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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ADENINE DEAMINASE (AAUR1117) FROM ARTHROBACTER AURESCENS
 
Authors :  Z. Zhang, A. M. Goble, F. M. Raushel, S. Swaminathan
Date :  11 May 11  (Deposition) - 25 May 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sgx, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, A. M. Goble, F. M. Raushel, S. Swaminathan
The Crystal Structure Of Adenine Deaminase (Aaur1117) From Arthrobacter Aurescens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ADENOSINE DEAMINASE 1
    Chains: A, B
    EC Number: 3.5.4.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-30A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ADD, ADD1, AAUR_1117
    Organism Scientific: ARTHROBACTER AURESCENS
    Organism Taxid: 290340
    Strain: TC1
    Synonym: ADENINE DEAMINASE, AAUR1117, ADENOSINE AMINOHYDROLASE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ADE2Ligand/IonADENINE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:19 , HIS A:21 , HIS A:199 , HIS A:223 , ASP A:280 , ADE A:345BINDING SITE FOR RESIDUE ZN A 344
2AC2SOFTWAREHIS A:21 , LEU A:59 , LEU A:63 , TYR A:66 , ASP A:171 , SER A:172 , HIS A:199 , GLU A:202 , HIS A:223 , ASP A:280 , ASP A:281 , ZN A:344 , HOH A:369BINDING SITE FOR RESIDUE ADE A 345
3AC3SOFTWAREHIS B:19 , HIS B:21 , HIS B:199 , ASP B:280 , ADE B:345BINDING SITE FOR RESIDUE ZN B 344
4AC4SOFTWAREHIS B:21 , LEU B:59 , PHE B:62 , TYR B:66 , ASP B:171 , SER B:172 , HIS B:199 , GLU B:202 , HIS B:223 , ASP B:280 , ASP B:281 , ZN B:344 , HOH B:375BINDING SITE FOR RESIDUE ADE B 345

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RYS)

(-) 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:335
 aligned with A1R3U3_PAEAT | A1R3U3 from UniProtKB/TrEMBL  Length:343

    Alignment length:335
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337     
         A1R3U3_PAEAT     8 TTSTAPPVAELHLHIEGTLQPELIFALAERNGIELPYEDIEELREKYEFTDLQSFLDLYYANMAVLQTEQDFTDMTRAYLERAAAGGVRHAEIMMDPQAHTSRGVALETCVNGVANALATSEEDFGVSTLLIAAFLRDMSEDSALEVLDQLLAMHAPIAGIGLDSAEVGNPPSKFERLYQRAAEAGLRRIAHAGEEGPASYITEALDVLHVERIDHGIRCMEDTDVVQRLVAEQVPLTVCPLSNVRLRAVDKLADHPLPEMLAIGLNVCVNSDDPAYFGGYVDDNFEQLVKVLEFSVPEQATLAANSIRSSFASDARKAVLLDEVTEWVKASVTP 342
               SCOP domains d3rysa_ A: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee...hhhhhhhhhhhhhhhhhh.......hhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhhhh...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee...hhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhh..eeehhhhhhhh....hhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rys A   8 TTSTAPPVAELHLHIEGTLQPELIFALAERNGIELPYEDIEELREKYEFTDLQSFLDLYYANMAVLQTEQDFTDMTRAYLERAAAGGVRHAEIMMDPQAHTSRGVALETCVNGVANALATSEEDFGVSTLLIAAFLRDMSEDSALEVLDQLLAMHAPIAGIGLDSAEVGNPPSKFERLYQRAAEAGLRRIAHAGEEGPASYITEALDVLHVERIDHGIRCMEDTDVVQRLVAEQVPLTVCPLSNVRLRAVDKLADHPLPEMLAIGLNVCVNSDDPAYFGGYVDDNFEQLVKVLEFSVPEQATLAANSIRSSFASDARKAVLLDEVTEWVKASVTP 342
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337     


Chain B from PDB  Type:PROTEIN  Length:327
 aligned with A1R3U3_PAEAT | A1R3U3 from UniProtKB/TrEMBL  Length:343

    Alignment length:327
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
         A1R3U3_PAEAT    12 APPVAELHLHIEGTLQPELIFALAERNGIELPYEDIEELREKYEFTDLQSFLDLYYANMAVLQTEQDFTDMTRAYLERAAAGGVRHAEIMMDPQAHTSRGVALETCVNGVANALATSEEDFGVSTLLIAAFLRDMSEDSALEVLDQLLAMHAPIAGIGLDSAEVGNPPSKFERLYQRAAEAGLRRIAHAGEEGPASYITEALDVLHVERIDHGIRCMEDTDVVQRLVAEQVPLTVCPLSNVRLRAVDKLADHPLPEMLAIGLNVCVNSDDPAYFGGYVDDNFEQLVKVLEFSVPEQATLAANSIRSSFASDARKAVLLDEVTEWVKA 338
               SCOP domains d3rysb_ B: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...hhhhhhhhhhhhhhhhhh.......hhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhhhh...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee...hhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhh.eeeehhhhhhhh....hhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rys B  12 APPVAELHLHIEGTLQPELIFALAERNGIELPYEDIEELREKYEFTDLQSFLDLYYANMAVLQTEQDFTDMTRAYLERAAAGGVRHAEIMMDPQAHTSRGVALETCVNGVANALATSEEDFGVSTLLIAAFLRDMSEDSALEVLDQLLAMHAPIAGIGLDSAEVGNPPSKFERLYQRAAEAGLRRIAHAGEEGPASYITEALDVLHVERIDHGIRCMEDTDVVQRLVAEQVPLTVCPLSNVRLRAVDKLADHPLPEMLAIGLNVCVNSDDPAYFGGYVDDNFEQLVKVLEFSVPEQATLAANSIRSSFASDARKAVLLDEVTEWVKA 338
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RYS)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A1R3U3_PAEAT | A1R3U3)
molecular function
    GO:0000034    adenine deaminase activity    Catalysis of the reaction: adenine + H2O = hypoxanthine + NH3.
    GO:0019239    deaminase activity    Catalysis of the removal of an amino group from a substrate, producing ammonia (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:0006146    adenine catabolic process    The chemical reactions and pathways resulting in the breakdown of adenine, 6-aminopurine, one of the 5 main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine.
    GO:0043103    hypoxanthine salvage    Any process that generates hypoxanthine, 6-hydroxy purine, from derivatives of it without de novo synthesis.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).

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