3O52 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

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

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

Date :   27 Jul 10 (Deposition) - 11 May 11 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Nudix, Gdp_mannose, Hydrolase, Biofilm, Tartrate, Nudix Fold, Gdp- Mannose Hydrolase (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, E
	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
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (2x)	:					E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	NA	6	Ligand/Ion	SODIUM ION
3	TAR	6	Ligand/Ion	D(-)-TARTARIC ACID

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	TAR	3	Ligand/Ion	D(-)-TARTARIC ACID

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	TAR	2	Ligand/Ion	D(-)-TARTARIC ACID

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION
3	TAR	2	Ligand/Ion	D(-)-TARTARIC ACID

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:44 , ALA A:85 , GLU A:127 , ILE A:129 , LYS A:176 , HOH A:205 , NA A:7114 , SER B:121 , PRO B:122 , GLY B:123	BINDING SITE FOR RESIDUE TAR A 7110
02	AC2	SOFTWARE	TYR A:183 , THR A:186 , HOH B:193	BINDING SITE FOR RESIDUE NA A 7113
03	AC3	SOFTWARE	ARG A:67 , TAR A:7110	BINDING SITE FOR RESIDUE NA A 7114
04	AC4	SOFTWARE	ARG A:36 , HOH A:267 , HOH A:268	BINDING SITE FOR RESIDUE TAR A 7112
05	AC5	SOFTWARE	SER A:121 , PRO A:122 , GLY A:123 , ARG B:44 , ARG B:67 , LEU B:87 , GLU B:127 , ILE B:129 , LYS B:176 , HOH B:217	BINDING SITE FOR RESIDUE TAR B 7110
06	AC6	SOFTWARE	LYS B:9 , ASN B:22 , THR B:24	BINDING SITE FOR RESIDUE NA B 7111
07	AC7	SOFTWARE	ILE C:12 , ASP C:15	BINDING SITE FOR RESIDUE TAR C 7110
08	AC8	SOFTWARE	ASP C:191	BINDING SITE FOR RESIDUE CL C 192
09	AC9	SOFTWARE	GLY C:123 , ARG D:44 , ARG D:67 , GLY D:86 , LEU D:87 , HOH D:258 , NA D:7112	BINDING SITE FOR RESIDUE TAR D 7110
10	BC1	SOFTWARE	LYS D:30 , ARG D:98 , VAL D:109	BINDING SITE FOR RESIDUE NA D 7111
11	BC2	SOFTWARE	ARG D:44 , LEU D:87 , GLU D:127 , HOH D:212 , TAR D:7110	BINDING SITE FOR RESIDUE NA D 7112
12	BC3	SOFTWARE	ARG E:44 , LEU E:87 , SER E:121 , PRO E:122 , GLY E:123 , GLU E:127 , ILE E:129 , LYS E:176 , HOH E:296 , NA E:7111	BINDING SITE FOR RESIDUE TAR E 7110
13	BC4	SOFTWARE	HOH B:297 , HOH E:296 , TAR E:7110	BINDING SITE FOR RESIDUE NA E 7111

(no "SS Bond" information available for 3O52)

Asymmetric Unit

No.	Residues
1	Gly A:32	-	Glu A:33
2	Asp B:138	-	Asn B:139

(no "SAP(SNP)/Variant" information available for 3O52)

Asymmetric Unit (1, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDK_ECOLI	43-180	5	A:43-180 B:43-180 C:43-180 D:43-180 E: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 -

Biological Unit 3 (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	- - - - E:43-180

(no "Exon" information available for 3O52)

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:175
 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 d3o52a_ 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..eee....hhhhhhhhhhhhhhh.ee...eeeeeee........eeeeeeeeee--------------..eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------NUDIX  PDB: A:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o52 A   3 QQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYS--------------DIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132    |    -       152       162       172       182         
                                                                                                                                                                137            152

Chain B from PDB  Type:PROTEIN  Length:176
 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 d3o52b_ B: ADP-ribose pyrophosphat ase homologue YffH                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeeeeeeeee.....ee.-.eeeee...eeeeeeee....eeeeeeeehhhhhh......eeee.eeee....hhhhhhhhhhhhhhh......eeeeeee........eeeeeeee....------------..eeeeeehhhhhhhhhhh...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------NUDIX  PDB: B:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o52 B   3 QQITLIKDKILSDNYFTLHNITYDLTRKDGEVIR-KREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDN------------DIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
                                    12        22        32   | |  42        52        62        72        82        92       102       112       122       132      |  -       152       162       172       182         
                                                            36 |                                                                                                  139          152                                       
                                                              38

Chain C from PDB  Type:PROTEIN  Length:177
 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 d3o52c_ 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....hhhhhhhhhhhhhhh.....eeeeeeee........eeeeeeee....------------..eeeeeehhhhhhhhhh....hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------NUDIX  PDB: C:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o52 C   3 QQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDN------------DIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      |  -       152       162       172       182         
                                                                                                                                                                  139          152

Chain D from PDB  Type:PROTEIN  Length:180
 aligned with NUDK_ECOLI | P37128 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:188
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183        
           NUDK_ECOLI     4 QITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGVEDEDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
               SCOP domains d3o52d_ D: 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.....eeeeeeee........eeeeeeee.......--------...eeeeeehhhhhhhhhh....hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------NUDIX  PDB: D:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o52 D   4 QITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRA--------EDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
                                    13        23        33        43        53        63        73        83        93       103       113       123       133        |-       153       163       173       183        
                                                                                                                                                                    142      151

Chain E from PDB  Type:PROTEIN  Length:177
 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 d3o52e_ E: ADP-ribose pyrophosphatase homologue YffH                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------NUDIX-3o52E01 E:44-184                                                                                                                       ------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------NUDIX-3o52E02 E:44-184                                                                                                                       ------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------NUDIX-3o52E03 E:44-184                                                                                                                       ------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------NUDIX-3o52E04 E:44-184                                                                                                                       ------- Pfam domains (4)
           Pfam domains (5) ------------------------------------------NUDIX-3o52E05 E:44-184                                                                                                                       ------- Pfam domains (5)
         Sec.struct. author ..eeeeeeeeeee....eeeeeeeeee.....eeeeeeeeee...eeeeeeee....eeeeeeeehhhhhh......eeee.eeee....hhhhhhhhhhhhhh..ee...eeeeeee........eeeeeee.ee.-------------..eeeeeehhhhhhhhhh....hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------NUDIX  PDB: E:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o52 E   2 TQQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSD-------------DIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      |  -         -|      161       171       181       191
                                                                                                                                                                  138           152

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	-	→ 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 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	d3o52a_	A:
1b	d3o52b_	B:
1c	d3o52c_	C:
1d	d3o52d_	D:
1e	d3o52e_	E:

(no "CATH Domain" information available for 3O52)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX (78)

Escherichia coli (strain K12) (28)

1a	NUDIX-3o52E01	E:44-184
1b	NUDIX-3o52E02	E:44-184
1c	NUDIX-3o52E03	E:44-184
1d	NUDIX-3o52E04	E:44-184
1e	NUDIX-3o52E05	E:44-184

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (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
		Asp B:138 - Asn B:139	[ RasMol ]
		Gly A:32 - Glu A:33	[ RasMol ]

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	3o52
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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 3o61 3o69 3o6z

3o61	E. COLI GDPMK E100A MUTANT IN COMPLEX WITH GDP-MANNOSE + MG++
3o69	E. COLI GDPMK E100A MUTANT IN COMPLEX WITH MG++
3o6z	E. COLI GDPMK IN COMPLEX WITH MG++

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 5)

Exons (0, 0)

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SCOP Domains (1, 5)

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