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Title :   CRYSTAL STRUCTURE OF A PUTATIVE ENZYME (POSSIBLE NUDIX HYDROLASE) FROM ESCHERICHIA COLI K12

Authors :   B. Nocek, E. Evdokimova, M. Kudritska, A. Savchenko, A. Edwards, A. Joa Midwest Center For Structural Genomics (Mcsg)

Date :   04 Jan 06 (Deposition) - 21 Feb 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Putative Protein, Mad, Structural Genomics, Escherichia Coli K12, Putative Nudix Hydrolase, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Nocek, E. Evdokimova, M. Kudritska, A. Savchenko, A. Edwards, A. Joachimiak
Crystal Structure Of A Putative Enzyme (Possible Nudix Hydrolase) From Escherichia Coli K12
To Be Published
PubMed: search

Molecule 1 - PUTATIVE NUDIX HYDROLASE YFCD
	Chains	:	A, B, C
	EC Number	:	3.6.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333
	Strain	:	K 12

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 32)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	GOL	9	Ligand/Ion	GLYCEROL
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 11)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 9)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (4, 11)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:45 , GLY A:47 , MSE A:48 , GLY A:49	BINDING SITE FOR RESIDUE SO4 A 401
02	AC2	SOFTWARE	LYS A:60 , ASP A:61 , HOH A:1034	BINDING SITE FOR RESIDUE SO4 A 402
03	AC3	SOFTWARE	ARG A:86 , PRO A:99 , PHE A:100 , HOH A:1015 , HOH A:1016 , HOH A:1050 , HIS C:125 , GLY C:126	BINDING SITE FOR RESIDUE SO4 A 403
04	AC4	SOFTWARE	HIS C:45 , GLY C:47 , MSE C:48 , GLY C:49	BINDING SITE FOR RESIDUE SO4 C 404
05	AC5	SOFTWARE	HIS A:125 , ARG C:86 , PRO C:99 , PHE C:100 , HOH C:928	BINDING SITE FOR RESIDUE SO4 C 405
06	AC6	SOFTWARE	ARG B:38 , HOH B:936	BINDING SITE FOR RESIDUE SO4 B 406
07	AC7	SOFTWARE	HIS B:45 , GLY B:47 , MSE B:48 , GLY B:49	BINDING SITE FOR RESIDUE ACT B 801
08	AC8	SOFTWARE	ALA A:23 , HOH A:913 , TRP B:140	BINDING SITE FOR RESIDUE ACT B 802
09	AC9	SOFTWARE	ARG B:86 , PRO B:99 , PHE B:100 , HIS B:125 , HOH B:964	BINDING SITE FOR RESIDUE ACT B 803
10	BC1	SOFTWARE	ALA B:23 , HOH B:935 , TRP C:140 , HOH C:983	BINDING SITE FOR RESIDUE ACT C 804
11	BC2	SOFTWARE	GLU A:88 , GOL A:904 , HOH A:957 , HOH A:1035 , HOH A:1041	BINDING SITE FOR RESIDUE MG A 910
12	BC3	SOFTWARE	ARG B:27 , ARG B:31 , ARG B:56 , LYS B:60 , ASP B:61 , VAL B:74 , GLU B:88 , HOH B:910 , HOH B:911	BINDING SITE FOR RESIDUE GOL B 900
13	BC4	SOFTWARE	HIS A:45 , HIS A:103 , SER A:121 , CYS A:122 , ASN A:168 , HOH A:996	BINDING SITE FOR RESIDUE GOL A 901
14	BC5	SOFTWARE	ASN A:16 , GLU A:17 , ARG A:36 , HOH A:1048	BINDING SITE FOR RESIDUE GOL A 902
15	BC6	SOFTWARE	GLU A:20 , VAL A:21 , ARG A:38	BINDING SITE FOR RESIDUE GOL A 903
16	BC7	SOFTWARE	ARG A:27 , ARG A:56 , LYS A:60 , GLY A:73 , VAL A:74 , MG A:910 , HOH A:1034 , HOH A:1041	BINDING SITE FOR RESIDUE GOL A 904
17	BC8	SOFTWARE	HIS C:45 , ALA C:101 , HIS C:103 , SER C:121 , CYS C:122 , ASN C:168 , HOH C:957	BINDING SITE FOR RESIDUE GOL C 905
18	BC9	SOFTWARE	VAL C:21 , ARG C:38	BINDING SITE FOR RESIDUE GOL C 906
19	CC1	SOFTWARE	ARG C:27 , ARG C:31 , ARG C:56 , LYS C:60 , GLY C:73 , VAL C:74 , HOH C:944	BINDING SITE FOR RESIDUE GOL C 907
20	CC2	SOFTWARE	ASN C:16 , GLU C:17 , ILE C:22 , ARG C:36 , HOH C:981	BINDING SITE FOR RESIDUE GOL C 908

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

Asymmetric Unit

No.	Residues
1	Gly A:126	-	Pro A:127
2	Gly B:126	-	Pro B:127
3	Gly C:126	-	Pro C:127

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	YFCD_ECOLI	35-163	3	A:35-163 B:35-163 C:35-163

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	YFCD_ECOLI	35-163	1	A:35-163 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	YFCD_ECOLI	35-163	1	- B:35-163 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	YFCD_ECOLI	35-163	1	- - C:35-163

(no "Exon" information available for 2FKB)

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
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Chain A from PDB  Type:PROTEIN  Length:161
 aligned with YFCD_ECOLI | P65556 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:161
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167 
           YFCD_ECOLI     8 STEWVDIVNEENEVIAQASREQMRAQCLRHRATYIVVHDGMGKILVQRRTETKDFLPGMLDATAGGVVQADEQLLESARREAEEELGIAGVPFAEHGQFYFEDKNCRVWGALFSCVSHGPFALQEDEVSEVCWLTPEEITARCDEFTPDSLKALALWMKRN 168
               SCOP domains d2fkba1 A:8-168 Hypothetical protein YfcD                                                                                                                         SCOP domains
               CATH domains 2fkbA00 A:8-168 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....eeeeeehhhhhhhh..eeeeeeeee.....eeeeee..........ee...........hhhhhhhhhhhhhhh......eeeeeeeeee..eeeeeeeeeee...........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------NUDIX  PDB: A:35-163 UniProt: 35-163                                                                                             ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fkb A   8 STEWVDIVNEENEVIAQASREQmRAQCLRHRATYIVVHDGmGKILVQRRTETKDFLPGmLDATAGGVVQADEQLLESARREAEEELGIAGVPFAEHGQFYFEDKNCRVWGALFSCVSHGPFALQEDEVSEVCWLTPEEITARCDEFTPDSLKALALWmKRN 168
                                    17        27  |     37        47|       57        67        77        87        97       107       117       127       137       147       157       167 
                                                 30-MSE            48-MSE            66-MSE                                                                                            165-MSE

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with YFCD_ECOLI | P65556 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:161
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167 
           YFCD_ECOLI     8 STEWVDIVNEENEVIAQASREQMRAQCLRHRATYIVVHDGMGKILVQRRTETKDFLPGMLDATAGGVVQADEQLLESARREAEEELGIAGVPFAEHGQFYFEDKNCRVWGALFSCVSHGPFALQEDEVSEVCWLTPEEITARCDEFTPDSLKALALWMKRN 168
               SCOP domains d2fkbb_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains 2fkbB00 B:8-168 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....eeeeeehhhhhhh...eeeeeeeee.....eeeeee..........ee...........hhhhhhhhhhhhhhh......eeeeeeeee....eeeeeeeeee...........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------NUDIX  PDB: B:35-163 UniProt: 35-163                                                                                             ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fkb B   8 STEWVDIVNEENEVIAQASREQmRAQCLRHRATYIVVHDGmGKILVQRRTETKDFLPGmLDATAGGVVQADEQLLESARREAEEELGIAGVPFAEHGQFYFEDKNCRVWGALFSCVSHGPFALQEDEVSEVCWLTPEEITARCDEFTPDSLKALALWmKRN 168
                                    17        27  |     37        47|       57        67        77        87        97       107       117       127       137       147       157       167 
                                                 30-MSE            48-MSE            66-MSE                                                                                            165-MSE

Chain C from PDB  Type:PROTEIN  Length:167
 aligned with YFCD_ECOLI | P65556 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
           YFCD_ECOLI     2 EQRRLASTEWVDIVNEENEVIAQASREQMRAQCLRHRATYIVVHDGMGKILVQRRTETKDFLPGMLDATAGGVVQADEQLLESARREAEEELGIAGVPFAEHGQFYFEDKNCRVWGALFSCVSHGPFALQEDEVSEVCWLTPEEITARCDEFTPDSLKALALWMKRN 168
               SCOP domains d2fkbc_ C: automated matches                                                                                                                                            SCOP domains
               CATH domains 2fkbC00 C:2-168 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...eeeee.....eeeeeehhhhhhhh..eeeeeeeee.....eeeeee..........ee..eeee.....hhhhhhhhhhhhhhh......eeeeeeeeee..eeeeeeeeeee...........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------NUDIX  PDB: C:35-163 UniProt: 35-163                                                                                             ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fkb C   2 EQRRLASTEWVDIVNEENEVIAQASREQmRAQCLRHRATYIVVHDGmGKILVQRRTETKDFLPGmLDATAGGVVQADEQLLESARREAEEELGIAGVPFAEHGQFYFEDKNCRVWGALFSCVSHGPFALQEDEVSEVCWLTPEEITARCDEFTPDSLKALALWmKRN 168
                                    11        21        31        41      | 51        61    |   71        81        91       101       111       121       131       141       151       161   |   
                                                       30-MSE            48-MSE            66-MSE                                                                                            165-MSE

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

Fold: Nudix (141)

Superfamily: Nudix (141)

Family: IPP isomerase-like (23)

Protein domain: automated matches (4)

Escherichia coli K-12 [TaxId: 83333] (1)

1a	d2fkbb_	B:
1b	d2fkbc_	C:

Protein domain: Hypothetical protein YfcD (1)

Escherichia coli [TaxId: 562] (1)

d2fkba1

A:8-168

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Nucleoside Triphosphate Pyrophosphohydrolase (89)

Homologous Superfamily: Nucleoside Triphosphate Pyrophosphohydrolase (89)

Escherichia coli k12. Organism_taxid: 83333. Strain: k 12. (1)

1a	2fkbC00	C:2-168
1b	2fkbA00	A:8-168
1c	2fkbB00	B:8-168

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (YFCD_ECOLI | P65556)

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:0016817	hydrolase activity, acting on acid anhydrides	Catalysis of the hydrolysis of any acid anhydride.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.

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	Cis Peptide Bonds
		Gly A:126 - Pro A:127	[ RasMol ]
		Gly B:126 - Pro B:127	[ RasMol ]
		Gly C:126 - Pro C:127	[ RasMol ]

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