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(-) Description

Title :  CRYSTAL STRUCTURE OF NE0047 IN COMPLEX WITH CYTOSINE
 
Authors :  A. Bitra, A. Biswas, R. Anand
Date :  24 Jun 13  (Deposition) - 22 Jan 14  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cda Fold, Deaminase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bitra, A. Biswas, R. Anand
Structural Basis Of The Substrate Specificity Of Cytidine Deaminase Superfamily Guanine Deaminase
Biochemistry V. 52 8106 2013
PubMed-ID: 24083949  |  Reference-DOI: 10.1021/BI400818E

(-) Compounds

Molecule 1 - CYTIDINE AND DEOXYCYTIDYLATE DEAMINASE ZINC-BINDING REGION
    Chains: A, B
    EC Number: 3.5.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NE0047
    Organism Scientific: NITROSOMONAS EUROPAEA
    Organism Taxid: 228410
    Strain: ATCC 19718 / NBRC 14298

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CYT1Ligand/Ion6-AMINOPYRIMIDIN-2(1H)-ONE
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:77 , CYS A:112 , CYS A:115BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREHIS B:77 , CYS B:112 , CYS B:115 , HOH B:307BINDING SITE FOR RESIDUE ZN B 201
3AC3SOFTWAREPHE B:48 , ASN B:66 , HIS B:77 , ASP B:142 , GLU B:143 , HOH B:307BINDING SITE FOR RESIDUE CYT B 202

(-) 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 4LD4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LD4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LD4)

(-) Exons   (0, 0)

(no "Exon" information available for 4LD4)

(-) 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
                                                                                                                                                                                                                             
               SCOP domains d4ld4a_ A: Putative deaminase NE0047                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhhhh.....eeeee......eeeeee.hhhhhh....hhhhhhhhhhhhhh.............eeeeee..hhhhhhhhhhhh..eeeeeehhhhhhh..........hhhhhhhhh..eee...hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ld4 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
                                                                                                                                                                                                                      
               SCOP domains d4ld4b_ B: Putative deaminase NE0047                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhhhh..eeeeeeeee.....eeeeeee..........hhhhhhhhhhhhhh............eeeeeee..hhhhhhhhhhhh..eeeeeehhhhhhh..........hhhhhhhhh..eee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ld4 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  (0, 0)

(no "CATH Domain" information available for 4LD4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LD4)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q82Y41_NITEU | Q82Y41: 2g84 4hrq 4hrw 4lc5 4lcn 4lco 4lcp 4ld2

(-) Related Entries Specified in the PDB File

2g84 4hrq 4hrw 4lc5 4lcn 4lco 4ld2 4ldp