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(-) Description

Title :  BACTERIAL CYTOSINE DEAMINASE D314G MUTANT.
 
Authors :  S. D. Mahan, G. C. Ireton, B. L. Stoddard, M. E. Black
Date :  31 Oct 03  (Deposition) - 05 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Cytosine Deaminase, Hydrolase, Alpha-Beta Barrel, Hexamer, Domain Swap, D314G Mutant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Mahan, G. C. Ireton, C. Knoeber, B. L. Stoddard, M. E. Black
Random Mutagenesis And Selection Of Escherichia Coli Cytosine Deaminase For Cancer Gene Therapy.
Protein Eng. Des. Sel. V. 17 625 2004
PubMed-ID: 15381761  |  Reference-DOI: 10.1093/PROTEIN/GZH074

(-) Compounds

Molecule 1 - CYTOSINE DEAMINASE
    Chains: A
    EC Number: 3.5.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CODA, B0337
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CYTOSINE AMINOHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2GOL1Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GOL6Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:61 , HIS A:63 , HIS A:214 , ASP A:313 , MG A:502 , HOH A:600BINDING SITE FOR RESIDUE FE A 501
2AC2SOFTWAREFE A:501 , HOH A:600 , HOH A:601 , HOH A:602 , HOH A:603 , HOH A:604 , HOH A:605BINDING SITE FOR RESIDUE MG A 502
3AC3SOFTWAREALA A:128 , LYS A:134 , GLU A:171 , ARG A:174 , LEU A:175 , HOH A:801 , HOH A:911 , HOH A:1043BINDING SITE FOR RESIDUE GOL A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R9X)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:72 -Pro A:73
2Tyr A:289 -Pro A:290

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CODA_ECOLI_001 *R13WCODA_ECOLI  ---  ---AR12W
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CODA_ECOLI_001 *R13WCODA_ECOLI  ---  ---AR12W
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R9X)

(-) Exons   (0, 0)

(no "Exon" information available for 1R9X)

(-) Sequences/Alignments

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:423
 aligned with CODA_ECOLI | P25524 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:423
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424   
           CODA_ECOLI     5 ALQTIINARLPGEEGLWQIHLQDGKISAIDAQSGVMPITENSLDAEQGLVIPPFVEPHIHLDTTQTAGQPNWNQSGTLFEGIERWAERKALLTHDDVKQRAWQTLKWQIANGIQHVRTHVDVSDATLTALKAMLEVKQEVAPWIDLQIVAFPQEGILSYPNGEALLEEALRLGADVVGAIPHFEFTREYGVESLHKTFALAQKYDRLIDVHCDEIDDEQSRFVETVAALAHHEGMGARVTASHTTAMHSYNGAYTSRLFRLLKMSGINFVANPLVNIHLQGRFDTYPKRRGITRVKEMLESGINVCFGHDDVFDPWYPLGTANMLQVLHMGLHVCQLMGYGQINDGLNLITHHSARTLNLQDYGIAAGNSANLIILPAENGFDALRRQVPVRYSVRGGKVIASTQPAQTTVYLEQPEAIDYKR 427
               SCOP domains d1r9xa1 A:4-55,A:376-426 Cytosine deaminase         d1r9xa2 A:56-375 Cytosine deaminase catalytic domain                                                                                                                                                                                                                                                                            d1r9xa1 A:4-55,A:376-426 Cytosine deaminase         SCOP domains
               CATH domains 1r9xA01 A:4-56,A:365-426 Urease, subunit C, domain 1 1r9xA02 A:57-364 Metal-dependent hydrolases                                                                                                                                                                                                                                                                         1r9xA01 A:4-56,A:365-426 Urease, subunit C, domain 1           CATH domains
               Pfam domains ------------------------------------------------Amidohydro_3-1r9xA01 A:52-378                                                                                                                                                                                                                                                                                                          ------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.......eeeeeee..eeeeeeee.........eee....eee..eeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.....hhhhhhhhhhhhhhh...eeeeeee.........hhhhhhhhhhhh...eeeehhhhh.hhhhhhhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhh.............hhhhhhhhh..eee...............hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..............eeee...hhhhhhhhh....eeee..eeeee.....eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) --------W------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r9x A   4 ALQTIINARLPGEEGLWQIHLQDGKISAIDAQSGVMPITENSLDAEQGLVIPPFVEPHIHLDTTQTAGQPNWNQSGTLFEGIERWAERKALLTHDDVKQRAWQTLKWQIANGIQHVRTHVDVSDATLTALKAMLEVKQEVAPWIDLQIVAFPQEGILSYPNGEALLEEALRLGADVVGAIPHFEFTREYGVESLHKTFALAQKYDRLIDVHCDEIDDEQSRFVETVAALAHHEGMGARVTASHTTAMHSYNGAYTSRLFRLLKMSGINFVANPLVNIHLQGRFDTYPKRRGITRVKEMLESGINVCFGHDGVFDPWYPLGTANMLQVLHMGLHVCQLMGYGQINDGLNLITHHSARTLNLQDYGIAAGNSANLIILPAENGFDALRRQVPVRYSVRGGKVIASTQPAQTTVYLEQPEAIDYKR 426
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423
   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  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (CODA_ECOLI | P25524)
molecular function
    GO:0004131    cytosine deaminase activity    Catalysis of the reaction: cytosine + H2O = uracil + NH3.
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0035888    isoguanine deaminase activity    Catalysis of the reaction: isoguanine + H2O = xanthine + NH3.
    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:0006209    cytosine catabolic process    The chemical reactions and pathways resulting in the breakdown of cytosine, 4-amino-2-hydroxypyrimidine, a pyrimidine derivative that is one of the five main bases found in nucleic acids; it occurs widely in cytidine derivatives.
    GO:0019858    cytosine metabolic process    The chemical reactions and pathways involving cytosine, 4-amino-2-hydroxypyrimidine, a pyrimidine derivative that is one of the five main bases found in nucleic acids; it occurs widely in cytidine derivatives.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CODA_ECOLI | P25524: 1k6w 1k70 1r9y 1r9z 1ra0 1ra5 1rak 3g77 3o7u 3r0d 3rn6

(-) Related Entries Specified in the PDB File

1k6w 1r9y 1r9z 1ra0 1ra5 1rak 1rb7