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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF THE D152A E.COLI GDP-MANNOSE HYDROLASE (YFFH) IN COMPLEX WITH MG++

Authors :   L. M. Amzel, S. B. Gabelli, A. N. Boto

Date :   29 Jul 10 (Deposition) - 11 May 11 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

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

Reference :   A. N. Boto, W. Xu, J. Jakoncic, A. Pannuri, T. Romeo, M. J. Bessman, S. B. Gabelli, L. M. Amzel
Structural Studies Of The Nudix Gdp-Mannose Hydrolase From E. Coli Reveals A New Motif For Mannose Recognition.
Proteins V. 79 2455 2011
PubMed-ID: 21638333 | Reference-DOI: 10.1002/PROT.23069

Molecule 1 - GDP-MANNOSE PYROPHOSPHATASE NUDK
	Chains	:	A, B
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	B2467, JW2451, NUDK, YFFH
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MG	3	Ligand/Ion	MAGNESIUM ION
3	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:85 , GLU A:104 , HOH A:311 , HOH A:324 , HOH A:417	BINDING SITE FOR RESIDUE MG A 202
2	AC2	SOFTWARE	GLU B:100 , GLU B:104 , GLU B:151 , MG B:202 , HOH B:229 , HOH B:414 , HOH B:415	BINDING SITE FOR RESIDUE MG B 201
3	AC3	SOFTWARE	ALA B:85 , GLU B:104 , GLU B:151 , MG B:201 , HOH B:214 , HOH B:240 , HOH B:347 , HOH B:414	BINDING SITE FOR RESIDUE MG B 202
4	AC4	SOFTWARE	ARG B:113	BINDING SITE FOR RESIDUE CL B 204
5	AC5	SOFTWARE	GLN B:4 , THR B:28	BINDING SITE FOR RESIDUE CL B 203
6	AC6	SOFTWARE	GLU B:94 , VAL B:95 , LYS B:99 , HOH B:327 , HOH B:350	BINDING SITE FOR RESIDUE PEG B 205
7	AC7	SOFTWARE	ARG B:64 , ILE B:81 , MET B:166 , GLU B:171	BINDING SITE FOR RESIDUE TRS B 206
8	AC8	SOFTWARE	ILE A:8 , ARG A:36 , ASP B:15 , THR B:19 , HIS B:21 , ASP B:43	BINDING SITE FOR RESIDUE PEG B 192

(no "SS Bond" information available for 3O6Z)

(no "Cis Peptide Bond" information available for 3O6Z)

(no "SAP(SNP)/Variant" information available for 3O6Z)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDK_ECOLI	43-180	2	A:43-180 B:43-180

(no "Exon" information available for 3O6Z)

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
	(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:181
 aligned with NUDK_ECOLI | P37128 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:190
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
           NUDK_ECOLI     2 TQQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGVEDEDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
               SCOP domains d3o6za_ A: ADP-ribose pyrophosphatase homologue YffH                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeee....eeeeeeeehhhhhh......eeee.eeee....hhhhhhhhhhhhhh-.....eeeeeeee........eeeeeeee......--------....eeeeeehhhhhhhhhhh...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------NUDIX  PDB: A:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o6z A   2 TQQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEET-YEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQR--------DEAIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
                                    11        21        31        41        51        61        71        81        91       101   | | 111       121       131       141       151       161       171       181       191
                                                                                                                                 105 |                               141      150                                         
                                                                                                                                   107

Chain B from PDB  Type:PROTEIN  Length:188
 aligned with NUDK_ECOLI | P37128 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:189
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         
           NUDK_ECOLI     3 QQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGVEDEDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
               SCOP domains d3o6zb_ B: ADP-ribose pyrophos phatase homologue YffH                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------NUDIX-3o6zB01 B:44-184                                                                                                                       ------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------NUDIX-3o6zB02 B:44-184                                                                                                                       ------- Pfam domains (2)
         Sec.struct. author ..eeeeeeeeeee...eeeeeeeee.....-.eeeeeeeee...eeeeeeee....eeeeeeeehhhhhh......eeee.eeee....hhhhhhhhhhhhhhh......eeeeeee........eeeeeeee.hhhhh............eeeeeehhhhhhhhhhh...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------NUDIX  PDB: B:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o6z B   3 QQITLIKDKILSDNYFTLHNITYDLTRKDG-VIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGVEDEAIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
                                    12        22        32 |      42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         
                                                        32 |                                                                                                                                                             
                                                          34

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: Nudix (141)

Superfamily: Nudix (141)

Family: MutT-like (82)

Protein domain: ADP-ribose pyrophosphatase homologue YffH (5)

Escherichia coli [TaxId: 562] (5)

1a	d3o6za_	A:
1b	d3o6zb_	B:

(no "CATH Domain" information available for 3O6Z)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX (78)

Escherichia coli (strain K12) (28)

1a	NUDIX-3o6zB01	B:44-184
1b	NUDIX-3o6zB02	B:44-184

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NUDK_ECOLI | P37128)


GO:0052751	GDP-mannose hydrolase activity	Catalysis of the reaction: GDP-mannose + H2O = GMP + mannose-1-phosphate.
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:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3o6z)

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	3o6z
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	NUDK_ECOLI \| P37128
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	3.6.1.-
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UniProtKB/Swiss-Prot
	NUDK_ECOLI \| P37128	:	1viu 3o52 3o61 3o69

3o52	E. COLI GDPMK IN COMPLEX WITH TARTRATE
3o61	E. COLI GDPMK E100A MUTANT IN COMPLEX WITH GDP-MANNOSE + MG++
3o69	E. COLI GDPMK E100A MUTANT IN COMPLEX WITH MG++

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (5, 5)

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