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(-) Description

Title :  CRYSTAL STRUCTURE OF GUANINE DEAMINASE FROM C. ACETOBUTYLICUM WITH BOUND GUANINE IN THE ACTIVE SITE
 
Authors :  D. Kumaran, S. K. Burley, S. Swaminathan, New York Sgx Research Cen Structural Genomics (Nysgxrc)
Date :  06 Sep 06  (Deposition) - 19 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Structure Initiative Ii (Psi-Ii), 9246A, Amidohydrolase, Guanine Deaminase, Nucleotide Transport And Metabolism, Structural Genomics, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kumaran, S. K. Burley, S. Swaminathan
Crystal Structure Of Guanine Deaminase From C. Acetobutylicum With Bound Guanine In The Active Site
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYTOSINE/GUANINE DEAMINASE RELATED PROTEIN
    Chains: A, B
    EC Number: 3.5.4.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGX3(BC)
    Expression System Strain: DE3+RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: CLOSTRIDIUM ACETOBUTYLICUM
    Organism Taxid: 272562
    Strain: ATCC 824

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2GOL1Ligand/IonGLYCEROL
3GUN2Ligand/IonGUANINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:73 , HIS A:75 , HIS A:229 , HIS A:269 , ASP A:320 , GUN A:503BINDING SITE FOR RESIDUE FE A 501
2AC2SOFTWAREHIS B:73 , HIS B:75 , HIS B:229 , HIS B:269 , ASP B:320 , GUN B:504BINDING SITE FOR RESIDUE FE B 502
3AC3SOFTWAREHIS A:75 , GLN A:78 , LEU A:90 , TRP A:93 , LEU A:94 , ARG A:202 , PHE A:203 , HIS A:229 , GLU A:232 , HIS A:269 , ASP A:320 , FE A:501 , HOH A:588BINDING SITE FOR RESIDUE GUN A 503
4AC4SOFTWAREHIS B:75 , GLN B:78 , LEU B:90 , TRP B:93 , LEU B:94 , ARG B:202 , PHE B:203 , HIS B:229 , GLU B:232 , HIS B:269 , ASP B:320 , FE B:502 , HOH B:510 , HOH B:527BINDING SITE FOR RESIDUE GUN B 504
5AC5SOFTWAREGLU A:172 , ASN A:173 , THR A:176 , GLN A:345 , GLY A:348 , LEU B:234BINDING SITE FOR RESIDUE GOL A 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I9U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I9U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I9U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I9U)

(-) Exons   (0, 0)

(no "Exon" information available for 2I9U)

(-) 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:419
 aligned with Q97MB6_CLOAB | Q97MB6 from UniProtKB/TrEMBL  Length:428

    Alignment length:419
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415         
         Q97MB6_CLOAB     6 NLKIFKGNLIFTKTSDKFTIMKDSYIVVIDGKIASVSSNLPDKYKGNPIIDFRNNIIIPGMNDLHAHASQYKNLGIGMDKELLPWLNNYTFPEEAKFLNVDYAKKTYGRLIKDLIKNGTTRVALFATLHKDSTIELFNMLIKSGIGAYVGKVNMDYNCPDYLTENYITSLNDTEEIILKYKDKSNIVKPIITPRFVPSCSNELMDGLGKLSYKYRLPVQSHLSENLDEIAVVKSLHKKSNFYGEVYDKFGLFGNTPTLMAHCIHSSKEEINLIKRNNVTIVHCPTSNFNLGSGMMPVRKYLNLGINVVLGSDISAGHTCSLFKVIAYAIQNSKIKWQESGKKDMFLSTSEAFYMATKKGGSFFGKVGSFEEGYDFDALVINDSNLYPEDYDLTERLERFIYLGDDRNIMKRYVCGNEIF 424
               SCOP domains d2i9ua1 A:9-66,A:377-427 Guanine deaminase                d2i9ua2 A:67-376 Guanine deaminase                                                                                                                                                                                                                                                                                    d2i9ua1 A:9-66,A:377-427 Guanine deaminase          SCOP domains
               CATH domains 2i9uA01 A:9-67,A:376-427 Urease, subunit C, domain 1       2i9uA02 A:68-375 Metal-dependent hydrolases                                                                                                                                                                                                                                                                         2i9uA01 A:9-67,A:376-427 Urease, subunit C, domain 1 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee..eeeeeeeeeeeee..eeeeee...hhhhh...eeeeeeeeeee.eeeeeee.hhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhh.eeeee.ee...........hhhhhhhhhhhhhhhhh.....eee..ee.hhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh....hhhhhhhhh.......eeeee....hhhhhhhhhhh..eeeehhhhhhhh.....hhhhhhhh..eeee..........hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh...............eeee.....hhhhhhhhhhhhhhhhhhhhh.eeeeee..eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i9u A   9 NLKIFKGNLIFTKTSDKFTIMKDSYIVVIDGKIASVSSNLPDKYKGNPIIDFRNNIIIPGMNDLHAHASQYKNLGIGMDKELLPWLNNYTFPEEAKFLNVDYAKKTYGRLIKDLIKNGTTRVALFATLHKDSTIELFNMLIKSGIGAYVGKVNMDYNCPDYLTENYITSLNDTEEIILKYKDKSNIVKPIITPRFVPSCSNELMDGLGKLSYKYRLPVQSHLSENLDEIAVVKSLHKKSNFYGEVYDKFGLFGNTPTLMAHCIHSSKEEINLIKRNNVTIVHCPTSNFNLGSGMMPVRKYLNLGINVVLGSDISAGHTCSLFKVIAYAIQNSKIKWQESGKKDMFLSTSEAFYMATKKGGSFFGKVGSFEEGYDFDALVINDSNLYPEDYDLTERLERFIYLGDDRNIMKRYVCGNEIF 427
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418         


Chain B from PDB  Type:PROTEIN  Length:419
 aligned with Q97MB6_CLOAB | Q97MB6 from UniProtKB/TrEMBL  Length:428

    Alignment length:419
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415         
         Q97MB6_CLOAB     6 NLKIFKGNLIFTKTSDKFTIMKDSYIVVIDGKIASVSSNLPDKYKGNPIIDFRNNIIIPGMNDLHAHASQYKNLGIGMDKELLPWLNNYTFPEEAKFLNVDYAKKTYGRLIKDLIKNGTTRVALFATLHKDSTIELFNMLIKSGIGAYVGKVNMDYNCPDYLTENYITSLNDTEEIILKYKDKSNIVKPIITPRFVPSCSNELMDGLGKLSYKYRLPVQSHLSENLDEIAVVKSLHKKSNFYGEVYDKFGLFGNTPTLMAHCIHSSKEEINLIKRNNVTIVHCPTSNFNLGSGMMPVRKYLNLGINVVLGSDISAGHTCSLFKVIAYAIQNSKIKWQESGKKDMFLSTSEAFYMATKKGGSFFGKVGSFEEGYDFDALVINDSNLYPEDYDLTERLERFIYLGDDRNIMKRYVCGNEIF 424
               SCOP domains d2i9ub1 B:9-66,B:377-427 Guanine deaminase                d2i9ub2 B:67-376 Guanine deaminase                                                                                                                                                                                                                                                                                    d2i9ub1 B:9-66,B:377-427 Guanine deaminase          SCOP domains
               CATH domains 2i9uB01 B:9-67,B:376-427 Urease, subunit C, domain 1       2i9uB02 B:68-375 Metal-dependent hydrolases                                                                                                                                                                                                                                                                         2i9uB01 B:9-67,B:376-427 Urease, subunit C, domain 1 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.......eeeeeeeeeee..eeeeee...hhhhh....eeeeeeeeee.eeeeeee.hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhh.eeeee........hhhhh.hhhhhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh....hhhhhhhhh.......eeeee....hhhhhhhhhhh..eeeehhhhhhhh.....hhhhhhhh..eeee..........hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..............eeee.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i9u B   9 NLKIFKGNLIFTKTSDKFTIMKDSYIVVIDGKIASVSSNLPDKYKGNPIIDFRNNIIIPGMNDLHAHASQYKNLGIGMDKELLPWLNNYTFPEEAKFLNVDYAKKTYGRLIKDLIKNGTTRVALFATLHKDSTIELFNMLIKSGIGAYVGKVNMDYNCPDYLTENYITSLNDTEEIILKYKDKSNIVKPIITPRFVPSCSNELMDGLGKLSYKYRLPVQSHLSENLDEIAVVKSLHKKSNFYGEVYDKFGLFGNTPTLMAHCIHSSKEEINLIKRNNVTIVHCPTSNFNLGSGMMPVRKYLNLGINVVLGSDISAGHTCSLFKVIAYAIQNSKIKWQESGKKDMFLSTSEAFYMATKKGGSFFGKVGSFEEGYDFDALVINDSNLYPEDYDLTERLERFIYLGDDRNIMKRYVCGNEIF 427
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418
   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  (2, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I9U)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q97MB6_CLOAB | Q97MB6)
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.

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