1WN6 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BLASTICIDIN S DEAMINASE (BSD) COMPLEXED WITH TETRAHEDRAL INTERMEDIATE OF BLASTICIDIN S

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

Date :   27 Jul 04 (Deposition) - 25 Oct 05 (Release) - 29 Apr 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Hydrolase, Cytidine Deaminase Family, Zinc, 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
	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
	Organism Scientific	:	ASPERGILLUS TERREUS
	Organism Taxid	:	33178
	Strain	:	S-712

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ARS	2	Ligand/Ion	ARSENIC
2	BST	2	Ligand/Ion	6-(4-AMINO-4-HYDROXY-2-OXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-3-[3-AMINO-5-(N-METHYL-GUANIDINO)-PENTANOYLAMINO]-3,6-DIHYDRO-2H-PYRAN-2-CARBOXYLIC ACID
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	ARS	4	Ligand/Ion	ARSENIC
2	BST	4	Ligand/Ion	6-(4-AMINO-4-HYDROXY-2-OXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-3-[3-AMINO-5-(N-METHYL-GUANIDINO)-PENTANOYLAMINO]-3,6-DIHYDRO-2H-PYRAN-2-CARBOXYLIC ACID
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:54 , CYS A:88 , CYS A:91 , BST A:1003 , HOH A:1021	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	CYS B:54 , CYS B:88 , CYS B:91 , BST B:1004 , HOH B:1011	BINDING SITE FOR RESIDUE ZN B 1002
3	AC3	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 , GLU A:56 , ARG A:82 , SER A:86 , PRO A:87 , CYS A:88 , CYS A:91 , TYR A:126 , TRP A:128 , ZN A:1001 , HOH A:1008 , HOH A:1066 , HOH A:1074 , TRP B:128	BINDING SITE FOR RESIDUE BST A 1003
4	AC4	SOFTWARE	GLU A:7 , CYS A:73	BINDING SITE FOR RESIDUE ARS A 1005
5	AC5	SOFTWARE	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 , GLU B:56 , ARG B:82 , SER B:86 , PRO B:87 , CYS B:88 , CYS B:91 , TYR B:126 , TRP B:128 , ZN B:1002 , HOH B:1063 , HOH B:1088 , HOH B:1096	BINDING SITE FOR RESIDUE BST B 1004
6	AC6	SOFTWARE	GLU B:7 , CYS B:73 , ILE B:105	BINDING SITE FOR RESIDUE ARS B 1006

(no "SS Bond" information available for 1WN6)

(no "Cis Peptide Bond" information available for 1WN6)

(no "SAP(SNP)/Variant" information available for 1WN6)

Asymmetric Unit (1, 2)

	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	2	A:54-95 B:54-95
1	CYT_DCMP_DEAMINASES_1	PS00903		BSD_ASPTN	54-95	2	A:54-95 B:54-95

Biological Unit 1 (1, 8)

	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
1	CYT_DCMP_DEAMINASES_1	PS00903		BSD_ASPTN	54-95	4	A:54-95 B:54-95

(no "Exon" information available for 1WN6)

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:126
 aligned with BSD_ASPTE | P0C2P0 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:126
                                    13        23        33        43        53        63        73        83        93       103       113       123      
            BSD_ASPTE     4 SQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVWE 129
               SCOP domains d1wn6a_ A: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....ee...hhhhhhhhhhhh...eeeee.....eeeeehhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:54-95       ---------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wn6 A   4 SQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVWE 129
                                    13        23        33        43        53        63        73        83        93       103       113       123

Chain A from PDB  Type:PROTEIN  Length:126
 aligned with BSD_ASPTN | P0C2P1 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:126
                                    13        23        33        43        53        63        73        83        93       103       113       123      
            BSD_ASPTN     4 SQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAVVKDSDGQPTAVGIRELLPSGYMNR 129
               SCOP domains d1wn6a_ A: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....ee...hhhhhhhhhhhh...eeeee.....eeeeehhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:54-95       ---------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wn6 A   4 SQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVWE 129
                                    13        23        33        43        53        63        73        83        93       103       113       123

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with BSD_ASPTE | P0C2P0 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:126
                                    12        22        32        42        52        62        72        82        92       102       112       122      
            BSD_ASPTE     3 LSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVW 128
               SCOP domains d1wn6b_ B: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....ee...hhhhhhhhhhhh...eeeee.....eeeeehhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:54-95       --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wn6 B   3 LSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVW 128
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with BSD_ASPTN | P0C2P1 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:126
                                    12        22        32        42        52        62        72        82        92       102       112       122      
            BSD_ASPTN     3 LSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAVVKDSDGQPTAVGIRELLPSGYMN 128
               SCOP domains d1wn6b_ B: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....ee...hhhhhhhhhhhh...eeeee.....eeeeehhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:54-95       --------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wn6 B   3 LSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGVNVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIKAIVKDSDGQPTAVGIRELLPSGYVW 128
                                    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 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	d1wn6a_	A:
1b	d1wn6b_	B:

(no "CATH Domain" information available for 1WN6)

(no "Pfam Domain" information available for 1WN6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BSD_ASPTN | P0C2P1)

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.

Chain A,B (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 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
		ARS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		BST	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wn6)

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	1wn6
		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
	BSD_ASPTE \| P0C2P0
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	BSD_ASPTN \| P0C2P1
		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)
	3.5.4.23
		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
	BSD_ASPTE \| P0C2P0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	BSD_ASPTN \| P0C2P1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	BSD_ASPTE \| P0C2P0	:	1wn5 2z3g 2z3h 2z3i 2z3j
	BSD_ASPTN \| P0C2P1	:	1wn5

1af2
1jtk
1wn5	THE SAME PROTEIN COMPLEXED WITH CACODYLIC ACID

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 12)

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