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(-) Description

Title :  CRYTSAL STRUCTURE OF NE0047 IN COMPLEX WITH 2'-DEOXY-GUANOSINE
 
Authors :  R. Anand, A. Bitra, A. Biswas
Date :  22 Jun 13  (Deposition) - 22 Jan 14  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2GNG1Ligand/Ion2'-DEOXY-GUANOSINE
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:77 , CYS A:112 , CYS A:115 , HOH A:362BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREPHE A:48 , ASN A:66 , HIS A:77 , ALA A:78 , GLU A:79 , ALA A:109 , GLU A:110 , CYS A:112 , PHE A:141 , ASP A:142 , EDO A:203 , HOH A:314 , HOH A:362 , TRP B:121BINDING SITE FOR RESIDUE GNG A 202
3AC3SOFTWAREASN A:66 , GNG A:202 , HOH A:363BINDING SITE FOR RESIDUE EDO A 203
4AC4SOFTWAREHIS B:77 , CYS B:112 , CYS B:115 , HOH B:303BINDING SITE FOR RESIDUE ZN B 201
5AC5SOFTWAREGLY B:8 , ARG B:67 , GLY B:71 , HOH B:376 , HOH B:380BINDING SITE FOR RESIDUE EDO B 202
6AC6SOFTWAREPHE B:48 , HIS B:77 , GLU B:110 , GLU B:143 , HOH B:303 , HOH B:304 , HOH B:314 , HOH B:322BINDING SITE FOR RESIDUE EDO B 203

(-) 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 4LCN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LCN)

(-) 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 d4lcna_ A: Putative deaminase NE0047                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4lcn 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:180
                                                                                                                                                                                                                    
               SCOP domains d4lcnb_ B: Putative deaminase NE0047                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeee.hhhhhh....hhhhhhhhhhhhhh............eeeeeee..hhhhhhhhhhhh..eeeeeehhhhhhh..........hhhhhhhhh..eee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lcn B   1 MNDALHIGLPPFLVQANNEPRVLAAPEARMGYVLELVRANIAADGGPFAAAVFERDSGLLIAAGTNRVVPGRCSAAHAEILALSLAQAKLDTHDLSADGLPACELVTSAEPCVMCFGAVIWSGVRSLVCAARSDDVEAIGFDEGPRPENWMGGLEARGITVTTGLLRDAACALLREYNAC 180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4lco 4lcp 4ld2 4ld4

(-) Related Entries Specified in the PDB File

2g84 NATIVE NE0047
4hrq NE0047-8-AZAGUANINE BOUND STRUCTURE
4hrw NE0047 (E79A) -8-AZAGUANINE BOUND STRUCTURE
4lc5
4lco
4lcp
4ld2
4ld4