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(-) Description

Title :  GDP-MANNOSE MANNOSYL HYDROLASE-CALCIUM-GDP PRODUCT COMPLEX
 
Authors :  Y. Zou, C. Li, J. S. Brunzelle, S. K. Nair
Date :  03 Sep 06  (Deposition) - 19 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nudix Enzyme, Lipopolysaccharide, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zou, C. Li, J. S. Brunzelle, S. K. Nair
Molecular Basis For Substrate Selectivity And Specificity By An Lps Biosynthetic Enzyme
Biochemistry V. 46 4294 2007
PubMed-ID: 17371001  |  Reference-DOI: 10.1021/BI061056U
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GDP-MANNOSE MANNOSYL HYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-14
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GMM
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: O128

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:50 , GLU B:70 , GLN B:123 , GDP B:800 , HOH B:1039BINDING SITE FOR RESIDUE CA B 201
2AC2SOFTWAREGLY A:50 , GLU A:70 , GLN A:123 , GDP A:820 , HOH A:1049BINDING SITE FOR RESIDUE CA A 202
3AC3SOFTWAREPHE 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 , CA B:201 , HOH B:801 , HOH B:812 , HOH B:817 , HOH B:828 , HOH B:882 , HOH B:903 , HOH B:913 , HOH B:914 , HOH B:945 , HOH B:1040 , HOH B:1043 , HOH B:1046BINDING SITE FOR RESIDUE GDP B 800
4AC4SOFTWAREPHE 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 , CA A:202 , HOH A:828 , HOH A:834 , HOH A:840 , HOH A:857 , HOH A:922 , HOH A:978 , HOH A:1005 , HOH A:1047 , HOH A:1051 , HOH A:1057BINDING SITE FOR RESIDUE GDP A 820

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I8U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:40 -Pro A:41
2Arg B:40 -Pro B:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I8U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I8U)

(-) Exons   (0, 0)

(no "Exon" information available for 2I8U)

(-) 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:149
 aligned with Q6XQ58_ECOLX | Q6XQ58 from UniProtKB/TrEMBL  Length:167

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
         Q6XQ58_ECOLX     1 MMFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVAEEELLLPDEQHDDYRWLTPDALLASENVHANSRVYF 149
               SCOP domains d2i8ua_ A: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.eeeeeeeee.....eeeeee........ee..eee.....hhhhhhhhhhhhhhh...hhhhheeeeeeeeee..........eeeeeeeeeee.hhhhh......eeeeeeehhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i8u A   1 MMFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVAEEELLLPDEQHDDYRWLTPDALLASENVHANSRVYF 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         


Chain B from PDB  Type:PROTEIN  Length:149
 aligned with Q6XQ58_ECOLX | Q6XQ58 from UniProtKB/TrEMBL  Length:167

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
         Q6XQ58_ECOLX     2 MFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVAEEELLLPDEQHDDYRWLTPDALLASENVHANSRVYFN 150
               SCOP domains d2i8ub_ B: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.eeeeeeeee.....eeeeee........ee..eee.....hhhhhhhhhhhhhhh...hhhhheeeeeeeeee..........eeeeeeeeeee.hhhhh......eeeeeeehhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i8u B   2 MFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVAEEELLLPDEQHDDYRWLTPDALLASENVHANSRVYFN 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
   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 2I8U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I8U)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6XQ58_ECOLX | Q6XQ58)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/TrEMBL
        Q6XQ58_ECOLX | Q6XQ58: 2i8t

(-) Related Entries Specified in the PDB File

2i8o GDP-MANNOSE MANNOSYL HYDROLASE
2i8p GDP-MANNOSE MANNOSYL HYDROLASE BOUND TO GDP
2i8q GDP-MANNOSE MANNOSYL HYDROLASE, H124L MUTANT BOUND TO GDP- MANNOSE
2i8r GDP-MANNOSE MANNOSYL HYDROLASE MUTANT H124L BOUND TO GDP- GLUCOSE
2i8s GDP-MANNOSE MANNOSYL HYDROLASE VARIANTS H124L BOUND TO GDP- BETA-L-FUCOSE
2i8t GDP-MANNOSE MANNOSYL HYDROLASE-CALCIUM-GDP-MANNOSE COMPLEX