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(-) Description

Title :  L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT K15W)
 
Authors :  D. Grueninger, G. E. Schulz
Date :  04 Jun 07  (Deposition) - 08 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (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, B
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): A 
Biological Unit 2 (4x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2EDO6Ligand/Ion1,2-ETHANEDIOL
3ZN5Ligand/IonZINC ION
Biological Unit 1 (2, 20)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2EDO12Ligand/Ion1,2-ETHANEDIOL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 20)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2EDO12Ligand/Ion1,2-ETHANEDIOL
3ZN-1Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:157 , HOH A:2170 , HOH A:2171 , ASP B:47 , HIS B:50BINDING SITE FOR RESIDUE ZN A1273
02AC2SOFTWAREHOH A:2172 , HIS B:141 , HIS B:143 , HIS B:212 , EDO B:1276 , HOH B:2184BINDING SITE FOR RESIDUE ZN A1274
03AC3SOFTWAREHIS A:141 , HIS A:143 , HIS A:212 , ACT A:1282 , HOH A:2179BINDING SITE FOR RESIDUE ZN A1275
04AC4SOFTWAREHIS A:46 , ASP A:47 , GLU B:200 , HIS B:204BINDING SITE FOR RESIDUE ZN A1276
05AC5SOFTWAREGLU A:200 , HIS A:204 , HOH A:2173 , HOH A:2174BINDING SITE FOR RESIDUE ZN A1277
06AC6SOFTWARELEU B:150 , THR B:151 , LEU B:154 , GLU B:155 , PHE B:161 , PRO B:210 , GLN B:249 , HOH B:2183BINDING SITE FOR RESIDUE EDO B1275
07AC7SOFTWAREZN A:1274 , HOH A:2172 , HIS B:143 , GLU B:171 , HIS B:212 , HOH B:2131 , HOH B:2184BINDING SITE FOR RESIDUE EDO B1276
08AC8SOFTWARETRP A:8 , ASP A:38 , ASP A:41 , ARG A:137 , HOH A:2175BINDING SITE FOR RESIDUE EDO A1278
09AC9SOFTWAREARG B:128 , ASP B:178 , GLN B:202 , LYS B:203 , HIS B:204 , SER B:205 , HOH B:2185BINDING SITE FOR RESIDUE EDO B1277
10BC1SOFTWAREGLY A:76 , ASN A:81 , ASP A:222 , HOH A:2130 , HOH A:2176BINDING SITE FOR RESIDUE EDO A1279
11BC2SOFTWAREARG A:28 , ASN A:29 , VAL A:174 , HOH A:2107BINDING SITE FOR RESIDUE EDO A1280
12BC3SOFTWARELYS A:23 , TRP A:25 , ASN A:146 , GLU A:232 , GLN A:236 , HOH A:2013 , HOH A:2137 , HOH A:2178BINDING SITE FOR RESIDUE ACT A1281
13BC4SOFTWARETRP B:15 , ALA B:16 , ASP B:19 , ASP B:222 , HOH B:2186BINDING SITE FOR RESIDUE ACT B1278
14BC5SOFTWAREASN B:29 , GLY B:31 , GLY B:76 , THR B:115 , HOH B:2044BINDING SITE FOR RESIDUE ACT B1279
15BC6SOFTWAREGLY A:30 , GLY A:31 , ASN A:32 , HIS A:141 , HIS A:143 , HIS A:212 , ZN A:1275 , HOH A:2179BINDING SITE FOR RESIDUE ACT A1282

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V29)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V29)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V29)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V29)

(-) Exons   (0, 0)

(no "Exon" information available for 2V29)

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

    Alignment length:274
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    
           RHAD_ECOLI     1 MQNITQSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDEIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 274
               SCOP domains d2v29a_ A: L-rhamnulose-1-phosphate aldolase                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2v29A00 A:1-274 L-fuculose-1-phosphate Aldolase                                                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhh....eeee....hhhhh..eeeee....hhhhh..hhhhheeeeee.....eeeeeee.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhh.....hhhhhhhhhhhh..hhhhhh...eee.......hhhhhhhhhhhhh...eeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v29 A   1 MQNITQSWFVQGMIWATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDEIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 274
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    


Chain B from PDB  Type:PROTEIN  Length:274
 aligned with RHAD_ECOLI | P32169 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:274
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    
           RHAD_ECOLI     1 MQNITQSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDEIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 274
               SCOP domains d2v29b_ B: L-rhamnulose-1-phosphate aldolase                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2v29B00 B:1-274 L-fuculose-1-phosphate Aldolase                                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) ----------Aldolase_II-2v29B01 B:11-239                                                                                                                                                                                                         ----------------------------------- Pfam domains (1)
           Pfam domains (2) ----------Aldolase_II-2v29B02 B:11-239                                                                                                                                                                                                         ----------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhh.....eee....hhhhh..eeeee....hhhhh..hhhhheeeeee.....eeeeeee.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhh.....hhhhhhhhhhhh..hhhhhh...eee.......hhhhhhhhhhhhh...eeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v29 B   1 MQNITQSWFVQGMIWATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDEIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 274
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  2v29
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  RHAD_ECOLI | P32169
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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 2v2a 2v2b 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)
2v2a L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A-K248G-R253A-E254A)
2v2b L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E117S-E192A-K248G-R253A-E254A)