2GT2 - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE E. COLI GDP-MANNOSE MANNOSYL HYDROLASE

Authors :   S. B. Gabelli, M. A. Bianchet, H. F. Azurmendi, A. S. Mildvan, L. M. Amzel

Date :   27 Apr 06 (Deposition) - 12 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Gdp-Mannose Hydrolase Gdp-Glucose Hydrolase Nudix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. B. Gabelli, H. F. Azurmendi, M. A. Bianchet, L. M. Amzel, A. S. Mildvan
X-Ray, Nmr, And Mutational Studies Of The Catalytic Cycle Of The Gdp-Mannose Mannosyl Hydrolase Reaction.
Biochemistry V. 45 11290 2006
PubMed-ID: 16981689 | Reference-DOI: 10.1021/BI061239G
(for further references see the PDB file header)

Molecule 1 - GDP-MANNOSE MANNOSYL HYDROLASE
	Chains	:	A, B, C, D
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NUDD, GMM, WCAH
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	GDPMH, COLANIC ACID BIOSYNTHESIS PROTEIN WCAH

		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)

(no "Ligand,Modified Residues,Ions" information available for 2GT2)

(no "Site" information available for 2GT2)

(no "SS Bond" information available for 2GT2)

Asymmetric Unit

No.	Residues
1	Arg A:40	-	Pro A:41
2	Arg B:40	-	Pro B:41
3	Arg C:40	-	Pro C:41
4	Arg D:40	-	Pro D:41

(no "SAP(SNP)/Variant" information available for 2GT2)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	GMM_ECOLI	13-153	4	A:14-154 B:14-154 C:14-154 D:14-154
2	NUDIX_BOX	PS00893	Nudix box signature.	GMM_ECOLI	50-71	4	A:51-72 B:51-72 C:51-72 D:51-72

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	GMM_ECOLI	13-153	2	A:14-154 B:14-154 - -
2	NUDIX_BOX	PS00893	Nudix box signature.	GMM_ECOLI	50-71	2	A:51-72 B:51-72 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	GMM_ECOLI	13-153	2	- - C:14-154 D:14-154
2	NUDIX_BOX	PS00893	Nudix box signature.	GMM_ECOLI	50-71	2	- - C:51-72 D:51-72

(no "Exon" information available for 2GT2)

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:151
 aligned with GMM_ECOLI | P32056 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
            GMM_ECOLI     2 FLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 159
               SCOP domains d2gt2a_ A: GDP-mannose mannosyl hydrolase NudD                                                                                                                 SCOP domains
               CATH domains 2gt2A00 A:3-160 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.eeeeeeeee.....eeeee.........ee..eee.....hhhhhhhhhhhhhhh...hhhhheeeeeeeeee..........eeeeeeeeeee.hhhhh.-------.eeeehhhhhhhh...hhhhhh..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------NUDIX  PDB: A:14-154 UniProt: 13-153                                                                                                         ------ PROSITE (1)
                PROSITE (2) ------------------------------------------------NUDIX_BOX  PDB: A:51-7---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gt2 A   3 FLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELL-------DYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 160
                                    12        22        32        42        52        62        72        82        92       102       112     |   -   |   132       142       152        
                                                                                                                                             118     126

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with GMM_ECOLI | P32056 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:156
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153      
            GMM_ECOLI     4 RQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 159
               SCOP domains d2gt2b_ B: GDP-mannose mannosyl hydrolase NudD                                                                                                               SCOP domains
               CATH domains 2gt2B00 B:5-160 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh.eeeeeeeee....eeeeee.........ee..eee.....hhhhhhhhhhhhhhh...hhhhheeeeeeeeee..........eeeeeeeeeee.hhhhh..------.eeeeehhhhhhh...hhhhhh..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------NUDIX  PDB: B:14-154 UniProt: 13-153                                                                                                         ------ PROSITE (1)
                PROSITE (2) ----------------------------------------------NUDIX_BOX  PDB: B:51-7---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gt2 B   5 RQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLL------DYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 160
                                    14        24        34        44        54        64        74        84        94       104       114    |    - |     134       144       154      
                                                                                                                                            119    126

Chain C from PDB  Type:PROTEIN  Length:155
 aligned with GMM_ECOLI | P32056 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
            GMM_ECOLI     1 MFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 159
               SCOP domains d2gt2c_ C: GDP-mannose mannosyl hydrolase NudD                                                                                                                  SCOP domains
               CATH domains 2gt2C00 C:2-160 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.eeeeeeeee.....eeeee.........ee..eee.....hhhhhhhhhhhhhhh...hhhhheeeeeeeeee..........eeeeeeeeeee.hhhhh....----.eeeehhhhhhhh...hhhhhh..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------NUDIX  PDB: C:14-154 UniProt: 13-153                                                                                                         ------ PROSITE (1)
                PROSITE (2) -------------------------------------------------NUDIX_BOX  PDB: C:51-7---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gt2 C   2 MFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLLPD----DYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 160
                                    11        21        31        41        51        61        71        81        91       101       111       121    |  131       141       151         
                                                                                                                                                 121  126

Chain D from PDB  Type:PROTEIN  Length:152
 aligned with GMM_ECOLI | P32056 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       
            GMM_ECOLI     3 LRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 159
               SCOP domains d2gt2d_ D: GDP-mannose mannosyl hydrolase NudD                                                                                                                SCOP domains
               CATH domains 2gt2D00 D:4-160 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.eeeeeeeee....eeeeee.........ee..eee.....hhhhhhhhhhhhhhh...hhhhheeeeeeeeee..........eeeeeeeeeee.hhhhh..-----..eeeeehhhhhhh...hhhhhh..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------NUDIX  PDB: D:14-154 UniProt: 13-153                                                                                                         ------ PROSITE (1)
                PROSITE (2) -----------------------------------------------NUDIX_BOX  PDB: D:51-7---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gt2 D   4 LRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLL-----DDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 160
                                    13        23        33        43        53        63        73        83        93       103       113     |   - |     133       143       153       
                                                                                                                                             119   125

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Nudix (141)

Superfamily: Nudix (141)

Family: GDP-mannose mannosyl hydrolase NudD (5)

Protein domain: GDP-mannose mannosyl hydrolase NudD (3)

Escherichia coli [TaxId: 562] (3)

1a	d2gt2a_	A:
1b	d2gt2b_	B:
1c	d2gt2c_	C:
1d	d2gt2d_	D:

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. Organism_taxid: 562. (17)

1a	2gt2C00	C:2-160
1b	2gt2D00	D:4-160
1c	2gt2A00	A:3-160
1d	2gt2B00	B:5-160

(no "Pfam Domain" information available for 2GT2)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (GMM_ECOLI | P32056)

molecular function
	GO:0047917	GDP-glucosidase activity	Catalysis of the reaction: GDP-D-glucose + H(2)O = D-glucose + GDP + H(+).
	GO:0008727	GDP-mannose mannosyl hydrolase activity	Catalysis of the reaction: GDP-alpha-D-mannose + H2O = GDP + D-mannose + H+.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0009103	lipopolysaccharide biosynthetic process	The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2gt2)

	Sites
(no "Sites" information available for 2gt2)

	Cis Peptide Bonds
		Arg A:40 - Pro A:41	[ RasMol ]
		Arg B:40 - Pro B:41	[ RasMol ]
		Arg C:40 - Pro C:41	[ RasMol ]
		Arg D:40 - Pro D:41	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2gt2
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GMM_ECOLI \| P32056
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.6.1.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GMM_ECOLI \| P32056
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	GMM_ECOLI \| P32056	:	1rya 2gt4

1rya	CRYSTAL STRUCTURE OF THE E. COLI GDP-MANNOSE MANNOSYL HYDROLASE IN COMPLEX WITH GDP AND MG
2gt4

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File