1OX7 - JenaLib

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Title :   CRYSTAL STRUCTURE OF YEAST CYTOSINE DEAMINASE APO-ENZYME: INORGANIC ZINC BOUND

Authors :   G. C. Ireton, M. E. Black, B. L. Stoddard

Date :   01 Apr 03 (Deposition) - 19 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.43

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

Keywords :   Aminohydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. C. Ireton, M. E. Black, B. L. Stoddard
The 1. 14 A Crystal Structure Of Yeast Cytosine Deaminase. Evolution Of Nucleotide Salvage Enzymes And Implications For Genetic Chemotherapy.
Structure V. 11 961 2003
PubMed-ID: 12906827 | Reference-DOI: 10.1016/S0969-2126(03)00153-9
(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 Plasmid	:	PET15B-(YCD)
	Expression System Strain	:	BL21-RIL (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	FCY1 OR YPR062W OR YP9499.17
	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, 19)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	4	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 , ZN B:403 , HOH B:507	BINDING SITE FOR RESIDUE ZN B 400
2	AC2	SOFTWARE	GLU A:64 , ZN A:402 , HOH A:549 , HOH A:550 , HOH A:551 , HOH A:552	BINDING SITE FOR RESIDUE ZN A 401
3	AC3	SOFTWARE	HIS A:62 , CYS A:91 , CYS A:94 , ZN A:401 , HOH A:550	BINDING SITE FOR RESIDUE ZN A 402
4	AC4	SOFTWARE	GLU B:264 , ZN B:400 , HOH B:504 , HOH B:506 , HOH B:507 , HOH B:508	BINDING SITE FOR RESIDUE ZN B 403
5	AC5	SOFTWARE	GLU A:75 , HOH A:774 , GLU B:328 , GLN B:350 , HOH B:519 , HOH B:576	BINDING SITE FOR RESIDUE CA B 404

(no "SS Bond" information available for 1OX7)

(no "Cis Peptide Bond" information available for 1OX7)

(no "SAP(SNP)/Variant" information available for 1OX7)

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:1-158 B:201-358	158 158

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:158
 aligned with FCY1_YEAST | Q12178 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
           FCY1_YEAST     1 MVTGGMASKWDQKGMDIAYEEAALGYKEGGVPIGGCLINNKDGSVLGRGHNMRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKIMKQFIDERPQDWFEDIGE 158
               SCOP domains d1ox7a_ A: Cytosine deaminase                                                                                                                                  SCOP domains
               CATH domains -1ox7A00 A:2-158 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:1-158 UniProt: 1-158                                                                                                                          Transcript 1
                 1ox7 A   1 mVTGGmASKWDQKGmDIAYEEAALGYKEGGVPIGGCLINNKDGSVLGRGHNmRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDmCTGAIImYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKImKQFIDERPQDWFEDIGE 158
                            |    |  10    |   20        30        40        50 |      60        70        80        90  |    100       110       120       130       140|      150        
                            |    |       15-MSE                               52-MSE                                   93-MSE  |                                      141-MSE             
                            1-MSE|                                                                                           100-MSE                                                      
                                 6-MSE

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 d1ox7b_ B: Cytosine deaminase                                                                                                                                     SCOP domains
               CATH domains 1ox7B00 B:198-358 Cytidine Deaminase, domain 2                                                                                                                    CATH domains
           Pfam domains (1) ----------dCMP_cyt_deam_1-1ox7B01 B:208-310                                                                      ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------dCMP_cyt_deam_1-1ox7B02 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
                 1ox7 B 198 GSSmVTGGmASKWDQKGmDIAYEEAALGYKEGGVPIGGCLINNKDGSVLGRGHNmRFQKGSATLHGEISTLENCGRLEGKVYKDTTLYTTLSPCDmCTGAIImYGIPRCVVGENVNFKSKGEKYLQTRGHEVVVVDDERCKKImKQFIDERPQDWFEDIGE 358
                               |   207       217       227       237       247    |  257       267       277       287     | 297  |    307       317       327       337   |   347       357 
                             201-MSE|      215-MSE                              252-MSE                                  293-MSE  |                                      341-MSE             
                                  206-MSE                                                                                       300-MSE

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	d1ox7a_	A:
1b	d1ox7b_	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	1ox7A00	A:2-158
1b	1ox7B00	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_1-1ox7B01	B:208-310
1b	dCMP_cyt_deam_1-1ox7B02	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	:	1p6o 1rb7 1uaq 1ysb 1ysd 2o3k

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 19)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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