3O61 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE E100A E.COLI GDP-MANNOSE HYDROLASE (YFFH) IN COMPLEX WITH GDP-MANNOSE AND MG++

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

Date :   28 Jul 10 (Deposition) - 11 May 11 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

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, C, D
	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	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 11)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GDD	4	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
3	MG	4	Ligand/Ion	MAGNESIUM ION
4	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GDD	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GDD	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:17 , GLY A:47 , ALA A:48 , ARG A:67 , ALA A:85 , GLY A:86 , LEU A:87 , GLU A:104 , GLU A:127 , ILE A:129 , GLU A:151 , LYS A:176 , MG A:202 , HOH A:206 , HOH A:210 , LYS B:38 , ARG B:39 , GLU B:40 , SER B:121 , PRO B:122	BINDING SITE FOR RESIDUE GDD A 3846
02	AC2	SOFTWARE	ALA A:85 , GLU A:104 , HOH A:206 , GDD A:3846	BINDING SITE FOR RESIDUE MG A 202
03	AC3	SOFTWARE	THR A:19	BINDING SITE FOR RESIDUE NA A 204
04	AC4	SOFTWARE	LYS A:38 , ARG A:39 , GLU A:40 , SER A:121 , PRO A:122 , GLY A:123 , HOH A:199 , TYR B:17 , PHE B:18 , ARG B:44 , GLY B:47 , ARG B:67 , ALA B:85 , GLY B:86 , LEU B:87 , GLU B:104 , GLU B:127 , ILE B:129 , GLU B:151 , LYS B:176 , HOH B:196 , MG B:202 , HOH B:204 , HOH B:219	BINDING SITE FOR RESIDUE GDD B 3846
05	AC5	SOFTWARE	ALA B:85 , GLU B:104 , HOH B:218 , HOH B:219 , GDD B:3846	BINDING SITE FOR RESIDUE MG B 202
06	AC6	SOFTWARE	TYR C:17 , PHE C:18 , ARG C:44 , GLY C:47 , ALA C:48 , ARG C:67 , ALA C:85 , GLY C:86 , LEU C:87 , GLU C:104 , GLU C:127 , ILE C:129 , LYS C:176 , MG C:202 , HOH C:209 , HOH C:215 , HOH C:217 , NA C:230 , LYS D:38 , ARG D:39 , GLU D:40 , SER D:121 , PRO D:122 , GLY D:123	BINDING SITE FOR RESIDUE GDD C 3846
07	AC7	SOFTWARE	ALA C:85 , GLU C:104 , HOH C:215 , HOH C:217 , GDD C:3846	BINDING SITE FOR RESIDUE MG C 202
08	AC8	SOFTWARE	ARG C:67 , GLU C:82 , SER C:83 , ALA C:85 , HOH C:217 , GDD C:3846	BINDING SITE FOR RESIDUE NA C 230
09	AC9	SOFTWARE	LYS C:38 , ARG C:39 , GLU C:40 , SER C:121 , PRO C:122 , TYR D:17 , ARG D:44 , ARG D:67 , ALA D:85 , GLY D:86 , LEU D:87 , GLU D:104 , GLU D:127 , ILE D:129 , ASP D:150 , GLU D:151 , LYS D:176 , MG D:202 , HOH D:223	BINDING SITE FOR RESIDUE GDD D 3846
10	BC1	SOFTWARE	ALA D:85 , GLU D:104 , HOH D:223 , GDD D:3846	BINDING SITE FOR RESIDUE MG D 202

(no "SS Bond" information available for 3O61)

Asymmetric Unit

No.	Residues
1	Glu C:151	-	Asp C:152

(no "SAP(SNP)/Variant" information available for 3O61)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDK_ECOLI	43-180	4	A:43-180 B:43-180 C:43-180 D:43-180

Biological Unit 1 (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 - -

Biological Unit 2 (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	- - C:43-180 D:43-180

(no "Exon" information available for 3O61)

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:187
 aligned with NUDK_ECOLI | P37128 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
           NUDK_ECOLI     1 MTQQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGVEDEDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
               SCOP domains d3o61a_ A: ADP-ribose pyrophosphatase homologue YffH                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeee....eeeeeeeehhhhhh......eeee..eee....hhhhhhhhhhhhhh.......eeeeeee........eeeeeeee.hhhhh.....----...eeeeeehhhhhhhhhhh...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------NUDIX  PDB: A:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o61 A   1 MTQQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKAAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGG----EDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     |   -|      160       170       180       190 
                                                                                                                                                                           146  151

Chain B from PDB  Type:PROTEIN  Length:187
 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 d3o61b_ B: 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....hhhhhhhhhhhhhhh......eeeeeee........eeeeeeee.hhhhh.......--...eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------NUDIX  PDB: B:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o61 B   3 QQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKAAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGV--EDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142     | 152       162       172       182         
                                                                                                                                                                           148  |                                        
                                                                                                                                                                              151

Chain C from PDB  Type:PROTEIN  Length:182
 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 d3o61c_ C: 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: C:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o61 C   2 TQQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKAAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRA--------EDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141|      151       161       171       181       191
                                                                                                                                                                      142      151

Chain D from PDB  Type:PROTEIN  Length:190
 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 d3o61d_ D: ADP-ribose pyrophosphatase homologue YffH                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------NUDIX-3o61D01 D:44-184                                                                                                                       ------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------NUDIX-3o61D02 D:44-184                                                                                                                       ------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------NUDIX-3o61D03 D:44-184                                                                                                                       ------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------NUDIX-3o61D04 D:44-184                                                                                                                       ------- Pfam domains (4)
         Sec.struct. author ..eeeeeeeeeeee...eeeeeeeeee.....eeeeeeeeee...eeeeeeee....eeeeeeeehhhhhh......eeee.eeee....hhhhhhhhhhhhhh.......eeeeeee........eeeeeeee..................eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------NUDIX  PDB: D:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o61 D   2 TQQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKAAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGVEDEDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

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: 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	d3o61a_	A:
1b	d3o61b_	B:
1c	d3o61c_	C:
1d	d3o61d_	D:

(no "CATH Domain" information available for 3O61)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX (78)

Escherichia coli (strain K12) (28)

1a	NUDIX-3o61D01	D:44-184
1b	NUDIX-3o61D02	D:44-184
1c	NUDIX-3o61D03	D:44-184
1d	NUDIX-3o61D04	D:44-184

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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 Unit
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	Cis Peptide Bonds
		Glu C:151 - Asp C:152	[ RasMol ]

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	3o61
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	NUDK_ECOLI \| P37128	:	1viu 3o52 3o69 3o6z

3o52	E. COLI GDPMK IN COMPLEX WITH TARTRATE
3o69	E. COLI GDPMK E100A MUTANT IN COMPLEX WITH MG++
3o6z	E. COLI GDPMK IN COMPLEX WITH MG++

Description

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Ligands, Modified Residues, Ions (4, 11)

Sites (10, 10)

SS Bonds (0, 0)

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