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Title :   CRYSTAL STRUCTURE OF THE 5'-DEOXYNUCLEOTIDASE YFBR MUTANT E72A COMPLEXED WITH CO(2+) AND DAMP

Authors :   M. D. Zimmerman, M. Proudfoot, A. Yakunin, W. Minor

Date :   27 Mar 07 (Deposition) - 04 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (3x)

Keywords :   Nucleotidase, 5'-Deoxynucleotidase, Yfbr, Hd Domain Phosphohydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. D. Zimmerman, M. Proudfoot, A. Yakunin, W. Minor
Structural Insight Into The Mechanism Of Substrate Specificity And Catalytic Activity Of An Hd-Domain Phosphohydrolase: The 5'-Deoxyribonucleotidase Yfbr From Escherichia Coli.
J. Mol. Biol. V. 378 215 2008
PubMed-ID: 18353368 | Reference-DOI: 10.1016/J.JMB.2008.02.036

Molecule 1 - 5'-DEOXYNUCLEOTIDASE YFBR
	Chains	:	A, B
	EC Number	:	3.1.3.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MODIFIED PET-15B
	Expression System Strain	:	ROSETTA2(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YFBR, B2291, JW2288
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	NUCLEOSIDE 5'-MONOPHOSPHATE PHOSPHOHYDROLASE, 5'- DEOXYRIBONUCLEOTIDASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CO	2	Ligand/Ion	COBALT (II) ION
2	D5M	2	Ligand/Ion	2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	D5M	2	Ligand/Ion	2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (2, 9)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	D5M	6	Ligand/Ion	2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
3	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:33 , HIS A:68 , ASP A:69 , ASP A:137 , HOH A:425	BINDING SITE FOR RESIDUE CO A 201
2	AC2	SOFTWARE	HIS B:33 , HIS B:68 , ASP B:69 , ASP B:137	BINDING SITE FOR RESIDUE CO B 201
3	AC3	SOFTWARE	ARG A:18 , TRP A:19 , HIS A:33 , ASP A:69 , ASP A:77 , PRO A:79 , THR A:80 , ASP A:137 , HOH A:425	BINDING SITE FOR RESIDUE D5M A 301
4	AC4	SOFTWARE	ARG B:18 , TRP B:19 , HIS B:33 , ASP B:69 , ASP B:77 , LEU B:78 , PRO B:79 , THR B:80 , PRO B:81 , ASP B:137	BINDING SITE FOR RESIDUE D5M B 301
5	AC5	SOFTWARE	GLU A:122 , TYR A:125 , LYS A:134 , ASP A:137	BINDING SITE FOR RESIDUE PEG A 401

(no "SS Bond" information available for 2PAU)

(no "Cis Peptide Bond" information available for 2PAU)

(no "SAP(SNP)/Variant" information available for 2PAU)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HD	PS51831	HD domain profile.	5DNU_ECOLI	30-142	2	A:30-142 B:30-142

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HD	PS51831	HD domain profile.	5DNU_ECOLI	30-142	2	A:30-142 B:30-142

Biological Unit 2 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HD	PS51831	HD domain profile.	5DNU_ECOLI	30-142	6	A:30-142 B:30-142

(no "Exon" information available for 2PAU)

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:176
 aligned with 5DNU_ECOLI | P76491 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:183
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183   
           5DNU_ECOLI     4 SHFFAHLSRLKLINRWPLMRNVRTENVSEHSLQVAMVAHALAAIKNRKFGGNVNAERIALLAMYHDASEVLTGDLPTPVKYFNSQIAQEYKAIEKIAQQKLVDMVPEELRDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAKTRLEATLEARRSQEMDYFMEIFVPSF 186
               SCOP domains d2paua_ A: 5'-nucleotidase YfbR                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhh.....-------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------HD  PDB: A:30-142 UniProt: 30-142                                                                                -------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pau A   4 SHFFAHLSRLKLINRWPLMRNVRTENVSEHSLQVAMVAHALAAIKNRKFGGNVNAERIALLAMYHDASAVLTGDLPTP-------IAQEYKAIEKIAQQKLVDMVPEELRDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAKTRLEATLEARRSQEMDYFMEIFVPSF 186
                                    13        23        33        43        53        63        73       | -     |  93       103       113       123       133       143       153       163       173       183   
                                                                                                        81      89

Chain B from PDB  Type:PROTEIN  Length:177
 aligned with 5DNU_ECOLI | P76491 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:185
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     
           5DNU_ECOLI     2 KQSHFFAHLSRLKLINRWPLMRNVRTENVSEHSLQVAMVAHALAAIKNRKFGGNVNAERIALLAMYHDASEVLTGDLPTPVKYFNSQIAQEYKAIEKIAQQKLVDMVPEELRDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAKTRLEATLEARRSQEMDYFMEIFVPSF 186
               SCOP domains d2paub_ B: 5'-nucleotidase YfbR                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhh.....--------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------HD  PDB: B:30-142 UniProt: 30-142                                                                                -------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pau B   2 KQSHFFAHLSRLKLINRWPLMRNVRTENVSEHSLQVAMVAHALAAIKNRKFGGNVNAERIALLAMYHDASAVLTGDLPTP--------AQEYKAIEKIAQQKLVDMVPEELRDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAKTRLEATLEARRSQEMDYFMEIFVPSF 186
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     
                                                                                                          81       90

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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: All alpha proteins (14657)

Fold: HD-domain/PDEase-like (204)

Superfamily: HD-domain/PDEase-like (204)

Family: HD domain (20)

Protein domain: 5'-nucleotidase YfbR (3)

Escherichia coli [TaxId: 562] (3)

1a	d2paua_	A:
1b	d2paub_	B:

(no "CATH Domain" information available for 2PAU)

(no "Pfam Domain" information available for 2PAU)

Asymmetric Unit(hide GO term definitions)

Chain A,B (5DNU_ECOLI | P76491)

molecular function
	GO:0050897	cobalt ion binding	Interacting selectively and non-covalently with a cobalt (Co) ion.
	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:0008252	nucleotidase activity	Catalysis of the reaction: a nucleotide + H2O = a nucleoside + phosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
biological process
	GO:0006226	dUMP biosynthetic process	The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0010139	pyrimidine deoxyribonucleotide salvage	The pathway by which pyrimidine bases or pyrimidine deoxyribonucleotides from pyrimidine nucleotide breakdown are converted back to pyrimidine deoxyribonucleotides. The salvage pathway is important where there is no de novo pyrimidine deoxyribonucleotide biosynthesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	5DNU_ECOLI \| P76491	:	2paq 2par

2paq	CRYSTAL STRUCTURE OF 5'-DEOXYNUCLEOTIDASE YFBR
2par	CRYSTAL STRUCTURE OF 5'-DEOXYNUCLEOTIDASE YFBR MUTANT E72A COMPLEXED WITH CO(2+) AND TMP

Description

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Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

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