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(-) Description

Title :  CRYSTAL STRUCTURE OF GUANINE DEAMINASE FROM BRADYRHIZOBIUM JAPONICUM
 
Authors :  R. Agarwal, S. K. Burley, S. Swaminathan, New York Sgx Research Cen Structural Genomics (Nysgxrc)
Date :  25 Jan 07  (Deposition) - 20 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.62
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Psi-Ii, Psi-2, 9231A, Guanine Deaminase, Guanine, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Agarwal, S. K. Burley, S. Swaminathan
Crystal Structure Of Guanine Deaminase From Bradyrhizobium Japonicum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BLR3880 PROTEIN
    Chains: A
    EC Number: 3.5.4.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON PLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BII3846, BLR3880
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 224911
    Strain: USDA 110
    Synonym: GUANINE DEAMINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1GUN1Ligand/IonGUANINE
2MSE10Mod. Amino AcidSELENOMETHIONINE
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 22)
No.NameCountTypeFull Name
1GUN2Ligand/IonGUANINE
2MSE20Mod. Amino AcidSELENOMETHIONINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:79 , HIS A:81 , HIS A:234 , ASP A:326 , GUN A:600 , HOH A:688BINDING SITE FOR RESIDUE ZN A 500
2AC2SOFTWAREHIS A:79 , HIS A:81 , LEU A:95 , TRP A:98 , LEU A:99 , PHE A:207 , HIS A:234 , GLU A:237 , HIS A:273 , ASP A:326 , ZN A:500 , HOH A:681 , HOH A:688 , HOH A:730BINDING SITE FOR RESIDUE GUN A 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OOD)

(-) 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:463
 aligned with Q89NG0_BRADU | Q89NG0 from UniProtKB/TrEMBL  Length:465

    Alignment length:465
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460     
         Q89NG0_BRADU     1 MTTVGIRGTFFDFVDDPWKHIGNEQAAARFHQDGLMVVTDGVIKAFGPYEKIAAAHPGVEITHIKDRIIVPGFIDGHIHLPQTRVLGAYGEQLLPWLQKSIYPEEIKYKDRNYAREGVKRFLDALLAAGTTTCQAFTSSSPVATEELFEEASRRNMRVIAGLTGIDRNAPAEFIDTPENFYRDSKRLIAQYHDKGRNLYAITPRFAFGASPELLKACQRLKHEHPDCWVNTHISENPAECSGVLVEHPDCQDYLGVYEKFDLVGPKFSGGHGVYLSNNEFRRMSKKGAAVVFCPCSNLFLGSGLFRLGRATDPEHRVKMSFGTDVGGGNRFSMISVLDDAYKVGMCNNTLLDGSIDPSRKDLAEAERNKLSPYRGFWSVTLGGAEGLYIDDKLGNFEPGKEADFVALDPNGGQLAQPWHQSLIADGAGPRTVDEAASMLFAVMMVGDDRCVDETWVMGKRLYKKS 465
               SCOP domains d2ooda1 A:3-72,A:398-467 Guanine deaminase                            d2ooda2 A:73-397 Guanine deaminase                                                                                                                                                                                                                                                                                                   d2ooda1 A:3-72,A:398-467 Gua  nine deaminase                           SCOP domains
               CATH domains 2oodA01 A:3-73,A:397-467 Urease, subunit C, domain 1                   2oodA02 A:74-396 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                        2oodA01 A:3-73,A:397-467 Urea  se, subunit C, domain 1                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee..hhhhh..hhhh.eeeeeeeeeeee...eeeeeehhhhhhhh...eeeeeeeeeeee.eeeeeee.hhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhh..eee..ee...........hhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh....hhhhhhhh.......eeee.....hhhhhhhhhhhh.eeeehhhhhhhh.....hhhhhh......eeee..........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh................eeee.......hhhhhhh..--.....hhhhhhhhhhhhhhhhhhh.eeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ood A   3 LTTVGIRGTFFDFVDDPWKHIGNEQAAARFHQDGLmVVTDGVIKAFGPYEKIAAAHPGVEITHIKDRIIVPGFIDGHIHLPQTRVLGAYGEQLLPWLQKSIYPEEIKYKDRNYAREGVKRFLDALLAAGTTTCQAFTSSSPVATEELFEEASRRNmRVIAGLTGIDRNAPAEFIDTPENFYRDSKRLIAQYHDKGRNLYAITPRFAFGASPELLKACQRLKHEHPDCWVNTHISENPAECSGVLVEHPDCQDYLGVYEKFDLVGPKFSGGHGVYLSNNEFRRmSKKGAAVVFCPCSNLFLGSGLFRLGRATDPEHRVKmSFGTDVGGGNRFSmISVLDDAYKVGmCNNTLLDGSIDPSRKDLAEAERNKLSPYRGFWSVTLGGAEGLYIDDKLGNFEPGKEADFVALDPNGGQLAQPWHQSLI--GAGPRTVDEAASmLFAVmmVGDDRCVDETWVmGKRLYKKS 467
                                    12        22        32     |  42        52        62        72        82        92       102       112       122       132       142       152     | 162       172       182       192       202       212       222       232       242       252       262       272       282  |    292       302       312       322       332  |    342    |  352       362       372       382       392       402       412       422  |  | 432       442  ||   452      |462     
                                                              38-MSE                                                                                                                 158-MSE                                                                                                                        285-MSE                             321-MSE       335-MSE     347-MSE                                                                       425  |         440-MSE||          459-MSE    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   428              445-MSE                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     446-MSE
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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  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q89NG0_BRADU | Q89NG0)
molecular function
    GO:0008892    guanine deaminase activity    Catalysis of the reaction: guanine + H2O = xanthine + 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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006147    guanine catabolic process    The chemical reactions and pathways resulting in the breakdown of guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important.
    GO:0046098    guanine metabolic process    The chemical reactions and pathways involving guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important.

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