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(-) Description

Title :  STRUCTURE OF THE E100A E.COLI GDP-MANNOSE HYDROLASE (YFFH) IN COMPLEX WITH 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 :  2.10
Chains :  Asym./Biol. Unit :  A,B
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

(-) Compounds

Molecule 1 - GDP-MANNOSE PYROPHOSPHATASE NUDK
    Chains: A, B
    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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MG4Ligand/IonMAGNESIUM ION
3NA3Ligand/IonSODIUM ION
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:85 , GLU A:104 , HOH A:213 , HOH A:297BINDING SITE FOR RESIDUE MG A 202
02AC2SOFTWAREASP A:15 , ASN A:16 , HIS B:188BINDING SITE FOR RESIDUE PEG A 6073
03AC3SOFTWAREGLU A:40 , ARG B:44BINDING SITE FOR RESIDUE NA A 210
04AC4SOFTWARETRP A:71BINDING SITE FOR RESIDUE CL A 214
05AC5SOFTWARETHR A:2 , GLN B:65 , PHE B:66 , ASP B:152 , HOH B:413BINDING SITE FOR RESIDUE NA A 219
06AC6SOFTWAREARG B:44 , HOH B:252BINDING SITE FOR RESIDUE NA B 215
07AC7SOFTWAREHOH B:236 , HOH B:305 , HOH B:307 , HOH B:308 , HOH B:405BINDING SITE FOR RESIDUE MG B 203
08AC8SOFTWAREALA B:85 , GLU B:104 , HOH B:199 , HOH B:218 , HOH B:315 , HOH B:365BINDING SITE FOR RESIDUE MG B 202
09AC9SOFTWAREHOH B:230 , HOH B:316 , HOH B:317 , HOH B:318 , HOH B:319 , HOH B:345BINDING SITE FOR RESIDUE MG B 250
10BC1SOFTWARETRP B:71BINDING SITE FOR RESIDUE CL B 210
11BC2SOFTWAREGLU B:92 , PRO B:93 , GLU B:94 , LYS B:114 , PHE B:132 , HOH B:302BINDING SITE FOR RESIDUE PEG B 192

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O69)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O69)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O69)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.NUDK_ECOLI43-180
 		  2A:43-180
B:43-180

(-) Exons   (0, 0)

(no "Exon" information available for 3O69)

(-) Sequences/Alignments

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
(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:176
 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 d3o69a_ A: ADP-ribose pyrophos phatase 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...------------...eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------NUDIX  PDB: A:43-180 UniProt: 43-180                                                                                                      ----------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o69 A   2 TQQITLIKDKILSDNYFTLHNITYDLTRKD-EVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLL-NDEPEVCIRKAAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSD------------EDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
                                    11        21        31 |      41        51        61        71        81      | 91       101       111       121       131      |  -       151       161       171       181       191
                                                        31 |                                                     88 |                                             138          151                                        
                                                          33                                                       90                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:189
 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 d3o69b_ B: ADP-ribose pyrophosphatase homologue YffH                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------NUDIX-3o69B01 B:44-184                                                                                                                       ------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------NUDIX-3o69B02 B:44-184                                                                                                                       ------- Pfam domains (2)
         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
                 3o69 B   3 QQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKAAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGVEDEDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O69)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NUDK_ECOLI | P37128)
molecular function
    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.

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  3o69
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  3.6.1.-
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NUDK_ECOLI | P37128: 1viu 3o52 3o61 3o6z

(-) Related Entries Specified in the PDB File

3o52 E. COLI GDPMK IN COMPLEX WITH TARTRATE
3o61 E. COLI GDPMK E100A MUTANT IN COMPLEX WITH GDP-MANNOSE + MG++
3o6z E. COLI GDPMK IN COMPLEX WITH MG++