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Title :   CRYSTAL STRUCTURE OF THE 5'-DEOXYNUCLEOTIDASE YFBR

Authors :   M. D. Zimmerman, M. Chruszcz, M. Cymborowski, M. Kudritska, W. Minor, M Center For Structural Genomics (Mcsg)

Date :   27 Mar 07 (Deposition) - 10 Apr 07 (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, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, 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	:	B834(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YFBR, B2291, JW2288
	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 (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 36)

No.	Name	Count	Type	Full Name
1	MSE	36	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2PAQ)

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

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

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

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 2PAQ)

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:177
 aligned with 5DNU_ECOLI | P76491 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:186
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      
           5DNU_ECOLI     2 KQSHFFAHLSRLKLINRWPLMRNVRTENVSEHSLQVAMVAHALAAIKNRKFGGNVNAERIALLAMYHDASEVLTGDLPTPVKYFNSQIAQEYKAIEKIAQQKLVDMVPEELRDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAKTRLEATLEARRSQEMDYFMEIFVPSFH 187
               SCOP domains d2paqa_ A: 5'-nucleotidase YfbR                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhh.....---------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------HD  PDB: A:30-142 UniProt: 30-142                                                                                --------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2paq A   2 KQSHFFAHLSRLKLINRWPLmRNVRTENVSEHSLQVAmVAHALAAIKNRKFGGNVNAERIALLAmYHDASEVLTGDLPTP---------QEYKAIEKIAQQKLVDmVPEELRDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAKTRLEATLEARRSQEmDYFmEIFVPSFH 187
                                    11        21|       31       |41        51        61    |   71        81        91       101     | 111       121       131       141       151       161       171   |   181      
                                               22-MSE           39-MSE                     66-MSE         81        91             107-MSE                                                             175-MSE        
                                                                                                                                                                                                           179-MSE

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with 5DNU_ECOLI | P76491 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:186
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      
           5DNU_ECOLI     2 KQSHFFAHLSRLKLINRWPLMRNVRTENVSEHSLQVAMVAHALAAIKNRKFGGNVNAERIALLAMYHDASEVLTGDLPTPVKYFNSQIAQEYKAIEKIAQQKLVDMVPEELRDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAKTRLEATLEARRSQEMDYFMEIFVPSFH 187
               SCOP domains d2paqb_ B: 5'-nucleotidase YfbR                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhh.....----------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------HD  PDB: B:30-142 UniProt: 30-142                                                                                --------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2paq B   2 KQSHFFAHLSRLKLINRWPLmRNVRTENVSEHSLQVAmVAHALAAIKNRKFGGNVNAERIALLAmYHDASEVLTGDLPTP----------EYKAIEKIAQQKLVDmVPEELRDIFAPLIDEHAYSDEEKSLVKQADALCAYLKCLEELAAGNNEFLLAKTRLEATLEARRSQEmDYFmEIFVPSFH 187
                                    11        21|       31       |41        51        61    |   71        81         -|      101     | 111       121       131       141       151       161       171   |   181      
                                               22-MSE           39-MSE                     66-MSE         81         92            107-MSE                                                             175-MSE        
                                                                                                                                                                                                           179-MSE

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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	d2paqa_	A:
1b	d2paqb_	B:

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

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

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	:	2par 2pau

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

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