1VQ2 - JenaLib

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Description

Title :   CRYSTAL STRUCTURE OF T4-BACTERIOPHAGE DEOXYCYTIDYLATE DEAMINASE, MUTANT R115E

Authors :   R. Almog, F. Maley, G. F. Maley, R. Maccoll, P. Van Roey

Date :   15 Dec 04 (Deposition) - 21 Dec 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)
Biol. Unit 2: A  (6x)

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

Reference :   R. Almog, F. Maley, G. F. Maley, R. Maccoll, P. Van Roey
Three-Dimensional Structure Of The R115E Mutant Of T4-Bacteriophage 2'-Deoxycytidylate Deaminase
Biochemistry V. 43 13715 2004
PubMed-ID: 15504034 | Reference-DOI: 10.1021/BI048928H

Compounds

Molecule 1 - DEOXYCYTIDYLATE DEAMINASE
	Chains	:	A
	EC Number	:	3.5.4.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CD
	Mutation	:	YES
	Organism Scientific	:	ENTEROBACTERIA PHAGE T4
	Organism Taxid	:	10665
	Synonym	:	DCMP DEAMINASE

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A
Biological Unit 2 (6x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 3)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	DDN	1	Ligand/Ion	3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	DDN	2	Ligand/Ion	3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	DDN	6	Ligand/Ion	3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	ZN	-1	Ligand/Ion	ZINC ION

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:104 , CYS A:132 , CYS A:135 , DDN A:308	BINDING SITE FOR RESIDUE ZN A 701
2	AC2	SOFTWARE	CYS A:19 , CYS A:49 , HIS A:94 , GLU A:102	BINDING SITE FOR RESIDUE ZN A 702
3	AC3	SOFTWARE	CYS A:19 , SER A:21 , TRP A:22 , VAL A:24 , ASN A:40 , ARG A:91 , HIS A:94 , SER A:95 , SER A:98 , GLU A:102 , HIS A:104 , ALA A:105 , GLU A:106 , PRO A:131 , CYS A:132 , CYS A:135 , TYR A:153 , LYS A:155 , ZN A:701	BINDING SITE FOR RESIDUE DDN A 308

SS Bonds (0, 0)

(no "SS Bond" information available for 1VQ2)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1VQ2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1VQ2)

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.	DCTD_BPT4	1-171	1	A:1-171
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	DCTD_BPT4	104-139	1	A:104-139

Biological Unit 1 (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.	DCTD_BPT4	1-171	2	A:1-171
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	DCTD_BPT4	104-139	2	A:104-139

Biological Unit 2 (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYT_DCMP_DEAMINASES_2	PS51747	Cytidine and deoxycytidylate deaminases domain profile.	DCTD_BPT4	1-171	6	A:1-171
2	CYT_DCMP_DEAMINASES_1	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.	DCTD_BPT4	104-139	6	A:104-139

Exons (0, 0)

(no "Exon" information available for 1VQ2)

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 A from PDB  Type:PROTEIN  Length:173
 aligned with DCTD_BPT4 | P16006 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   
            DCTD_BPT4     1 MKASTVLQIAYLVSQESKCCSWKVGAVIEKNGRIISTGYNGSPAGGVNCCDYAAEQGWLLNKPKHAIIQGHKPECVSFGSTDRFVLAKEHRSAHSEWSSKNEIHAELNAILFAARNGSSIEGATMYVTLSPCPDCAKAIAQSGIKKLVYCETYDKNKPGWDDILRNAGIEVFNVPKKNLNKLNWENINEFCGE 193
               SCOP domains d1vq2a_ A: Deoxycytidylate deaminase                                                                                                                                                              SCOP domains
               CATH domains 1vq2A00 A:1-193 Cytidine Deaminase, domain 2                                                                                                                                                      CATH domains
               Pfam domains dCMP_cyt_deam_1-1vq2A01 A:1-151                                                                                                                        ------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.........eeeeee..eeeeeee........hhhhhhhhhh.ee..--------------------..ee...hhhhhhhhhhhhh.hhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhh...eeeeee.........hhhhhhh..eeee.hhhhh...hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CYT_DCMP_DEAMINASES_2  PDB: A:1-171 UniProt: 1-171                                                                                                                         ---------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:104-13------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vq2 A   1 MKASTVLQIAYLVSQESKCCSWKVGAVIEKNGRIISTGYNGSPAGGVNCCDYAAEQGWLLNK--------------------RFVLAKEHRSAHSEWSSKNEIHAELNAILFAAENGSSIEGATMYVTLSPCPDCAKAIAQSGIKKLVYCETYDKNKPGWDDILRNAGIEVFNVPKKNLNKLNWENINEFCGE 193
                                    10        20        30        40        50        60 |       -         -  |     90       100       110       120       130       140       150       160       170       180       190   
                                                                                        62                   83

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)

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: Deoxycytidylate deaminase-like (29)

Protein domain: Deoxycytidylate deaminase (1)

Bacteriophage T4 [TaxId: 10665] (1)

d1vq2a_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

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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)

Enterobacteria phage t4. Organism_taxid: 10665. (1)

1vq2A00

A:1-193

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CDA (39)

Family: dCMP_cyt_deam_1 (28)

Enterobacteria phage T4 (Bacteriophage T4) (1)

dCMP_cyt_deam_1-1vq2A01

A:1-151

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A (DCTD_BPT4 | P16006)

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:0004132	dCMP deaminase activity	Catalysis of the reaction: dCMP + H2O = dUMP + 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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0009165	nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
	GO:0006220	pyrimidine nucleotide metabolic process	The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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Description

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