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(-) Description

Title :  CRYSTAL STRUCTURE OF BLASTICIDIN S DEAMINASE FROM COCCIDIOIDES IMMITIS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  20 Aug 10  (Deposition) - 15 Sep 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ssgcid, Blasticidin S Deaminase, Seattle Structural Genomics Center For Infectious Disease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Ssgcid, J. Abendroth, A. S. Gardberg, B. Staker
Crystal Structure Of Blasticidin S Deaminase From Coccidioides Immitis
To Be Published
PubMed: search

(-) Compounds

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: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: COCCIDIOIDES IMMITIS
    Organism Taxid: 5501

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3ZN4Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:57 , CYS A:91 , CYS A:94 , EDO A:151BINDING SITE FOR RESIDUE ZN A 150
02AC2SOFTWARECYS B:57 , CYS B:91 , CYS B:94 , EDO B:151BINDING SITE FOR RESIDUE ZN B 150
03AC3SOFTWARECYS C:57 , CYS C:91 , CYS C:94 , EDO C:151BINDING SITE FOR RESIDUE ZN C 150
04AC4SOFTWARECYS D:57 , CYS D:91 , CYS D:94 , EDO D:151BINDING SITE FOR RESIDUE ZN D 150
05AC5SOFTWAREASN A:53 , GLY A:54 , ARG A:93 , ASN B:53 , ARG B:93 , ASN C:53 , GLY C:54 , ARG C:93 , ASN D:53 , ARG D:93BINDING SITE FOR RESIDUE CL C 138
06AC6SOFTWAREVAL A:32 , CYS A:57 , GLU A:59 , ALA A:79 , PRO A:90 , CYS A:91 , CYS A:94 , HOH A:145 , ZN A:150BINDING SITE FOR RESIDUE EDO A 151
07AC7SOFTWAREVAL B:32 , CYS B:57 , GLU B:59 , ALA B:79 , PRO B:90 , CYS B:91 , CYS B:94 , ZN B:150 , HOH B:243BINDING SITE FOR RESIDUE EDO B 151
08AC8SOFTWAREVAL C:32 , CYS C:57 , GLU C:59 , ALA C:79 , PRO C:90 , CYS C:91 , CYS C:94 , ZN C:150 , HOH C:154BINDING SITE FOR RESIDUE EDO C 151
09AC9SOFTWAREVAL D:32 , CYS D:57 , GLU D:59 , ALA D:79 , SER D:89 , PRO D:90 , CYS D:91 , CYS D:94 , HOH D:141 , ZN D:150BINDING SITE FOR RESIDUE EDO D 151
10BC1SOFTWAREVAL D:43 , PHE D:44 , SER D:45 , VAL D:65 , HOH D:383BINDING SITE FOR RESIDUE EDO D 152

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OJ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OJ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OJ6)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.BSD_COCIM57-98
 
 
 		  4A:57-98
B:57-98
C:57-98
D:57-98

(-) Exons   (0, 0)

(no "Exon" information available for 3OJ6)

(-) Sequences/Alignments

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:134
 aligned with BSD_COCIM | P0CI02 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:134
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    
            BSD_COCIM     4 EPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWDKDYDRI 137
               SCOP domains d3oj6a_ A: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....eee..hhhhhhhhhhhh...eeee......eeee.hhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:57-98       --------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oj6 A   4 EPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWDKDYDRI 137
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    


Chain A from PDB  Type:PROTEIN  Length:134
 aligned with E1C9L5_COCIT | E1C9L5 from UniProtKB/TrEMBL  Length:150

    Alignment length:134
                                    26        36        46        56        66        76        86        96       106       116       126       136       146    
         E1C9L5_COCIT    17 EPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWDKDYDRI 150
               SCOP domains d3oj6a_ A: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....eee..hhhhhhhhhhhh...eeee......eeee.hhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oj6 A   4 EPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWDKDYDRI 137
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    


Chain B from PDB  Type:PROTEIN  Length:134
 aligned with BSD_COCIM | P0CI02 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:135
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     
            BSD_COCIM     2 APEPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWDKDYDR 136
               SCOP domains d3oj6b_ B: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhhhhhh........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....eee..hhhhhhhhhhhh...eeee......eeee.hhhh.......-.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:57-98       -------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oj6 B   2 APEPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWD-DYDR 136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 |   
                                                                                                                                                           131 |   
                                                                                                                                                             133   


Chain B from PDB  Type:PROTEIN  Length:134
 aligned with E1C9L5_COCIT | E1C9L5 from UniProtKB/TrEMBL  Length:150

    Alignment length:135
                                    24        34        44        54        64        74        84        94       104       114       124       134       144     
         E1C9L5_COCIT    15 APEPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWDKDYDR 149
               SCOP domains d3oj6b_ B: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhhhhhh........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....eee..hhhhhhhhhhhh...eeee......eeee.hhhh.......-.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oj6 B   2 APEPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWD-DYDR 136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 |   
                                                                                                                                                           131 |   
                                                                                                                                                             133   


Chain C from PDB  Type:PROTEIN  Length:128
 aligned with BSD_COCIM | P0CI02 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:128
                                    13        23        33        43        53        63        73        83        93       103       113       123        
            BSD_COCIM     4 EPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWD 131
               SCOP domains d3oj6c_ C: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....eee..hhhhhhhhhhhh...eeeeee..eeeeee.hhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: C:57-98       --------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oj6 C   4 EPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWD 131
                                    13        23        33        43        53        63        73        83        93       103       113       123        


Chain C from PDB  Type:PROTEIN  Length:128
 aligned with E1C9L5_COCIT | E1C9L5 from UniProtKB/TrEMBL  Length:150

    Alignment length:128
                                    26        36        46        56        66        76        86        96       106       116       126       136        
         E1C9L5_COCIT    17 EPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWD 144
               SCOP domains d3oj6c_ C: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....eee..hhhhhhhhhhhh...eeeeee..eeeeee.hhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oj6 C   4 EPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWD 131
                                    13        23        33        43        53        63        73        83        93       103       113       123        


Chain D from PDB  Type:PROTEIN  Length:134
 aligned with BSD_COCIM | P0CI02 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:134
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    
            BSD_COCIM     4 EPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWDKDYDRI 137
               SCOP domains d3oj6d_ D: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....eee..hhhhhhhhhhhh...eeee......eeee.hhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: D:57-98       --------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oj6 D   4 EPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWDKDYDRI 137
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    


Chain D from PDB  Type:PROTEIN  Length:134
 aligned with E1C9L5_COCIT | E1C9L5 from UniProtKB/TrEMBL  Length:150

    Alignment length:134
                                    26        36        46        56        66        76        86        96       106       116       126       136       146    
         E1C9L5_COCIT    17 EPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWDKDYDRI 150
               SCOP domains d3oj6d_ D: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh........eeeeeee....eeeee.........hhhhhhhhhhhhh....eeeeeeee....eee..hhhhhhhhhhhh...eeee......eeee.hhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oj6 D   4 EPLSAAGQNLIDTATSVINGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGGPCAELVVLGVAAAAGATKLTHIVAIANEGRGILSPCGRCRQVLADLHPGIKAIVIGKEGPKMVAVEELLPSIYAWDKDYDRI 137
                                    13        23        33        43        53        63        73        83        93       103       113       123       133
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OJ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3OJ6)

(-) Gene Ontology  (6, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (BSD_COCIM | P0CI02)
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,C,D   (E1C9L5_COCIT | E1C9L5)
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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.

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 Related Entries

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