1WKQ - JenaLib

Title :   CRYSTAL STRUCTURE OF BACILLUS SUBTILIS GUANINE DEAMINASE. THE FIRST DOMAIN-SWAPPED STRUCTURE IN THE CYTIDINE DEAMINASE SUPERFAMILY

Authors :   S. H. Liaw, Y. J. Chang, C. T. Lai

Date :   01 Jun 04 (Deposition) - 13 Jul 04 (Release) - 15 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.17

Chains :   Asym./Biol. Unit : A,B

Keywords :   Guanine Deaminase, Domain Swap, The Cytidine Deaminase Superfamily, Substrate Specificity, Structural Plasticity, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. H. Liaw, Y. J. Chang, C. T. Lai, H. C. Chang, G. G. Chang
Crystal Structure Of Bacillus Subtilis Guanine Deaminase: The First Domain-Swapped Structure In The Cytidine Deaminase Superfamily
J. Biol. Chem. V. 279 35479 2004
PubMed-ID: 15180998 | Reference-DOI: 10.1074/JBC.M405304200
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 3)

Exons (0, 0)

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:158
 aligned with GUAD_BACSU | O34598 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:158
                              1                                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148        
           GUAD_BACSU     - --MNHETFLKRAVTLACEGVNAGIGGPFGAVIVKDGAIIAEGQNNVTTSNDPTAHAEVTAIRKACKVLGAYQLDDCILYTSCEPCPMCLGAIYWARPKAVFYAAEHTDAAEAGFDDSFIYKEIDKPAEERTIPFYQVTLTEHLSPFQAWRNFANKKEY 156
               SCOP domains d1wkqa_ A: Guanine deaminase GuaD                                                                                                                              SCOP domains
               CATH domains 1wkqA00 A:-2-156 Cytidine Deaminase, domain 2                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh......eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh..eeeeeehhhhhhhh..hhhhhhhhhhhhhhhh...eee......hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --CYT_DCMP_DEAMINASES_2  PDB: A:1-132 UniProt: 1-132                                                                                  ------------------------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:53-90   ------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wkq A  -2 HAMNHETFLKRAVTLACEGVNAGIGGPFGAVIVKDGAIIAEGQNNVTTSNDPTAHAEVTAIRKACKVLGAYQLDDCILYTSCEPCPMCLGAIYWARPKAVFYAAEHTDAAEAGFDDSFIYKEIDKPAEERTIPFYQVTLTEHLSPFQAWRNFANKKEY 156
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148        
                             ||                                                                                                                                                           
                            -1|                                                                                                                                                           
                              1

Chain B from PDB  Type:PROTEIN  Length:155
 aligned with GUAD_BACSU | O34598 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     
           GUAD_BACSU     2 NHETFLKRAVTLACEGVNAGIGGPFGAVIVKDGAIIAEGQNNVTTSNDPTAHAEVTAIRKACKVLGAYQLDDCILYTSCEPCPMCLGAIYWARPKAVFYAAEHTDAAEAGFDDSFIYKEIDKPAEERTIPFYQVTLTEHLSPFQAWRNFANKKEY 156
               SCOP domains d1wkqb_ B: Guanine deaminase GuaD                                                                                                                           SCOP domains
               CATH domains 1wkqB00 B:2-156 Cytidine Deaminase, domain 2                                                                                                                CATH domains
           Pfam domains (1) dCMP_cyt_deam_1-1wkqB01 B:2-102                                                                      ------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) dCMP_cyt_deam_1-1wkqB02 B:2-102                                                                      ------------------------------------------------------ Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhh......eeeeee..eeeeeee.hhhhhh....hhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh..eeeeeehhhhhhhh..hhhhhhhhhhhhhhhh...eee......hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CYT_DCMP_DEAMINASES_2  PDB: - UniProt: 1-132                                                                                       ------------------------ PROSITE (1)
                PROSITE (2) ---------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:53-90   ------------------------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wkq B   2 NHETFLKRAVTLACEGVNAGIGGPFGAVIVKDGAIIAEGQNNVTTSNDPTAHAEVTAIRKACKVLGAYQLDDCILYTSCEPCPMCLGAIYWARPKAVFYAAEHTDAAEAGFDDSFIYKEIDKPAEERTIPFYQVTLTEHLSPFQAWRNFANKKEY 156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GUAD_BACSU | O34598)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0019239	deaminase activity	Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3).
	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: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:0009451	RNA modification	The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
	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:0006144	purine nucleobase metabolic process	The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.

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