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(-) Description

Title :  CYTIDINE AND DEOXYCYTIDYLATE DEAMINASE ZINC-BINDING REGION FROM NITROSOMONAS EUROPAEA.
 
Authors :  J. Osipiuk, T. Skarina, O. Onopriyenko, A. Savchenko, A. Edwards, A. Jo Midwest Center For Structural Genomics (Mcsg)
Date :  01 Mar 06  (Deposition) - 04 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cytidine And Deoxycytidylate Deaminase, Zinc-Binding Region, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, T. Skarina, O. Onopriyenko, A. Savchenko, A. Edwards, A. Joachimiak
X-Ray Crystal Structure Of Cytidine And Deoxycytidylate Deaminase Zinc-Binding Region From Nitrosomonas Europaea.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYTIDINE AND DEOXYCYTIDYLATE DEAMINASE ZINC-BINDING REGION
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NE0047
    Organism Scientific: NITROSOMONAS EUROPAEA
    Organism Taxid: 228410
    Strain: ATCC 19718

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2EDO3Ligand/Ion1,2-ETHANEDIOL
3NA1Ligand/IonSODIUM ION
4ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:77 , CYS A:112 , CYS A:115 , HOH A:714BINDING SITE FOR RESIDUE ZN A 506
2AC2SOFTWAREHIS B:77 , CYS B:112 , CYS B:115 , HOH B:703BINDING SITE FOR RESIDUE ZN B 507
3AC3SOFTWAREGLU B:155 , VAL B:161 , HOH B:519 , HOH B:669 , HOH B:698BINDING SITE FOR RESIDUE NA B 508
4AC4SOFTWAREPHE A:48 , GLU A:79 , GLU A:110 , GLU A:143 , HOH A:532 , HOH A:545 , HOH A:617 , HOH A:714BINDING SITE FOR RESIDUE EDO A 501
5AC5SOFTWAREGLY B:8 , ARG B:67 , PRO B:70 , GLY B:71 , HOH B:675BINDING SITE FOR RESIDUE EDO B 502
6AC6SOFTWAREPHE B:48 , GLU B:79 , GLU B:110 , GLU B:143 , HOH B:524 , HOH B:533 , HOH B:630 , HOH B:703BINDING SITE FOR RESIDUE EDO B 503
7AC7SOFTWAREASP A:135 , CYS A:171 , ARG A:175 , HOH A:675 , HOH A:678 , HOH A:700BINDING SITE FOR RESIDUE BME A 504
8AC8SOFTWAREASP B:135 , CYS B:171 , HOH B:553 , HOH B:569 , HOH B:708BINDING SITE FOR RESIDUE BME B 505

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:180 -A:189

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G84)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G84)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2G84)

(-) Exons   (0, 0)

(no "Exon" information available for 2G84)

(-) 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:189
 aligned with Q82Y41_NITEU | Q82Y41 from UniProtKB/TrEMBL  Length:193

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
         Q82Y41_NITEU     1 MNDALHIGLPPFLVQANNEPRVLAAPEARMGYVLELVRANIAADGGPFAAAVFERDSGLLIAAGTNRVVPGRCSAAHAEILALSLAQAKLDTHDLSADGLPACELVTSAEPCVMCFGAVIWSGVRSLVCAARSDDVEAIGFDEGPRPENWMGGLEARGITVTTGLLRDAACALLREYNACNGVIYNARC 189
               SCOP domains d2g84a1 A:1-189 Putative deaminase NE0047                                                                                                                                                     SCOP domains
               CATH domains --------2g84A01 A:9-181 Cytidine Deaminase, domain 2                                                                                                                                 -------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeee...........hhhhhhhhhhhhhhh...........eeeeeee..hhhhhhhhhhhh..eeeeeehhhhhhhh.........hhhhhhhhh..eee...hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g84 A   1 MNDALHIGLPPFLVQANNEPRVLAAPEARMGYVLELVRANIAADGGPFAAAVFERDSGLLIAAGTNRVVPGRCSAAHAEILALSLAQAKLDTHDLSADGLPACELVTSAEPCVMCFGAVIWSGVRSLVCAARSDDVEAIGFDEGPRPENWMGGLEARGITVTTGLLRDAACALLREYNACNGVIYNARC 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         


Chain B from PDB  Type:PROTEIN  Length:182
 aligned with Q82Y41_NITEU | Q82Y41 from UniProtKB/TrEMBL  Length:193

    Alignment length:182
                              1                                                                                                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178  
         Q82Y41_NITEU     - --MNDALHIGLPPFLVQANNEPRVLAAPEARMGYVLELVRANIAADGGPFAAAVFERDSGLLIAAGTNRVVPGRCSAAHAEILALSLAQAKLDTHDLSADGLPACELVTSAEPCVMCFGAVIWSGVRSLVCAARSDDVEAIGFDEGPRPENWMGGLEARGITVTTGLLRDAACALLREYNAC 180
               SCOP domains d2g84b_ B: Putative deaminase NE0047                                                                                                                                                   SCOP domains
               CATH domains 2g84B00 B:-1-180 Cytidine Deaminase, domain 2                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeee...........hhhhhhhhhhhhhhh...........eeeeeee..hhhhhhhhhhhh..eeeeeehhhhhhh..........hhhhhhhhh..eee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g84 B  -1 GHMNDALHIGLPPFLVQANNEPRVLAAPEARMGYVLELVRANIAADGGPFAAAVFERDSGLLIAAGTNRVVPGRCSAAHAEILALSLAQAKLDTHDLSADGLPACELVTSAEPCVMCFGAVIWSGVRSLVCAARSDDVEAIGFDEGPRPENWMGGLEARGITVTTGLLRDAACALLREYNAC 180
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178
   Legend:   → Mismatch (orange background)
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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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G84)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q82Y41_NITEU | Q82Y41)
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: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.

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 Related Entries

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        Q82Y41_NITEU | Q82Y41: 4hrq 4hrw 4lc5 4lcn 4lco 4lcp 4ld2 4ld4

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