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Asym./Biol. Unit (Jmol Viewer)

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Title :   YEAST CYTOSINE DEAMINASE DOUBLE MUTANT

Authors :   A. Korkegian, M. E. Black, D. Baker, B. L. Stoddard

Date :   08 Feb 05 (Deposition) - 17 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Hydrolase, Cytosine Deaminase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Korkegian, M. E. Black, D. Baker, B. L. Stoddard
Computational Thermostabilization Of An Enzyme.
Science V. 308 857 2005
PubMed-ID: 15879217 | Reference-DOI: 10.1126/SCIENCE.1107387
(for further references see the PDB file header)

Molecule 1 - CYTOSINE DEAMINASE
	Chains	:	A, B
	EC Number	:	3.5.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	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 (2, 5)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:64 , ZN A:501 , HOH A:1128 , HOH A:1129 , HOH A:1132 , HOH A:1133	BINDING SITE FOR RESIDUE ZN A 500
2	AC2	SOFTWARE	HIS A:62 , CYS A:91 , CYS A:94 , ZN A:500 , HOH A:1133	BINDING SITE FOR RESIDUE ZN A 501
3	AC3	SOFTWARE	HIS B:262 , CYS B:291 , CYS B:294 , ZN B:503 , HOH B:1131	BINDING SITE FOR RESIDUE ZN B 502
4	AC4	SOFTWARE	GLU B:264 , ZN B:502 , HOH B:1130 , HOH B:1131 , HOH B:1134 , HOH B:1135	BINDING SITE FOR RESIDUE ZN B 503
5	AC5	SOFTWARE	GLY B:326 , ASP B:346 , HOH B:1064 , HOH B:1090 , HOH B:1136	BINDING SITE FOR RESIDUE CA B 504

(no "SS Bond" information available for 1YSD)

(no "Cis Peptide Bond" information available for 1YSD)

(no "SAP(SNP)/Variant" information available for 1YSD)

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:3-158 B:201-358	156 158

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:156
 aligned with FCY1_YEAST | Q12178 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      
           FCY1_YEAST     3 TGGMASKWDQKGMDIAYEEAALGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKIMKQFIDERPQDWFEDIGE 158
               SCOP domains d1ysda1 A:3-158 Cytosine deaminase                                                                                                                           SCOP domains
               CATH domains 1ysdA00 A:3-158 Cytidine Deaminase, domain 2                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeee.hhhhhh....hhhhhhhhhhh..hhhhhh.eeeeeee..hhhhhhhhhhhh..eeeeee......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:3-158 UniProt: 1-158 [INCOMPLETE]                                                                                                           Transcript 1
                 1ysd A   3 TGGMASKWDQKGMDIAYEEALLGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKLMKQFIDERPQDWFEDIGE 158
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with FCY1_YEAST | Q12178 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:161
                               1                                                                                                                                                             
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157 
           FCY1_YEAST     - ---MVTGGMASKWDQKGMDIAYEEAALGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKIMKQFIDERPQDWFEDIGE 158
               SCOP domains d1ysdb_ B: Cytosine deaminase                                                                                                                                     SCOP domains
               CATH domains 1ysdB00 B:198-358 Cytidine Deaminase, domain 2                                                                                                                    CATH domains
           Pfam domains (1) ----------dCMP_cyt_deam_1-1ysdB01 B:208-310                                                                      ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------dCMP_cyt_deam_1-1ysdB02 B:208-310                                                                      ------------------------------------------------ Pfam domains (2)
         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: 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:201-358 UniProt: 1-158                                                                                                                        Transcript 1
                 1ysd B 198 GSSMVTGGMASKWDQKGMDIAYEEALLGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKLMKQFIDERPQDWFEDIGE 358
                                   207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357

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 '\|'

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	d1ysda1	A:3-158
1b	d1ysdb_	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	1ysdA00	A:3-158
1b	1ysdB00	B:198-358

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_1-1ysdB01	B:208-310
1b	dCMP_cyt_deam_1-1ysdB02	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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