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Title :   CRYSTAL STRUCTURE OF THE E. COLI GDP-MANNOSE MANNOSYL HYDROLASE IN COMPLEX WITH GDP AND MG

Authors :   S. B. Gabelli, M. A. Bianchet, P. M. Legler, A. S. Mildvan, L. M. Amzel

Date :   20 Dec 03 (Deposition) - 22 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

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

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

Reference :   S. B. Gabelli, M. A. Bianchet, H. F. Azurmendi, Z. Xia, V. Sarawat, A. S. Mildvan, L. M. Amzel
Structure And Mechanism Of Gdp-Mannose Glycosyl Hydrolase, A Nudix Enzyme That Cleaves At Carbon Instead Of Phosphorus.
Structure V. 12 927 2004
PubMed-ID: 15274914 | Reference-DOI: 10.1016/J.STR.2004.03.028
(for further references see the PDB file header)

Molecule 1 - GDP-MANNOSE MANNOSYL HYDROLASE
	Chains	:	A, B
	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, WCAH, GMM, B2051
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	GDPMH, COLANIC ACID BIOSYNTHESIS PROTEIN WCAH

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 7)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:50 , GLU A:70 , GLN A:123 , GDP A:770 , HOH A:1002	BINDING SITE FOR RESIDUE MG A 1001
2	AC2	SOFTWARE	GLY B:50 , GLU B:70 , GLN B:123 , GDP B:771 , HOH B:1004	BINDING SITE FOR RESIDUE MG B 1002
3	AC3	SOFTWARE	SER B:28 , GLU B:114	BINDING SITE FOR RESIDUE CL B 1003
4	AC4	SOFTWARE	PHE A:3 , LEU A:4 , PHE A:9 , ARG A:37 , ASN A:39 , GLY A:50 , GLY A:51 , ARG A:52 , GLU A:70 , PHE A:94 , TYR A:103 , GLN A:123 , TRS A:870 , MG A:1001 , HOH A:1002 , HOH A:1003 , HOH A:1010 , HOH A:1018 , HOH A:1040 , HOH A:1075 , HOH A:1078 , HOH A:1102 , HOH A:1103 , HOH A:1132 , HOH A:1153	BINDING SITE FOR RESIDUE GDP A 770
5	AC5	SOFTWARE	PHE B:3 , LEU B:4 , PHE B:9 , ARG B:37 , ASN B:39 , GLY B:50 , GLY B:51 , ARG B:52 , GLU B:70 , PHE B:94 , TYR B:103 , GLN B:123 , TRS B:871 , MG B:1002 , HOH B:1004 , HOH B:1006 , HOH B:1007 , HOH B:1012 , HOH B:1034 , HOH B:1067 , HOH B:1082 , HOH B:1135 , HOH B:1164 , HOH B:1179 , HOH B:1189	BINDING SITE FOR RESIDUE GDP B 771
6	AC6	SOFTWARE	SER A:20 , ASP A:22 , ARG A:37 , PHE A:47 , HIS A:88 , TYR A:90 , TYR A:103 , GDP A:770 , HOH A:1005	BINDING SITE FOR RESIDUE TRS A 870
7	AC7	SOFTWARE	SER B:20 , ASP B:22 , ARG B:37 , PHE B:47 , HIS B:88 , TYR B:90 , TYR B:103 , GDP B:771 , HOH B:1009	BINDING SITE FOR RESIDUE TRS B 871

(no "SS Bond" information available for 1RYA)

Asymmetric/Biological Unit

No.	Residues
1	Arg A:40	-	Pro A:41
2	Arg B:40	-	Pro B:41

(no "SAP(SNP)/Variant" information available for 1RYA)

Asymmetric/Biological Unit (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

(no "Exon" information available for 1RYA)

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
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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 d1ryaa_ A: GDP-mannose mannosyl hydrolase NudD                                                                                                                   SCOP domains
               CATH domains 1ryaA00 A:1-160 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.eeeeeeeee.....eeeeee........ee..eee.....hhhhhhhhhhhhhhh...hhhhheeeeeeeeee..........eeeeeeeeeee.hhhhh......eeeeeeehhhhhhhh...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
                 1rya A   1 MMFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 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 d1ryab_ B: GDP-mannose mannosyl hydrolase NudD                                                                                                                   SCOP domains
               CATH domains 1ryaB00 B:1-160 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.eeeeeeeee.....eeeeee........ee..eee.....hhhhhhhhhhhhhhh...hhhhheeeeeeeeee..........eeeeeeeeeee.hhhhh......eeeeeeehhhhhhhh...hhhhhh.......eeee.. 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
                 1rya B   1 MMFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL 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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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	d1ryaa_	A:
1b	d1ryab_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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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	1ryaA00	A:1-160
1b	1ryaB00	B:1-160

(no "Pfam Domain" information available for 1RYA)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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/Biological Unit
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Description

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Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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