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Title :   CRYSTAL STRUCTURE OF HUMAN CYTIDINE DEAMINASE

Authors :   S. J. Chung, J. C. Fromme, G. L. Verdine

Date :   13 Sep 02 (Deposition) - 04 Nov 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Human, Enzyme, Cytidine Deaminase, Amine Hydrolase, Inhibitor, Diazepinone, Leukemia, Chemotherapy, Anticancer, Drug, Phi-Phi Interaction, Edge-To-Face Interaction, Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Chung, J. C. Fromme, G. L. Verdine
Structure Of Human Cytidine Deaminase Bound To A Potent Inhibitor
J. Med. Chem. V. 48 658 2005
PubMed-ID: 15689149 | Reference-DOI: 10.1021/JM0496279

Molecule 1 - CYTIDINE DEAMINASE
	Chains	:	A, B
	EC Number	:	3.5.4.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CYTIDINE AMINOHYDROLASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	BRD	2	Ligand/Ion	1-BETA-RIBOFURANOSYL-1,3-DIAZEPINONE
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	BRD	4	Ligand/Ion	1-BETA-RIBOFURANOSYL-1,3-DIAZEPINONE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:65 , GLU A:67 , CYS A:99 , CYS A:102	BINDING SITE FOR RESIDUE ZN A 147
2	AC2	SOFTWARE	CYS B:65 , CYS B:99 , CYS B:102 , HOH B:151	BINDING SITE FOR RESIDUE ZN B 147
3	AC3	SOFTWARE	PHE A:36 , VAL A:38 , ASN A:54 , GLU A:56 , ILE A:64 , CYS A:65 , ALA A:66 , GLU A:67 , HOH A:159 , ALA B:58 , CYS B:59 , TYR B:60	BINDING SITE FOR RESIDUE BRD A 148
4	AC4	SOFTWARE	ALA A:58 , CYS A:59 , TYR A:60 , PRO A:61 , PHE B:36 , VAL B:38 , ASN B:54 , GLU B:56 , ILE B:64 , CYS B:65 , ALA B:66 , GLU B:67 , SER B:97 , HOH B:151 , HOH B:157	BINDING SITE FOR RESIDUE BRD B 149

(no "SS Bond" information available for 1MQ0)

(no "Cis Peptide Bond" information available for 1MQ0)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_021559	K	27	Q	CDD_HUMAN	Polymorphism	2072671	A/B	Q	27	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_021559	K	27	Q	CDD_HUMAN	Polymorphism	2072671	A/B	Q	27	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric 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.	CDD_HUMAN	13-140	2	A:13-140 B:13-140
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	CDD_HUMAN	65-106	2	A:65-106 B: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_HUMAN	13-140	4	A:13-140 B:13-140
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	CDD_HUMAN	65-106	4	A:65-106 B:65-106

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000375071	1a	ENSE00001465671	chr1:20915441-20915776	336	CDD_HUMAN	1-52	52	2	A:13-52 B:13-52	40 40
1.2	ENST00000375071	2	ENSE00001041262	chr1:20931421-20931532	112	CDD_HUMAN	52-89	38	2	A:52-89 B:52-89	38 38
1.3	ENST00000375071	3	ENSE00001041265	chr1:20940335-20940392	58	CDD_HUMAN	89-108	20	2	A:89-108 B:89-108	20 20
1.4b	ENST00000375071	4b	ENSE00001906111	chr1:20944945-20945401	457	CDD_HUMAN	109-146	38	2	A:109-142 B:109-142	34 34

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:130
 aligned with CDD_HUMAN | P32320 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:130
                                    22        32        42        52        62        72        82        92       102       112       122       132       142
            CDD_HUMAN    13 ECVQQLLVCSQEAKKSAYCPYSHFPVGAALLTQEGRIFKGCNIENACYPLGICAERTAIQKAVSEGYKDFRAIAIASDMQDDFISPCGACRQVMREFGTNWPVYMTKPDGTYIVMTVQELLPSSFGPEDL 142
               SCOP domains d1mq0a_ A: mono-domain cytidine deaminase                                                                                          SCOP domains
               CATH domains 1mq0A00 A:13-142 Cytidine Deaminase, domain 2                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh........eeeeee.....eeeee.....hhhhh.hhhhhhhhhhhhh......eeeeee.........hhhhhhhhhh.....eeeee.....eeeeehhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------Q------------------------------------------------------------------------------------------------------------------- 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 1 (1) Exon 1.1a  PDB: A:13-52 UniProt: 1-52   ------------------------------------Exon 1.3            Exon 1.4b  PDB: A:109-142          Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.2  PDB: A:52-89 UniProt: 52-89 ----------------------------------------------------- Transcript 1 (2)
                 1mq0 A  13 ECVQQLLVCSQEAKQSAYCPYSHFPVGAALLTQEGRIFKGCNIENACYPLGICAERTAIQKAVSEGYKDFRAIAIASDMQDDFISPCGACRQVMREFGTNWPVYMTKPDGTYIVMTVQELLPSSFGPEDL 142
                                    22        32        42        52        62        72        82        92       102       112       122       132       142

Chain B from PDB  Type:PROTEIN  Length:130
 aligned with CDD_HUMAN | P32320 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:130
                                    22        32        42        52        62        72        82        92       102       112       122       132       142
            CDD_HUMAN    13 ECVQQLLVCSQEAKKSAYCPYSHFPVGAALLTQEGRIFKGCNIENACYPLGICAERTAIQKAVSEGYKDFRAIAIASDMQDDFISPCGACRQVMREFGTNWPVYMTKPDGTYIVMTVQELLPSSFGPEDL 142
               SCOP domains d1mq0b_ B: mono-domain cytidine deaminase                                                                                          SCOP domains
               CATH domains 1mq0B00 B:13-142 Cytidine Deaminase, domain 2                                                                                      CATH domains
           Pfam domains (1) dCMP_cyt_deam_1-1mq0B01 B:13-118                                                                          ------------------------ Pfam domains (1)
           Pfam domains (2) dCMP_cyt_deam_1-1mq0B02 B:13-118                                                                          ------------------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhh........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhh.....eeeeeeee.........hhhhhhhhhhh....eeeee.....eeeeehhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------Q------------------------------------------------------------------------------------------------------------------- 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 1 (1) Exon 1.1a  PDB: B:13-52 UniProt: 1-52   ------------------------------------Exon 1.3            Exon 1.4b  PDB: B:109-142          Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.2  PDB: B:52-89 UniProt: 52-89 ----------------------------------------------------- Transcript 1 (2)
                 1mq0 B  13 ECVQQLLVCSQEAKQSAYCPYSHFPVGAALLTQEGRIFKGCNIENACYPLGICAERTAIQKAVSEGYKDFRAIAIASDMQDDFISPCGACRQVMREFGTNWPVYMTKPDGTYIVMTVQELLPSSFGPEDL 142
                                    22        32        42        52        62        72        82        92       102       112       122       132       142

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: Cytidine deaminase-like (78)

Superfamily: Cytidine deaminase-like (76)

Family: Cytidine deaminase (22)

Protein domain: mono-domain cytidine deaminase (8)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d1mq0a_	A:
1b	d1mq0b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

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

Topology: Cytidine Deaminase; domain 2 (44)

Homologous Superfamily: Cytidine Deaminase, domain 2 (32)

Human (Homo sapiens) (1)

1a	1mq0A00	A:13-142
1b	1mq0B00	B:13-142

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: CDA (39)

Family: dCMP_cyt_deam_1 (28)

Homo sapiens (Human) (2)

1a	dCMP_cyt_deam_1-1mq0B01	B:13-118
1b	dCMP_cyt_deam_1-1mq0B02	B:13-118

Asymmetric Unit(hide GO term definitions)

Chain A,B (CDD_HUMAN | P32320)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0009972	cytidine deamination	The removal of amino group in the presence of water.
	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: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.
	GO:0043097	pyrimidine nucleoside salvage	Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
	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.
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.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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1jtk	CYTIDINE DEAMINASE FROM B. SUBTILIS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (4, 8)

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