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(-) Description

Title :  L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI ( MUTANT E117S-E192A-K248G-R253A-E254A)
 
Authors :  D. Grueninger, G. E. Schulz
Date :  04 Jun 07  (Deposition) - 08 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Zinc Enzyme, Metal-Binding, Surface Mutation, 2-Ketose Degradation, Protein-Protein Interface, Lyase, Aldolase, Class Ii, Rare Sugar, Cleavage Of L-Rhamnulose-1-Phosphate To Dihydroxyacetone Phosphate, Bacterial L-Rhamnose Metabolism, Rhamnose Metabolism, Protein Engineering, Domain Motion For Mechanical Support Of Catalysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Grueninger, G. E. Schulz
Antenna Domain Mobility And Enzymatic Reaction Of L-Rhamnulose-1-Phosphate Aldolase.
Biochemistry V. 47 607 2008
PubMed-ID: 18085797  |  Reference-DOI: 10.1021/BI7012799
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHAMNULOSE-1-PHOSPHATE ALDOLASE
    Chains: A
    EC Number: 4.1.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223-3
    Expression System Strain: JM105
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2PGR1Ligand/IonR-1,2-PROPANEDIOL
3PO41Ligand/IonPHOSPHATE ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2PGR4Ligand/IonR-1,2-PROPANEDIOL
3PO44Ligand/IonPHOSPHATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:141 , HIS A:143 , HIS A:212 , ACT A:1276 , HOH A:2212BINDING SITE FOR RESIDUE ZN A1274
2AC2SOFTWAREHIS A:46 , ASP A:47 , GLU A:200 , HIS A:204BINDING SITE FOR RESIDUE ZN A1275
3AC3SOFTWAREASN A:29 , GLY A:31 , ASN A:32 , HIS A:141 , HIS A:143 , HIS A:212 , ZN A:1274 , HOH A:2212 , HOH A:2213BINDING SITE FOR RESIDUE ACT A1276
4AC4SOFTWAREARG A:80 , GLN A:83 , LEU A:84 , HOH A:2214 , HOH A:2215 , HOH A:2216BINDING SITE FOR RESIDUE PGR A1277
5AC5SOFTWAREASN A:29 , SER A:75 , GLY A:76 , THR A:115 , SER A:116 , HOH A:2124BINDING SITE FOR RESIDUE PO4 A1278

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V2B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V2B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V2B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V2B)

(-) Exons   (0, 0)

(no "Exon" information available for 2V2B)

(-) Sequences/Alignments

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:272
 aligned with RHAD_ECOLI | P32169 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:272
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  
           RHAD_ECOLI     2 QNITQSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDEIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALA 273
               SCOP domains d2v2ba_ A: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2v2bA00 A:2-273 L-fuculose-1-phosphate Aldolase                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------Aldolase_II-2v2bA01 A:11-239                                                                                                                                                                                                         ---------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhh....eeee....hhhhh..eeeee....hhhhh..hhhhheeeeee.....eeeeeee.........hhhhhhhhhhhhhhhhh....eeeee.hhhhhhhh.....hhhhhhhhhhhh..hhhhhh...eee.......hhhhhhhhhhhh....eeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v2b A   2 QNITQSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSSLPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDAIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMGQTISAAELIALGKRFGVTPLASALA 273
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Aldolase_II] (19)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (RHAD_ECOLI | P32169)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008994    rhamnulose-1-phosphate aldolase activity    Catalysis of the reaction: L-rhamnulose 1-phosphate = glycerone phosphate + (S)-lactaldehyde.
biological process
    GO:0019323    pentose catabolic process    The chemical reactions and pathways resulting in the breakdown of a pentose, any monosaccharide with a chain of five carbon atoms in the molecule.
    GO:0019301    rhamnose catabolic process    The chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose.
    GO:0019299    rhamnose metabolic process    The chemical reactions and pathways involving rhamnose, the hexose 6-deoxy-L-mannose. Rhamnose occurs commonly as a compound of plant glycosides, in polysaccharides of gums and mucilages, and in bacterial polysaccharides. It is also a component of some plant cell wall polysaccharides and frequently acts as the sugar components of flavonoids.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RHAD_ECOLI | P32169: 1gt7 1ojr 2uyu 2uyv 2v29 2v2a 2v9e 2v9f 2v9g 2v9i 2v9l 2v9m 2v9n 2v9o

(-) Related Entries Specified in the PDB File

1gt7 L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI
1ojr L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A)
2uyu L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A88F-E192A)
2uyv L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT Q6Y-E192A)
2v29 L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT K15W)
2v2a L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A-K248G-R253A- E254A)
2v9e L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A-K248W-A273S)
2v9f L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A-K248W-A273S)
2v9g L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT Q6Y-L84W-E192A)
2v9i L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A-K248W-L274STOP )
2v9l L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT Q6Y-E192A)
2v9m L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A87M-T109F-E192A)
2v9n L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A88F-E192A)
2v9o L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A87M-T109F-E192A)