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(-) Description

Title :  1.6 A CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE FROM BURKHOLDERIA PSEUDOMALLEI
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Date :  01 Jul 08  (Deposition) - 15 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Burkholderia, Pseudomallei, Cytidine, Deaminase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
1. 6 A Crystal Structure Of Cytidine Deaminase From Burkholderia Pseudomallei
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTIDINE DEAMINASE
    Chains: A, B, C, D
    EC Number: 3.5.4.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BG1861RC
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: CDD, BPSS1959
    Organism Common: PSEUDOMONAS PSEUDOMALLEI
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 28450
    Strain: 1710B

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1MRD4Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
2PO41Ligand/IonPHOSPHATE ION
3ZN4Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS D:53 , CYS D:88 , CYS D:91BINDING SITE FOR RESIDUE ZN D 131
2AC2SOFTWARECYS C:53 , CYS C:88 , CYS C:91BINDING SITE FOR RESIDUE ZN C 131
3AC3SOFTWARECYS B:53 , CYS B:88 , CYS B:91BINDING SITE FOR RESIDUE ZN B 131
4AC4SOFTWARECYS A:53 , CYS A:88 , CYS A:91BINDING SITE FOR RESIDUE ZN A 131
5AC5SOFTWARETHR B:2 , HIS B:3BINDING SITE FOR RESIDUE PO4 B 132
6AC6SOFTWARELEU A:129 , ALA B:46 , SER B:47 , TYR B:48 , PHE D:24 , ASN D:42 , GLU D:44 , CYS D:51BINDING SITE FOR RESIDUE MRD D 132
7AC7SOFTWAREASN A:42 , GLU A:44 , ALA C:46 , SER C:47 , TYR C:48 , LEU D:129BINDING SITE FOR RESIDUE MRD A 132
8AC8SOFTWAREALA A:46 , SER A:47 , TYR A:48 , ASN C:42 , GLU C:44BINDING SITE FOR RESIDUE MRD C 132
9AC9SOFTWAREASN B:42 , GLU B:44 , ALA D:46 , SER D:47 , TYR D:48BINDING SITE FOR RESIDUE MRD B 133

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DMO)

(-) Exons   (0, 0)

(no "Exon" information available for 3DMO)

(-) 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:133
 aligned with Q3JJN0_BURP1 | Q3JJN0 from UniProtKB/TrEMBL  Length:130

    Alignment length:133
                               1                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127   
         Q3JJN0_BURP1     - ---MTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAFYLA 130
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dmoA00 A:-2-130 Cytidine Deaminase, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh......eeeeeeee........hhhhhhhhhhhhh...eeeee.....eeeeehhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dmo A  -2 HHHMTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAFYLA 130
                                     7        17        27        37        47        57        67        77        87        97       107       117       127   


Chain A from PDB  Type:PROTEIN  Length:133
 aligned with Q63IV7_BURPS | Q63IV7 from UniProtKB/TrEMBL  Length:130

    Alignment length:133
                               1                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127   
         Q63IV7_BURPS     - ---MTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAFYLA 130
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dmoA00 A:-2-130 Cytidine Deaminase, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh......eeeeeeee........hhhhhhhhhhhhh...eeeee.....eeeeehhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dmo A  -2 HHHMTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAFYLA 130
                                     7        17        27        37        47        57        67        77        87        97       107       117       127   


Chain B from PDB  Type:PROTEIN  Length:127
 aligned with Q3JJN0_BURP1 | Q3JJN0 from UniProtKB/TrEMBL  Length:130

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
         Q3JJN0_BURP1     1 MTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAF 127
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dmoB00 B:1-127 Cytidine Deaminase, domain 2                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh......eeeeeeee........hhhhhhhhhhhhh...eeeeee....eeeeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dmo B   1 MTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAF 127
                                    10        20        30        40        50        60        70        80        90       100       110       120       


Chain B from PDB  Type:PROTEIN  Length:127
 aligned with Q63IV7_BURPS | Q63IV7 from UniProtKB/TrEMBL  Length:130

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
         Q63IV7_BURPS     1 MTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAF 127
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dmoB00 B:1-127 Cytidine Deaminase, domain 2                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh......eeeeeeee........hhhhhhhhhhhhh...eeeeee....eeeeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dmo B   1 MTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAF 127
                                    10        20        30        40        50        60        70        80        90       100       110       120       


Chain C from PDB  Type:PROTEIN  Length:127
 aligned with Q3JJN0_BURP1 | Q3JJN0 from UniProtKB/TrEMBL  Length:130

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
         Q3JJN0_BURP1     1 MTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAF 127
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dmoC00 C:1-127 Cytidine Deaminase, domain 2                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh......eeeeeeee........hhhhhhhhhhhhh...eeeeee....eeeeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dmo C   1 MTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAF 127
                                    10        20        30        40        50        60        70        80        90       100       110       120       


Chain C from PDB  Type:PROTEIN  Length:127
 aligned with Q63IV7_BURPS | Q63IV7 from UniProtKB/TrEMBL  Length:130

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
         Q63IV7_BURPS     1 MTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAF 127
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dmoC00 C:1-127 Cytidine Deaminase, domain 2                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...........eeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh......eeeeeeee........hhhhhhhhhhhhh...eeeeee....eeeeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dmo C   1 MTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAF 127
                                    10        20        30        40        50        60        70        80        90       100       110       120       


Chain D from PDB  Type:PROTEIN  Length:133
 aligned with Q3JJN0_BURP1 | Q3JJN0 from UniProtKB/TrEMBL  Length:130

    Alignment length:133
                               1                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127   
         Q3JJN0_BURP1     - ---MTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAFYLA 130
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dmoD00 D:-2-130 Cytidine Deaminase, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh......eeeeeeee........hhhhhhhhhhhhh...eeeee.....eeeeehhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dmo D  -2 HHHMTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAFYLA 130
                                     7        17        27        37        47        57        67        77        87        97       107       117       127   


Chain D from PDB  Type:PROTEIN  Length:133
 aligned with Q63IV7_BURPS | Q63IV7 from UniProtKB/TrEMBL  Length:130

    Alignment length:133
                               1                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127   
         Q63IV7_BURPS     - ---MTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAFYLA 130
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dmoD00 D:-2-130 Cytidine Deaminase, domain 2                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh......eeeeeeee........hhhhhhhhhhhhh...eeeee.....eeeeehhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dmo D  -2 HHHMTHHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSALAAGYRPGEFAAIAVVGETHGPIAPCGACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLLPDAFYLA 130
                                     7        17        27        37        47        57        67        77        87        97       107       117       127
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3DMO)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q63IV7_BURPS | Q63IV7)
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:0004126    cytidine deaminase activity    Catalysis of the reaction: cytidine + H2O = uridine + NH3.
    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.
biological process
    GO:0009972    cytidine deamination    The removal of amino group in the presence of water.

Chain A,B,C,D   (Q3JJN0_BURP1 | Q3JJN0)
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:0004126    cytidine deaminase activity    Catalysis of the reaction: cytidine + H2O = uridine + NH3.
    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:0009972    cytidine deamination    The removal of amino group in the presence of water.

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