3IJF - JenaLib

Title :   CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE FROM MYCOBACTERIUM TUBERCULOSIS

Authors :   W. F. De Azevedo Jr. , L. A. Basso, D. S. Santos

Date :   04 Aug 09 (Deposition) - 02 Mar 10 (Release) - 02 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.99

Chains :   Asym. Unit : X
Biol. Unit 1: X  (4x)
Biol. Unit 2: X  (2x)
Biol. Unit 3: X  (2x)

Keywords :   Mycobacterium Tuberculosis, Cytidine Deaminase, Drug Target, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. A. Sanchez-Quitian, C. Z. Schneider, R. G. Ducati, W. F. De Azevedo, C. Bloch, L. A. Basso, D. S. Santos
Structural And Functional Analyses Of Mycobacterium Tuberculosis Rv3315C-Encoded Metal-Dependent Homotetrameric Cytidine Deaminase.
J. Struct. Biol. V. 169 413 2010
PubMed-ID: 20035876 | Reference-DOI: 10.1016/J.JSB.2009.12.019

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	CDD_MYCTO	4-126	1	X:4-125
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	CDD_MYCTU	4-126	1	X:4-125
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	CDD_MYCTO	56-96	1	X:56-96
2	CYT_DCMP_DEAMINASES_1	PS00903		CDD_MYCTU	56-96	1	X:56-96

Biological Unit 1 (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_MYCTO	4-126	4	X:4-125
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	CDD_MYCTU	4-126	4	X:4-125
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	CDD_MYCTO	56-96	4	X:56-96
2	CYT_DCMP_DEAMINASES_1	PS00903		CDD_MYCTU	56-96	4	X:56-96

Biological Unit 2 (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_MYCTO	4-126	2	X:4-125
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	CDD_MYCTU	4-126	2	X:4-125
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	CDD_MYCTO	56-96	2	X:56-96
2	CYT_DCMP_DEAMINASES_1	PS00903		CDD_MYCTU	56-96	2	X:56-96

Biological Unit 3 (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_MYCTO	4-126	2	X:4-125
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	CDD_MYCTU	4-126	2	X:4-125
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	CDD_MYCTO	56-96	2	X:56-96
2	CYT_DCMP_DEAMINASES_1	PS00903		CDD_MYCTU	56-96	2	X:56-96

Exons (0, 0)

Sequences/Alignments

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 X from PDB  Type:PROTEIN  Length:123
 aligned with CDD_MYCTO | P9WPH2 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:123
                                    12        22        32        42        52        62        72        82        92       102       112       122   
            CDD_MYCTO     3 DVDWNMLRGNATQAAAGAYVPYSRFAVGAAALVDDGRVVTGCNVENVSYGLTLCAECAVVCALHSTGGGRLLALACVDGHGSVLMPCGRCRQVLLEHGGSELLIDHPVRPRRLGDLLPDAFGL 125
               SCOP domains d3ijfx_ X: automated matches                                                                                                SCOP domains
               CATH domains 3ijfX00 X:3-125 Cytidine Deaminase, domain 2                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhh...ee......eehhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -CYT_DCMP_DEAMINASES_2  PDB: X:4-125 UniProt: 4-126                                                                         PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: X:56-96      ----------------------------- PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ijf X   3 DVDWNMLRGNATQAAAGAYVPYSRFAVGAAALVDDGRVVTGCNVENVSYGLTLCAECAVVCALHSTGGGRLLALACVDGHGSVLMPCGRCRQVLLEHGGSELLIDHPVRPRRLGDLLPDAFGL 125
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain X from PDB  Type:PROTEIN  Length:123
 aligned with CDD_MYCTU | P9WPH3 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:123
                                    12        22        32        42        52        62        72        82        92       102       112       122   
            CDD_MYCTU     3 DVDWNMLRGNATQAAAGAYVPYSRFAVGAAALVDDGRVVTGCNVENVSYGLTLCAECAVVCALHSTGGGRLLALACVDGHGSVLMPCGRCRQVLLEHGGSELLIDHPVRPRRLGDLLPDAFGL 125
               SCOP domains d3ijfx_ X: automated matches                                                                                                SCOP domains
               CATH domains 3ijfX00 X:3-125 Cytidine Deaminase, domain 2                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..........eeeeeee....eeeee.....hhhhh.hhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhh...ee......eehhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -CYT_DCMP_DEAMINASES_2  PDB: X:4-125 UniProt: 4-126                                                                         PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: X:56-96      ----------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ijf X   3 DVDWNMLRGNATQAAAGAYVPYSRFAVGAAALVDDGRVVTGCNVENVSYGLTLCAECAVVCALHSTGGGRLLALACVDGHGSVLMPCGRCRQVLLEHGGSELLIDHPVRPRRLGDLLPDAFGL 125
                                    12        22        32        42        52        62        72        82        92       102       112       122

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (11, 17)

Asymmetric Unit(hide GO term definitions)

Chain X (CDD_MYCTU | P9WPH3)

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:0047844	deoxycytidine deaminase activity	Catalysis of the reaction: deoxycytidine + H2O = deoxyuridine + 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:0009972	cytidine deamination	The removal of amino group in the presence of water.
	GO:0043100	pyrimidine nucleobase salvage	Any process that generates pyrimidine nucleobases, 1,3-diazine organic nitrogenous bases, from derivatives of them without de novo synthesis.
	GO:0046109	uridine biosynthetic process	The chemical reactions and pathways resulting in the formation of uridine, uracil riboside, a ribonucleoside very widely distributed but occurring almost entirely as phosphoric esters in ribonucleotides and ribonucleic acids.
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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain X (CDD_MYCTO | P9WPH2)

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: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:0009972	cytidine deamination	The removal of amino group in the presence of water.

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