----------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z3i A   2 PLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAQLVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVWEG 130
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with BSD_ASPTE | P0C2P0 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
            BSD_ASPTE     2 PLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVWEG 130
               SCOP domains d2z3ib_ B: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.........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
                 2z3i B   2 PLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAQLVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVWEG 130
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with BSD_ASPTE | P0C2P0 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
            BSD_ASPTE     2 PLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVWEG 130
               SCOP domains d2z3ic_ C: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         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: C:54-95       ----------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z3i C   2 PLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAQLVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVWEG 130
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain D from PDB  Type:PROTEIN  Length:129
 aligned with BSD_ASPTE | P0C2P0 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
            BSD_ASPTE     2 PLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVWEG 130
               SCOP domains d2z3id_ D: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --dCMP_cyt_deam_1-2z3iD01 D:4-108                                                                          ---------------------- Pfam domains (1)
           Pfam domains (2) --dCMP_cyt_deam_1-2z3iD02 D:4-108                                                                          ---------------------- Pfam domains (2)
           Pfam domains (3) --dCMP_cyt_deam_1-2z3iD03 D:4-108                                                                          ---------------------- Pfam domains (3)
           Pfam domains (4) --dCMP_cyt_deam_1-2z3iD04 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
                 2z3i D   2 PLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAQLVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVWEG 130
                                    11        21        31        41        51        61        71        81        91       101       111       121

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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	d2z3ia_	A:
1b	d2z3ib_	B:
1c	d2z3ic_	C:
1d	d2z3id_	D:

(no "CATH Domain" information available for 2Z3I)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CDA (39)

Family: dCMP_cyt_deam_1 (28)

Aspergillus terreus (5)

1a	dCMP_cyt_deam_1-2z3iD01	D:4-108
1b	dCMP_cyt_deam_1-2z3iD02	D:4-108
1c	dCMP_cyt_deam_1-2z3iD03	D:4-108
1d	dCMP_cyt_deam_1-2z3iD04	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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	2z3i
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	3.5.4.23
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	BSD_ASPTE \| P0C2P0	:	1wn5 1wn6 2z3g 2z3h 2z3j

Description

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Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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