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(-) Description

Title :  CRYSTAL STRUCTURE OF AN AMIDOHYDROLASE FROM AN ENVIRONMENTAL SAMPLE OF SARGASSO SEA
 
Authors :  R. Agarwal, S. K. Burley, S. Swaminathan, New York Sgx Research Cen Structural Genomics (Nysgxrc)
Date :  27 Mar 07  (Deposition) - 03 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Nysgxrc, 9339A, Psi-Ii, Amidohydrolase, Sargasso Sea, Environmental Sample, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. S. Hall, R. Agarwal, D. Hitchcock, J. M. Sauder, S. K. Burley, S. Swaminathan, F. M. Raushel
Discovery And Structure Determination Of The Orphan Enzyme Isoxanthopterin Deaminase.
Biochemistry V. 49 4374 2010
PubMed-ID: 20415463  |  Reference-DOI: 10.1021/BI100252S

(-) Compounds

Molecule 1 - PUTATIVE CYTOSINE/GUANINE DEAMINASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:76 , HIS A:78 , HIS A:248 , HIS A:285 , ASP A:336 , HOH A:551BINDING SITE FOR RESIDUE ZN A 493

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PAJ)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PAJ)

(-) 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:421
 aligned with IXPDE_UNKP | P0CI72 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:475
                                    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       347       357       367       377       387       397       407       417       427       437       447       457       467       477     
           IXPDE_UNKP     8 PSTLIRNAAAIMTGGRGTADDPSRVPGPDIRIVGDTIDAIGALAPRPGETIVDATDCVIYPAWVNTHHHLFQSLLKGEPAGLDATLTPWLAATPYRFRALFDERRFRLAARIGLIELARSGCATVADHNYVYYPGMPFDSSAILFEEAEKLGLRFVLLRGGATQTRQLEADLPTALRPETLDAYVADIERLAARYHDASPRAMRRVVMAPTTVLYSISPREMRETAAVARRLGLRMHSHLSETVGYQDSAYSMYGKSPVAFCGEHDWLGSDVWYAHLVKVDADEIALLAQTGTGVAHCPQSNGRLGSGICPVREMADAGVPVSIGVDGAASNEAADMISEVHMTWLAQRARLGMLAQPAYRGGSFEGGAGAASIAEVIHWGTAGGARVMGLDEVGKVAVGYAADIAVYRLDDPRYFGLHDPAIGPVASGGRPSVMALFSAGKRVVVDDLIEGVDIKELGGEARRVVRELLREVVV 482
               SCOP domains d2paja1 A:10-69,A:406-484 Hypothetical protein GOS_1943094  d2paja2 A:70-405 Hy                 pothetical protein GOS_1943094                                                                                                                                                                                                                                                                              d2paja1 A:10-69,A:406-484 Hypothetical protein GOS_1943094                      SCOP domains
               CATH domains 2pajA01 A:10-71,A:402-458 Urease, subunit C, domain 1         2pajA02 A:72-401                  Metal-dependent hydrolases                                                                                                                                                                                                                                                                              2pajA01 A:10-71,A:402-458 Urease, subunit C, domain 1    2pajA03 A:459-484          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee..................eeee..eeeee.........eeee....eeee.ee....hhhhhhh....-----------------hhhhhhhhhhhhhhhhhhhhhhh..eeeeee...........hhhhhhhhhhhhh..eeeeee.............hhhhh..hhhhhhhhhhhhhhhh........eeeee.........hhhhhhhhhhhhhhh..eeeee..-------------..hhhhhhhhh......eeee.....hhhhhhhhhhhh.eeeehhhhhhh.-----...hhhhhh..eee..hhhhhh...hhhhhhhhhhhhhhhh.-------------------.hhhhhhhhhhhhhhhhhh..............eeeee..hhhhh...hhhhhhhhh....eeeeeee..eeeee.......hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2paj A  10 PSTLIRNAAAIMTGGRGTADDPSRVPGPDIRIVGDTIDAIGALAPRPGETIVDATDCVIYPAWVNTHHHLFQSLLKGEP-----------------FRALFDERRFRLAARIGLIELARSGCATVADHNYVYYPGMPFDSSAILFEEAEKLGLRFVLLRGGATQTRQLEADLPTALRPETLDAYVADIERLAARYHDASPRAMRRVVMAPTTVLYSISPREMRETAAVARRLGLRMHSHLS-------------GKSPVAFCGEHDWLGSDVWYAHLVKVDADEIALLAQTGTGVAHCPQSNGRL-----PVREMADAGVPVSIGVDGAASNEAADMISEVHMTWLAQRARL-------------------ASIAEVIHWGTAGGARVMGLDEVGKVAVGYAADIAVYRLDDPRYFGLHDPAIGPVASGGRPSVMALFSAGKRVVVDDLIEGVDIKELGGEARRVVRELLREVVV 484
                                    19        29        39        49        59        69        79        |-         -      |109       119       129       139       149       159       169       179       189       199       209       219       229       239       249|        -    |  269       279       289       299       309    |    -|      329       339       349       359 |       -         - |     389       399       409       419       429       439       449       459       469       479     
                                                                                                         88               106                                                                                                                                             250           264                                               314   320                                      361                 381
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (IXPDE_UNKP | P0CI72)
molecular function
    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:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0050228    pterin deaminase activity    Catalysis of the reaction: 2-amino-4-hydroxypteridine + H2O = 2,4-dihydroxypteridine + NH3.

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