2GT4 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE Y103F MUTANT OF THE GDP-MANNOSE MANNOSYL HYDROLASE IN COMPLEX WITH GDP-MANNOSE AND MG+2

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

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

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Gdp-Mannose Hydrolase Gdp-Glucose Hydrolase Nudix Gdp Gdp- Fucose (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
	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	:	YEFC
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI K12
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	GDPMH, COLANIC ACID BIOSYNTHESIS PROTEIN WCAH

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	GDD	3	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
3	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	GDD	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	GDD	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:139 , ARG B:37 , THR B:38 , ASN B:39 , ARG B:40 , PRO B:41 , GDD B:201 , MG B:401 , HOH B:415 , HOH B:416 , HOH B:417	BINDING SITE FOR RESIDUE BMA B 202
2	AC2	SOFTWARE	LYS C:36 , ARG C:37 , THR C:38 , ASN C:39 , GDD C:201 , MG C:401 , HOH C:413 , HOH C:425 , HOH C:449 , HOH C:507	BINDING SITE FOR RESIDUE BMA C 202
3	AC3	SOFTWARE	GLY A:50 , GLU A:70 , GDD A:201 , HOH A:411 , HOH A:455	BINDING SITE FOR RESIDUE MG A 401
4	AC4	SOFTWARE	GLY B:50 , GLU B:70 , GDD B:201 , BMA B:202 , HOH B:402 , HOH B:417	BINDING SITE FOR RESIDUE MG B 401
5	AC5	SOFTWARE	GLY C:50 , GLU C:70 , GDD C:201 , BMA C:202 , HOH C:413 , HOH C:425	BINDING SITE FOR RESIDUE MG C 401
6	AC6	SOFTWARE	PHE A:3 , LEU A:4 , PHE A:9 , SER A:20 , ASP A:22 , ARG A:37 , PHE A:47 , GLY A:50 , GLY A:51 , ARG A:52 , GLU A:70 , HIS A:88 , TYR A:90 , PHE A:103 , MG A:401 , HOH A:422 , HOH A:424 , HOH A:434 , HOH A:446 , HOH A:480	BINDING SITE FOR RESIDUE GDD A 201
7	AC7	SOFTWARE	ALA A:137 , PHE B:3 , LEU B:4 , PHE B:9 , SER B:20 , ASP B:22 , ARG B:37 , GLY B:50 , GLY B:51 , ARG B:52 , GLU B:70 , HIS B:88 , TYR B:90 , PHE B:94 , PHE B:103 , BMA B:202 , MG B:401 , HOH B:403 , HOH B:415 , HOH B:416 , HOH B:417 , HOH B:451 , HOH B:468 , HOH B:479	BINDING SITE FOR RESIDUE GDD B 201
8	AC8	SOFTWARE	PHE C:3 , LEU C:4 , PHE C:9 , SER C:20 , ASP C:22 , ARG C:37 , ASN C:39 , PHE C:47 , GLY C:50 , GLY C:51 , ARG C:52 , GLU C:70 , HIS C:88 , TYR C:90 , PHE C:94 , PHE C:103 , BMA C:202 , MG C:401 , HOH C:402 , HOH C:406 , HOH C:413 , HOH C:416 , HOH C:442 , HOH C:446 , HOH C:449 , HOH C:505	BINDING SITE FOR RESIDUE GDD C 201

(no "SS Bond" information available for 2GT4)

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

(no "SAP(SNP)/Variant" information available for 2GT4)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	GMM_ECOLI	13-153	3	A:14-154 B:14-154 C:14-154
2	NUDIX_BOX	PS00893	Nudix box signature.	GMM_ECOLI	50-71	3	A:51-72 B:51-72 C: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
2	NUDIX_BOX	PS00893	Nudix box signature.	GMM_ECOLI	50-71	2	- - C:51-72

(no "Exon" information available for 2GT4)

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:160
 aligned with GMM_ECOLI | P32056 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:160
                             1                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
            GMM_ECOLI     - -MFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 159
               SCOP domains d2gt4a_ A: GDP-mannose mannosyl hydrolase NudD                                                                                                                   SCOP domains
               CATH domains 2gt4A00 A:1-160 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.eeeeeeeee.....eeeeee.......eee..eee.....hhhhhhhhhhhhhhh...hhhhheeeeeeeeee..........eeeeeeeeeee.hhhhh..hhhhhh.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
                 2gt4 A   1 MMFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHFVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with GMM_ECOLI | P32056 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:160
                             1                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
            GMM_ECOLI     - -MFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 159
               SCOP domains d2gt4b_ B: GDP-mannose mannosyl hydrolase NudD                                                                                                                   SCOP domains
               CATH domains 2gt4B00 B:1-160 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.eeeeeeeee.....eeeee.........ee..eee.....hhhhhhhhhhhhhhh...hhhhheeeeeeeeee..........eeeeeeeeeee.hhhhh...hhhhh.eeeehhhhhhh....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
                 2gt4 B   1 MMFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHFVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:160
 aligned with GMM_ECOLI | P32056 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:160
                             1                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
            GMM_ECOLI     - -MFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 159
               SCOP domains d2gt4c_ C: GDP-mannose mannosyl hydrolase NudD                                                                                                                   SCOP domains
               CATH domains 2gt4C00 C:1-160 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.eeeeeeeee.....eeeee.........ee..eee.....hhhhhhhhhhhhhh....hhhhheeeeeeeeee..........eeeeeeeeeee.hhhhh..hhhhhh.eeeehhhhhhh....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
                 2gt4 C   1 MMFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHFVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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(

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Folds(

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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	d2gt4a_	A:
1b	d2gt4b_	B:
1c	d2gt4c_	C:

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: k12. (1)

1a	2gt4A00	A:1-160
1b	2gt4B00	B:1-160
1c	2gt4C00	C:1-160

(no "Pfam Domain" information available for 2GT4)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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
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	Cis Peptide Bonds
		Arg A:40 - Pro A:41	[ RasMol ]
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		Arg C:40 - Pro C:41	[ RasMol ]

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	GMM_ECOLI \| P32056	:	1rya 2gt2

1rya	CRYSTAL STRUCTURE OF THE E. COLI GDP-MANNOSE MANNOSYL HYDROLASE IN COMPLEX WITH GDP AND MG
2gt2	CRYSTAL STRUCTURE OF THE E. COLI GDP-MANNOSE MANNOSYL HYDROLASE

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Ligands, Modified Residues, Ions (3, 8)

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