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Title :   STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF YFCE, A PHOSPHOESTERASE FROM E. COLI

Authors :   D. J. Miller, L. Shuvalova, E. Evdokimova, A. Savchenko, A. Yakunin, W. F. Anderson, Midwest Center For Structural Genomics (Mcsg)

Date :   25 Mar 04 (Deposition) - 17 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Yfce, Structural Genomics, Phosphoesterase, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. J. Miller, L. Shuvalova, E. Evdokimova, A. Savchenko, A. Yakunin, W. F. Anderson
Structural And Biochemical Characterization Of Yfce, A Phosphoesterase From E. Coli
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL PROTEIN YFCE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	469008
	Gene	:	YFCE, B2300, C2843, Z3562, ECS3184
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 14)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION
2	ZN	8	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:9 , ASP A:37 , ASN A:73 , HIS A:105 , HIS A:127 , ZN A:302 , SO4 A:501	BINDING SITE FOR RESIDUE ZN A 301
02	AC2	SOFTWARE	ASP A:9 , HIS A:11 , ASP A:37 , HIS A:129 , ZN A:301 , SO4 A:501	BINDING SITE FOR RESIDUE ZN A 302
03	AC3	SOFTWARE	ASP B:37 , ASN B:73 , HIS B:105 , HIS B:127 , ZN B:304 , SO4 B:502	BINDING SITE FOR RESIDUE ZN B 303
04	AC4	SOFTWARE	ASP B:9 , HIS B:11 , ASP B:37 , HIS B:129 , ZN B:303 , SO4 B:502	BINDING SITE FOR RESIDUE ZN B 304
05	AC5	SOFTWARE	ASP C:37 , ASN C:73 , HIS C:105 , HIS C:127 , ZN C:306 , SO4 C:503	BINDING SITE FOR RESIDUE ZN C 305
06	AC6	SOFTWARE	ASP C:9 , HIS C:11 , ASP C:37 , HIS C:129 , ZN C:305 , SO4 C:503	BINDING SITE FOR RESIDUE ZN C 306
07	AC7	SOFTWARE	ASP D:9 , HIS D:11 , ASP D:37 , HIS D:129 , ZN D:308 , SO4 D:505	BINDING SITE FOR RESIDUE ZN D 307
08	AC8	SOFTWARE	ASP D:37 , ASN D:73 , HIS D:105 , HIS D:127 , ZN D:307 , SO4 D:505	BINDING SITE FOR RESIDUE ZN D 308
09	AC9	SOFTWARE	HIS A:11 , ASP A:37 , ARG A:44 , ASN A:45 , ASN A:73 , CYS A:74 , HIS A:127 , HIS A:129 , ZN A:301 , ZN A:302 , HOH A:544	BINDING SITE FOR RESIDUE SO4 A 501
10	BC1	SOFTWARE	HIS B:11 , ASP B:37 , ASN B:45 , ASN B:73 , CYS B:74 , HIS B:127 , HIS B:129 , ZN B:303 , ZN B:304 , HOH B:537	BINDING SITE FOR RESIDUE SO4 B 502
11	BC2	SOFTWARE	ASP C:37 , ASN C:73 , HIS C:127 , HIS C:129 , ZN C:305 , ZN C:306	BINDING SITE FOR RESIDUE SO4 C 503
12	BC3	SOFTWARE	ARG C:71 , PRO C:90	BINDING SITE FOR RESIDUE SO4 C 504
13	BC4	SOFTWARE	HIS D:11 , ASP D:37 , ASN D:45 , ASN D:73 , HIS D:127 , HIS D:129 , ZN D:307 , ZN D:308	BINDING SITE FOR RESIDUE SO4 D 505
14	BC5	SOFTWARE	ARG D:71 , PRO D:90 , HOH D:591	BINDING SITE FOR RESIDUE SO4 D 506

(no "SS Bond" information available for 1SU1)

(no "Cis Peptide Bond" information available for 1SU1)

(no "SAP(SNP)/Variant" information available for 1SU1)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0025	PS01269	Uncharacterized protein family UPF0025 signature.	YFCE_ECOLI	121-145	4	A:121-145 B:121-145 C:121-145 D:121-145

(no "Exon" information available for 1SU1)

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:184
 aligned with YFCE_ECOLI | P67095 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    
           YFCE_ECOLI     1 MMKLMFASDIHGSLPATERVLELFAQSGAQWLVILGDVLNHGPRNALPEGYAPAKVAERLNEVAHKVIAVRGNCDSEVDQMLLHFPITAPWQQVLLEKQRLFLTHGHLFGPENLPALNQNDVLVYGHTHLPVAEQRGEIFHFNPGSVSIPKGGNPASYGMLDNDVLSVIALNDQSIIAQVAINP 184
               SCOP domains d1su1a_ A: Phosphodiesterase yfcE                                                                                                                                                        SCOP domains
               CATH domains 1su1A00 A:1-184  [code=3.60.21.10, no name defined]                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhh..eeee.................hhhhhhhhhhhhhh.eee......hhhhhhhh.......eeeee....eeeee.................eee.......eeeee..eeeee.............eeeeee..eeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------UPF0025  PDB: A:121-145  --------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1su1 A   1 MMKLMFASDIHGSLPATERVLELFAQSGAQWLVILGDVLNHGPRNALPEGYAPAKVVERLNEVAHKVIAVRGNCDSEVDQMLLHFPITAPWQQVLLEKQRLFLTHGHLFGPENLPALNQNDVLVYGHTHLPVAEQRGEIFHFNPGSVSIPKGGNPASYGMLDNDVLSVIALNDQSIIAQVAINP 184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:184
 aligned with YFCE_ECOLI | P67095 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    
           YFCE_ECOLI     1 MMKLMFASDIHGSLPATERVLELFAQSGAQWLVILGDVLNHGPRNALPEGYAPAKVAERLNEVAHKVIAVRGNCDSEVDQMLLHFPITAPWQQVLLEKQRLFLTHGHLFGPENLPALNQNDVLVYGHTHLPVAEQRGEIFHFNPGSVSIPKGGNPASYGMLDNDVLSVIALNDQSIIAQVAINP 184
               SCOP domains d1su1b_ B: Phosphodiesterase yfcE                                                                                                                                                        SCOP domains
               CATH domains 1su1B00 B:1-184  [code=3.60.21.10, no name defined]                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhh..eeee.................hhhhhhhhhhhhhh.eee......hhhhhhhh........eeee....eeee..................eee.......eeeee..eeeee.............eeeeee..eeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------UPF0025  PDB: B:121-145  --------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1su1 B   1 MMKLMFASDIHGSLPATERVLELFAQSGAQWLVILGDVLNHGPRNALPEGYAPAKVVERLNEVAHKVIAVRGNCDSEVDQMLLHFPITAPWQQVLLEKQRLFLTHGHLFGPENLPALNQNDVLVYGHTHLPVAEQRGEIFHFNPGSVSIPKGGNPASYGMLDNDVLSVIALNDQSIIAQVAINP 184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain C from PDB  Type:PROTEIN  Length:182
 aligned with YFCE_ECOLI | P67095 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
           YFCE_ECOLI     2 MKLMFASDIHGSLPATERVLELFAQSGAQWLVILGDVLNHGPRNALPEGYAPAKVAERLNEVAHKVIAVRGNCDSEVDQMLLHFPITAPWQQVLLEKQRLFLTHGHLFGPENLPALNQNDVLVYGHTHLPVAEQRGEIFHFNPGSVSIPKGGNPASYGMLDNDVLSVIALNDQSIIAQVAIN 183
               SCOP domains d1su1c_ C: Phosphodiesterase yfcE                                                                                                                                                      SCOP domains
               CATH domains 1su1C00 C:2-183  [code=3.60.21.10, no name defined]                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh..eeee.................hhhhhhhhhhhhhh.eee......hhhhhhhh.......eeeee....eeeee.................eee......eeeeee..eeeeee............eeeeee..eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------UPF0025  PDB: C:121-145  -------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1su1 C   2 MKLMFASDIHGSLPATERVLELFAQSGAQWLVILGDVLNHGPRNALPEGYAPAKVVERLNEVAHKVIAVRGNCDSEVDQMLLHFPITAPWQQVLLEKQRLFLTHGHLFGPENLPALNQNDVLVYGHTHLPVAEQRGEIFHFNPGSVSIPKGGNPASYGMLDNDVLSVIALNDQSIIAQVAIN 183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain D from PDB  Type:PROTEIN  Length:182
 aligned with YFCE_ECOLI | P67095 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
           YFCE_ECOLI     2 MKLMFASDIHGSLPATERVLELFAQSGAQWLVILGDVLNHGPRNALPEGYAPAKVAERLNEVAHKVIAVRGNCDSEVDQMLLHFPITAPWQQVLLEKQRLFLTHGHLFGPENLPALNQNDVLVYGHTHLPVAEQRGEIFHFNPGSVSIPKGGNPASYGMLDNDVLSVIALNDQSIIAQVAIN 183
               SCOP domains d1su1d_ D: Phosphodiesterase yfcE                                                                                                                                                      SCOP domains
               CATH domains 1su1D00 D:2-183  [code=3.60.21.10, no name defined]                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh..eeee.................hhhhhhhhhhhhhh.eee......hhhhhhhh.......eeeeee..eeeeee.................eee.......eeeee..eeeee.............eeeeee..eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------UPF0025  PDB: D:121-145  -------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1su1 D   2 MKLMFASDIHGSLPATERVLELFAQSGAQWLVILGDVLNHGPRNALPEGYAPAKVVERLNEVAHKVIAVRGNCDSEVDQMLLHFPITAPWQQVLLEKQRLFLTHGHLFGPENLPALNQNDVLVYGHTHLPVAEQRGEIFHFNPGSVSIPKGGNPASYGMLDNDVLSVIALNDQSIIAQVAIN 183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Metallo-dependent phosphatases (115)

Superfamily: Metallo-dependent phosphatases (115)

Family: YfcE-like (12)

Protein domain: Phosphodiesterase yfcE (1)

Escherichia coli [TaxId: 562] (1)

1a	d1su1a_	A:
1b	d1su1b_	B:
1c	d1su1c_	C:
1d	d1su1d_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Purple Acid Phosphatase; chain A, domain 2 (87)

Homologous Superfamily: [code=3.60.21.10, no name defined] (83)

Escherichia coli. Organism_taxid: 562. (4)

1a	1su1A00	A:1-184
1b	1su1D00	D:2-183
1c	1su1B00	B:1-184
1d	1su1C00	C:2-183

(no "Pfam Domain" information available for 1SU1)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (YFCE_ECOLI | P67095)

molecular function
	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.
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.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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