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Title :   CRYSTAL STRUCTURE OF MOUSE CYTIDINE DEAMINASE COMPLEXED WITH 3-DEAZAURIDINE

Authors :   A. H. Teh

Date :   06 Apr 05 (Deposition) - 11 Apr 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.36

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A,B,C,D  (2x)

Keywords :   Mouse, Cytidine Deaminase, Zinc, 3-Deazauridine, Substrate Dissociation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. H. Teh, M. Kimura, M. Yamamoto, N. Tanaka, I. Yamaguchi, T. Kumasaka
The 1. 48 A Resolution Crystal Structure Of The Homotetrameric Cytidine Deaminase From Mouse
Biochemistry V. 45 7825 2006
PubMed-ID: 16784234 | Reference-DOI: 10.1021/BI060345F
(for further references see the PDB file header)

Molecule 1 - CYTIDINE DEAMINASE
	Chains	:	A, B, C, D
	EC Number	:	3.5.4.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21C
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (2x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION
2	URD	4	Ligand/Ion	1-((2R,3R,4S,5R)-TETRAHYDRO-3,4-DIHYDROXY-5-(HYDROXYMETHYL)FURAN-2-YL)PYRIDINE-2,4(1H,3H)-DIONE
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION
2	URD	4	Ligand/Ion	1-((2R,3R,4S,5R)-TETRAHYDRO-3,4-DIHYDROXY-5-(HYDROXYMETHYL)FURAN-2-YL)PYRIDINE-2,4(1H,3H)-DIONE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 10)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	URD	8	Ligand/Ion	1-((2R,3R,4S,5R)-TETRAHYDRO-3,4-DIHYDROXY-5-(HYDROXYMETHYL)FURAN-2-YL)PYRIDINE-2,4(1H,3H)-DIONE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:65 , CYS A:99 , CYS A:102 , HOH A:1006	BINDING SITE FOR RESIDUE ZN A 147
2	AC2	SOFTWARE	CYS B:65 , CYS B:99 , CYS B:102 , HOH B:1003	BINDING SITE FOR RESIDUE ZN B 147
3	AC3	SOFTWARE	CYS C:65 , CYS C:99 , CYS C:102 , HOH C:1004	BINDING SITE FOR RESIDUE ZN C 147
4	AC4	SOFTWARE	CYS D:65 , CYS D:99 , CYS D:102 , HOH D:1005	BINDING SITE FOR RESIDUE ZN D 147
5	AC5	SOFTWARE	GLN A:130 , ALA A:135 , HOH A:1010 , HOH A:1070	BINDING SITE FOR RESIDUE SO4 A 1005
6	AC6	SOFTWARE	PHE A:36 , VAL A:38 , ASN A:54 , GLU A:56 , CYS A:65 , ALA A:66 , GLU A:67 , ILE A:96 , SER A:97 , PRO A:98 , HOH A:1007 , ALA C:58 , CYS C:59 , TYR C:60 , PRO C:61	BINDING SITE FOR RESIDUE URD A 1001
7	AC7	SOFTWARE	PHE A:137 , PHE B:36 , VAL B:38 , ASN B:54 , GLU B:56 , CYS B:65 , ALA B:66 , GLU B:67 , SER B:97 , HOH B:1003 , HOH B:1004 , ALA D:58 , CYS D:59 , TYR D:60 , PRO D:61	BINDING SITE FOR RESIDUE URD B 1002
8	AC8	SOFTWARE	ALA A:58 , CYS A:59 , TYR A:60 , PRO A:61 , PHE C:36 , VAL C:38 , ASN C:54 , GLU C:56 , VAL C:64 , CYS C:65 , ALA C:66 , GLU C:67 , SER C:97 , PRO C:98 , HOH C:1005	BINDING SITE FOR RESIDUE URD C 1003
9	AC9	SOFTWARE	ALA B:58 , CYS B:59 , TYR B:60 , PRO B:61 , PHE D:36 , VAL D:38 , ASN D:54 , GLU D:56 , CYS D:65 , ALA D:66 , GLU D:67 , SER D:97 , PRO D:98 , HOH D:1005 , HOH D:1006	BINDING SITE FOR RESIDUE URD D 1004

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

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

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	CDD_MOUSE	13-140	4	A:13-140 B:13-140 C:13-140 D:13-140
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	CDD_MOUSE	65-106	4	A:65-106 B:65-106 C:65-106 D:65-106

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	CDD_MOUSE	13-140	4	A:13-140 B:13-140 C:13-140 D:13-140
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	CDD_MOUSE	65-106	4	A:65-106 B:65-106 C:65-106 D:65-106

Biological Unit 2 (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	CDD_MOUSE	13-140	8	A:13-140 B:13-140 C:13-140 D:13-140
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	CDD_MOUSE	65-106	8	A:65-106 B:65-106 C:65-106 D:65-106

(no "Exon" information available for 1ZAB)

Asymmetric 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:137
 aligned with CDD_MOUSE | P56389 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:137
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       
            CDD_MOUSE    10 VEPEHVQRLLLSSREAKKSAYCPYSRFPVGAALLTGDGRIFSGCNIENACYPLGVCAERTAIQKAISEGYKDFRAIAISSDLQEEFISPCGACRQVMREFGTDWAVYMTKPDGTFVVRTVQELLPASFGPEDLQKIQ 146
               SCOP domains d1zaba1 A:10-146 mono-domain cytidine deaminase                                                                                           SCOP domains
               CATH domains 1zabA00 A:10-146 Cytidine Deaminase, domain 2                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeeee.........hhhhhhhhhhh....eeeee.....eeeeehhhhh....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CYT_DCMP_DEAMINASES_2  PDB: A:13-140 UniProt: 13-140                                                                            ------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:65-106      ---------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zab A  10 VEPEHVQRLLLSSREAKKSAYCPYSRFPVGAALLTGDGRIFSGCNIENACYPLGVCAERTAIQKAISEGYKDFRAIAISSDLQEEFISPCGACRQVMREFGTDWAVYMTKPDGTFVVRTVQELLPASFGPEDLQKIQ 146
                                    19        29        39        49        59        69        79        89        99       109       119       129       139

Chain B from PDB  Type:PROTEIN  Length:134
 aligned with CDD_MOUSE | P56389 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:134
                                    19        29        39        49        59        69        79        89        99       109       119       129       139    
            CDD_MOUSE    10 VEPEHVQRLLLSSREAKKSAYCPYSRFPVGAALLTGDGRIFSGCNIENACYPLGVCAERTAIQKAISEGYKDFRAIAISSDLQEEFISPCGACRQVMREFGTDWAVYMTKPDGTFVVRTVQELLPASFGPEDLQ 143
               SCOP domains d1zabb_ B: automated matches                                                                                                           SCOP domains
               CATH domains 1zabB00 B:10-143 Cytidine Deaminase, domain 2                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeeee.........hhhhhhhhhhh....eeeee.....eeeeehhhhh....hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CYT_DCMP_DEAMINASES_2  PDB: B:13-140 UniProt: 13-140                                                                            --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:65-106      ------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zab B  10 VEPEHVQRLLLSSREAKKSAYCPYSRFPVGAALLTGDGRIFSGCNIENACYPLGVCAERTAIQKAISEGYKDFRAIAISSDLQEEFISPCGACRQVMREFGTDWAVYMTKPDGTFVVRTVQELLPASFGPEDLQ 143
                                    19        29        39        49        59        69        79        89        99       109       119       129       139

Chain C from PDB  Type:PROTEIN  Length:136
 aligned with CDD_MOUSE | P56389 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:136
                                    18        28        38        48        58        68        78        88        98       108       118       128       138      
            CDD_MOUSE     9 AVEPEHVQRLLLSSREAKKSAYCPYSRFPVGAALLTGDGRIFSGCNIENACYPLGVCAERTAIQKAISEGYKDFRAIAISSDLQEEFISPCGACRQVMREFGTDWAVYMTKPDGTFVVRTVQELLPASFGPEDLQK 144
               SCOP domains d1zabc_ C: automated matches                                                                                                             SCOP domains
               CATH domains 1zabC00 C:9-144 Cytidine Deaminase, domain 2                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeeee.........hhhhhhhhhhh....eeeee.....eeeeehhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----CYT_DCMP_DEAMINASES_2  PDB: C:13-140 UniProt: 13-140                                                                            ---- PROSITE (1)
                PROSITE (2) --------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: C:65-106      -------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zab C   9 AVEPEHVQRLLLSSREAKKSAYCPYSRFPVGAALLTGDGRIFSGCNIENACYPLGVCAERTAIQKAISEGYKDFRAIAISSDLQEEFISPCGACRQVMREFGTDWAVYMTKPDGTFVVRTVQELLPASFGPEDLQK 144
                                    18        28        38        48        58        68        78        88        98       108       118       128       138

Chain D from PDB  Type:PROTEIN  Length:137
 aligned with CDD_MOUSE | P56389 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:137
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       
            CDD_MOUSE    10 VEPEHVQRLLLSSREAKKSAYCPYSRFPVGAALLTGDGRIFSGCNIENACYPLGVCAERTAIQKAISEGYKDFRAIAISSDLQEEFISPCGACRQVMREFGTDWAVYMTKPDGTFVVRTVQELLPASFGPEDLQKIQ 146
               SCOP domains d1zabd_ D: automated matches                                                                                                              SCOP domains
               CATH domains 1zabD00 D:10-146 Cytidine Deaminase, domain 2                                                                                             CATH domains
           Pfam domains (1) --dCMP_cyt_deam_1-1zabD01 D:12-118                                                                           ---------------------------- Pfam domains (1)
           Pfam domains (2) --dCMP_cyt_deam_1-1zabD02 D:12-118                                                                           ---------------------------- Pfam domains (2)
           Pfam domains (3) --dCMP_cyt_deam_1-1zabD03 D:12-118                                                                           ---------------------------- Pfam domains (3)
           Pfam domains (4) --dCMP_cyt_deam_1-1zabD04 D:12-118                                                                           ---------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeeee.........hhhhhhhhhhh....eeeee.....eeeeehhhhh....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CYT_DCMP_DEAMINASES_2  PDB: D:13-140 UniProt: 13-140                                                                            ------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: D:65-106      ---------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zab D  10 VEPEHVQRLLLSSREAKKSAYCPYSRFPVGAALLTGDGRIFSGCNIENACYPLGVCAERTAIQKAISEGYKDFRAIAISSDLQEEFISPCGACRQVMREFGTDWAVYMTKPDGTFVVRTVQELLPASFGPEDLQKIQ 146
                                    19        29        39        49        59        69        79        89        99       109       119       129       139

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 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: Cytidine deaminase (22)

Protein domain: automated matches (9)

Mouse (Mus musculus) [TaxId: 10090] (3)

1a	d1zabb_	B:
1b	d1zabd_	D:
1c	d1zabc_	C:

Protein domain: mono-domain cytidine deaminase (8)

Mouse (Mus musculus) [TaxId: 10090] (1)

d1zaba1

A:10-146

Asymmetric 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)

House mouse (Mus musculus) (3)

1a	1zabA00	A:10-146
1b	1zabC00	C:9-144
1c	1zabB00	B:10-143
1d	1zabD00	D:10-146

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CDA (39)

Family: dCMP_cyt_deam_1 (28)

Mus musculus (Mouse) (1)

1a	dCMP_cyt_deam_1-1zabD01	D:12-118
1b	dCMP_cyt_deam_1-1zabD02	D:12-118
1c	dCMP_cyt_deam_1-1zabD03	D:12-118
1d	dCMP_cyt_deam_1-1zabD04	D:12-118

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CDD_MOUSE | P56389)

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:0004126	cytidine deaminase activity	Catalysis of the reaction: cytidine + H2O = uridine + 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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0001882	nucleoside binding	Interacting selectively and non-covalently with a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0009972	cytidine deamination	The removal of amino group in the presence of water.
	GO:0030308	negative regulation of cell growth	Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
	GO:0045980	negative regulation of nucleotide metabolic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleotides.
	GO:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Cis Peptide Bonds
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	CDD_MOUSE \| P56389	:	2fr5 2fr6

2fr5	THE SAME PROTEIN COMPLEXED WITH TETRAHYDROURIDINE.
2fr6	THE SAME PROTEIN COMPLEXED WITH CYTIDINE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

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