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Title :   YEAST CYTOSINE DEAMINASE D92E TRIPLE MUTANT BOUND TO TRANSITION STATE ANALOGUE HPY

Authors :   A. M. Korkegian, B. L. Stoddard

Date :   01 Dec 06 (Deposition) - 16 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Homodimer, Transition State Analogue, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Stolworthy, A. M. Korkegian, C. Willmon, B. L. Stoddard, M. E. Black
Crystal Structure Of Yeast Cytosine Deaminase D92E Triple Mutant Bound To Transition State Analogue Hpy
To Be Published
PubMed: search

Molecule 1 - CYTOSINE DEAMINASE
	Chains	:	A, B
	EC Number	:	3.5.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	FCY1
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	CYTOSINE AMINOHYDROLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	HPY	2	Ligand/Ion	4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE
3	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS B:262 , CYS B:291 , CYS B:294 , HPY B:410	BINDING SITE FOR RESIDUE ZN B 400
2	AC2	SOFTWARE	HIS A:62 , CYS A:91 , CYS A:94 , HPY A:411	BINDING SITE FOR RESIDUE ZN A 401
3	AC3	SOFTWARE	GLU A:128 , GLN A:150 , HOH A:423 , HOH A:435 , GLU B:275	BINDING SITE FOR RESIDUE CA B 403
4	AC4	SOFTWARE	ILE B:233 , ASN B:251 , HIS B:262 , GLY B:263 , GLU B:264 , CYS B:291 , CYS B:294 , ASP B:355 , ZN B:400	BINDING SITE FOR RESIDUE HPY B 410
5	AC5	SOFTWARE	ILE A:33 , ASN A:51 , HIS A:62 , GLY A:63 , GLU A:64 , PRO A:90 , CYS A:91 , CYS A:94 , ASP A:155 , ZN A:401	BINDING SITE FOR RESIDUE HPY A 411

(no "SS Bond" information available for 2O3K)

(no "Cis Peptide Bond" information available for 2O3K)

(no "SAP(SNP)/Variant" information available for 2O3K)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	FCY1_YEAST	9-129	2	A:9-129 B:209-329
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	FCY1_YEAST	62-98	2	A:62-98 B:262-298

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YPR062W	1	YPR062W.1	XVI:677162-677638	477	FCY1_YEAST	1-158	158	2	A:5-158 B:206-358	154 153

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
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Chain A from PDB  Type:PROTEIN  Length:154
 aligned with FCY1_YEAST | Q12178 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:154
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154    
           FCY1_YEAST     5 GMASKWDQKGMDIAYEEAALGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKIMKQFIDERPQDWFEDIGE 158
               SCOP domains d2o3ka_ A: Cytosine deaminase                                                                                                                              SCOP domains
               CATH domains 2o3kA00 A:5-158 Cytidine Deaminase, domain 2                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeee.hhhhhh....hhhhhhhhhhh..hhhhhh.eeeee....hhhhhhhhhhhh..eeee........hhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----CYT_DCMP_DEAMINASES_2  PDB: A:9-129 UniProt: 9-129                                                                       ----------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:62-98  ------------------------------------------------------------ PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:5-158 UniProt: 1-158 [INCOMPLETE]                                                                                                         Transcript 1
                 2o3k A   5 GMASKWDQKGMDIAYEEALLGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCEMCTGAIIMYGIPRCVIGENVNFKSKGEKYLQTRGHEVVVVDDERCKKLMKQFIDERPQDWFEDIGE 158
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with FCY1_YEAST | Q12178 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:153
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155   
           FCY1_YEAST     6 MASKWDQKGMDIAYEEAALGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKIMKQFIDERPQDWFEDIGE 158
               SCOP domains d2o3kb_ B: Cytosine deaminase                                                                                                                             SCOP domains
               CATH domains 2o3kB00 B:206-358 Cytidine Deaminase, domain 2                                                                                                            CATH domains
           Pfam domains (1) --dCMP_cyt_deam_1-2o3kB01 B:208-310                                                                      ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --dCMP_cyt_deam_1-2o3kB02 B:208-310                                                                      ------------------------------------------------ Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeee.hhhhhh....hhhhhhhhhhh..hhhhhh.eeeeeee..hhhhhhhhhhh...eeeeee......hhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CYT_DCMP_DEAMINASES_2  PDB: B:209-329 UniProt: 9-129                                                                     ----------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:262-298------------------------------------------------------------ PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:206-358 UniProt: 1-158 [INCOMPLETE]                                                                                                      Transcript 1
                 2o3k B 206 MASKWDQKGMDIAYEEALLGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCEMCTGAIIMYGIPRCVIGENVNFKSKGEKYLQTRGHEVVVVDDERCKKLMKQFIDERPQDWFEDIGE 358
                                   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355

Legend:		→ Mismatch	(orange background)
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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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Cytidine deaminase-like (78)

Superfamily: Cytidine deaminase-like (76)

Family: Deoxycytidylate deaminase-like (29)

Protein domain: Cytosine deaminase (7)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (7)

1a	d2o3ka_	A:
1b	d2o3kb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Cytidine Deaminase; domain 2 (44)

Homologous Superfamily: Cytidine Deaminase, domain 2 (32)

Baker's yeast (Saccharomyces cerevisiae) (8)

1a	2o3kB00	B:206-358
1b	2o3kA00	A:5-158

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CDA (39)

Family: dCMP_cyt_deam_1 (28)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (8)

1a	dCMP_cyt_deam_1-2o3kB01	B:208-310
1b	dCMP_cyt_deam_1-2o3kB02	B:208-310

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (FCY1_YEAST | Q12178)

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:0004131	cytosine deaminase activity	Catalysis of the reaction: cytosine + H2O = uracil + 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:0044206	UMP salvage	Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.
	GO:0046087	cytidine metabolic process	The chemical reactions and pathways involving cytidine, cytosine riboside, a widely distributed nucleoside.
	GO:0019858	cytosine metabolic process	The chemical reactions and pathways involving cytosine, 4-amino-2-hydroxypyrimidine, a pyrimidine derivative that is one of the five main bases found in nucleic acids; it occurs widely in cytidine derivatives.
	GO:0008655	pyrimidine-containing compound salvage	Any process that generates a pyrimidine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a pyrimidine base, from derivatives of them without de novo synthesis.

Asymmetric/Biological Unit
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	FCY1_YEAST \| Q12178	:	1ox7 1p6o 1rb7 1uaq 1ysb 1ysd

1ysb	CRYSTAL STRUCTURE OF YEAST CYTOSINE DEAMINASE TRIPLE MUTANT (A23L,V108I,I140L)

Description

Compounds

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Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

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