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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ADENOSINE DEAMINASE WITH ADENINE BOUND FROM PSEUDOMONAS AERUGINOSA
 
Authors :  Z. Zhang, S. K. Burley, S. Swaminathan, New York Sgx Research Cente Structural Genomics (Nysgxrc)
Date :  19 Oct 10  (Deposition) - 22 Dec 10  (Release) - 22 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Psii, Sgx, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, S. K. Burley, S. Swaminathan
The Crystal Structure Of Adenosine Deaminase With Adenine Bound From Pseudomonas Aeruginosa
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ADENOSINE DEAMINASE
    Chains: A, B
    EC Number: 3.5.4.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC - PSGX3 (BC)
    Expression System Strain: BL21 (DE3) CODON+RIL (P)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ADD, PA0148
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: ADENOSINE AMINOHYDROLASE

 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  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1ADE2Ligand/IonADENINE
2MSE8Mod. Amino AcidSELENOMETHIONINE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE
2MSE4Mod. Amino AcidSELENOMETHIONINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE
2MSE4Mod. Amino AcidSELENOMETHIONINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:16 , HIS A:18 , HIS A:196 , HIS A:220 , ASP A:277 , ADE A:328BINDING SITE FOR RESIDUE ZN A 327
2AC2SOFTWAREHIS A:18 , LEU A:56 , LEU A:60 , TYR A:63 , SER A:169 , HIS A:196 , GLU A:199 , HIS A:220 , ASP A:277 , ASP A:278 , ZN A:327 , HOH A:400BINDING SITE FOR RESIDUE ADE A 328
3AC3SOFTWAREHIS B:16 , HIS B:18 , HIS B:196 , HIS B:220 , ASP B:277 , ADE B:328BINDING SITE FOR RESIDUE ZN B 327
4AC4SOFTWAREHIS B:18 , LEU B:56 , LEU B:60 , TYR B:63 , SER B:169 , HIS B:196 , GLU B:199 , HIS B:220 , ASP B:277 , ASP B:278 , ZN B:327 , HOH B:350BINDING SITE FOR RESIDUE ADE B 328

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PAO)

(-) 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:313
 aligned with ADE_PSEAE | Q9I6Y4 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:313
                                    11        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   
            ADE_PSEAE     2 YEWLNALPKAELHLHLEGTLEPELLFALAERNRIALPWNDVETLRKAYAFNNLQEFLDLYYAGADVLRTEQDFYDLTWAYLQKCKAQNVVHVEPFFDPQTHTDRGIPFEVVLAGIRAALRDGEKLLGIRHGLILSFLRHLSEEQAQKTLDQALPFRDAFIAVGLDSSEVGHPPSKFQRVFDRARSEGFLTVAHAGEEGPPEYIWEALDLLKVERIDHGVRAFEDERLMRRLIDEQIPLTVCPLSNTKLCVFDDMSQHTILDMLERGVKVTVNSDDPAYFGGYVTENFHALQQSLGMTEEQARRLAQNSLDARL 314
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.eee...hhhhhhhhhhhhhhhhhh.......hhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.eeee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhh.ee..eeeee...hhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhhh..ee.eee....hhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhh..eeehhhhhhhh....hhhhhhhhhhhhhh..eee...hhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pao A   4 YEWLNALPKAELHLHLEGTLEPELLFALAERNRIALPWNDVETLRKAYAFNNLQEFLDLYYAGADVLRTEQDFYDLTWAYLQKCKAQNVVHVEPFFDPQTHTDRGIPFEVVLAGIRAALRDGEKLLGIRHGLILSFLRHLSEEQAQKTLDQALPFRDAFIAVGLDSSEVGHPPSKFQRVFDRARSEGFLTVAHAGEEGPPEYIWEALDLLKVERIDHGVRAFEDERLmRRLIDEQIPLTVCPLSNTKLCVFDDmSQHTILDmLERGVKVTVNSDDPAYFGGYVTENFHALQQSLGmTEEQARRLAQNSLDARL 316
                                    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   
                                                                                                                                                                                                                                                             231-MSE                   257-MSE 265-MSE                           299-MSE             


Chain B from PDB  Type:PROTEIN  Length:314
 aligned with ADE_PSEAE | Q9I6Y4 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:314
                                    11        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    
            ADE_PSEAE     2 YEWLNALPKAELHLHLEGTLEPELLFALAERNRIALPWNDVETLRKAYAFNNLQEFLDLYYAGADVLRTEQDFYDLTWAYLQKCKAQNVVHVEPFFDPQTHTDRGIPFEVVLAGIRAALRDGEKLLGIRHGLILSFLRHLSEEQAQKTLDQALPFRDAFIAVGLDSSEVGHPPSKFQRVFDRARSEGFLTVAHAGEEGPPEYIWEALDLLKVERIDHGVRAFEDERLMRRLIDEQIPLTVCPLSNTKLCVFDDMSQHTILDMLERGVKVTVNSDDPAYFGGYVTENFHALQQSLGMTEEQARRLAQNSLDARLV 315
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.eee...hhhhhhhhhhhhhhhhhh.......hhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.eeee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhh.ee.eeeeee...hhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhh....eeee.hhhh.hhhhhhhhhhhh..eeehhhhhhhh....hhhhhhhhhhhhh...eee...hhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pao B   4 YEWLNALPKAELHLHLEGTLEPELLFALAERNRIALPWNDVETLRKAYAFNNLQEFLDLYYAGADVLRTEQDFYDLTWAYLQKCKAQNVVHVEPFFDPQTHTDRGIPFEVVLAGIRAALRDGEKLLGIRHGLILSFLRHLSEEQAQKTLDQALPFRDAFIAVGLDSSEVGHPPSKFQRVFDRARSEGFLTVAHAGEEGPPEYIWEALDLLKVERIDHGVRAFEDERLmRRLIDEQIPLTVCPLSNTKLCVFDDmSQHTILDmLERGVKVTVNSDDPAYFGGYVTENFHALQQSLGmTEEQARRLAQNSLDARLV 317
                                    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    
                                                                                                                                                                                                                                                             231-MSE                   257-MSE 265-MSE                           299-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3PAO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ADE_PSEAE | Q9I6Y4)
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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 Related Entries

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UniProtKB/Swiss-Prot
        ADE_PSEAE | Q9I6Y4: 3ou8 3pan 3pbm

(-) Related Entries Specified in the PDB File

3ou8 RELATED ID: NYSGXRC-9608A RELATED DB: TARGETDB