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(-) Description

Title :  L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI ( MUTANT Q6Y-E192A)
 
Authors :  D. Grueninger, G. E. Schulz
Date :  20 Apr 07  (Deposition) - 15 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Aggregation, Zinc Enzyme, Fibrillation, Metal-Binding, Oligomerization, Interface Design, Surface Mutation, 2-Ketose Degradation, Protein-Protein Interface, Zinc, Lyase, Aldolase, Class Ii, Rare Sugar, Cleavage Of L-Rhamnulose-1-Phosphate To Dihydroxyacetoneph Bacterial L-Rhamnose Metabolism, Rhamnose Metabolism, Protein Engineering (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Grueninger, N. Treiber, M. O. P. Ziegler, J. W. A. Koetter, M. -S. Schulze, G. E. Schulz
Designed Protein-Protein Association.
Science V. 319 206 2008
PubMed-ID: 18187656  |  Reference-DOI: 10.1126/SCIENCE.1150421
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHAMNULOSE-1-PHOSPHATE ALDOLASE
    Chains: A, B, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1TLA5Ligand/IonL(+)-TARTARIC ACID
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1TLA10Ligand/IonL(+)-TARTARIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:29 , GLY A:30 , GLY A:31 , ASN A:32 , SER A:75 , GLY A:76 , THR A:115 , SER A:116 , GLU A:117 , ZN A:1276 , TLA A:1277 , HOH A:2123 , HOH A:2162 , HOH A:2253BINDING SITE FOR RESIDUE TLA A1275
2AC2SOFTWAREASN B:29 , GLY B:30 , GLY B:31 , ASN B:32 , THR B:115 , SER B:116 , GLU B:117 , HIS B:141 , HIS B:143 , HIS B:212 , ZN B:1276 , HOH B:2094 , HOH B:2099 , HOH B:2259 , HOH B:2260 , HOH B:2261 , HOH B:2262 , HOH B:2263 , HOH B:2264 , HOH B:2266 , GLU C:171BINDING SITE FOR RESIDUE TLA B1275
3AC3SOFTWAREASN C:29 , GLY C:30 , GLY C:31 , ASN C:32 , THR C:115 , SER C:116 , HIS C:141 , HIS C:143 , HIS C:212 , ZN C:1276 , HOH C:2048 , HOH C:2053 , HOH C:2119 , HOH C:2232 , GLU D:171BINDING SITE FOR RESIDUE TLA C1275
4AC4SOFTWAREASN D:29 , GLY D:30 , GLY D:31 , ASN D:32 , SER D:75 , GLY D:76 , THR D:115 , SER D:116 , GLU D:117 , HIS D:141 , HIS D:143 , ZN D:1276 , HOH D:2222 , HOH D:2224BINDING SITE FOR RESIDUE TLA D1275
5AC5SOFTWAREHIS A:141 , HIS A:143 , HIS A:212 , TLA A:1275 , TLA A:1277 , HOH A:2253BINDING SITE FOR RESIDUE ZN A1276
6AC6SOFTWAREHIS B:141 , HIS B:143 , HIS B:212 , TLA B:1275BINDING SITE FOR RESIDUE ZN B1276
7AC7SOFTWAREHIS C:141 , HIS C:143 , HIS C:212 , TLA C:1275 , GLU D:171BINDING SITE FOR RESIDUE ZN C1276
8AC8SOFTWAREHIS D:141 , HIS D:143 , HIS D:212 , TLA D:1275 , HOH D:2222 , HOH D:2224BINDING SITE FOR RESIDUE ZN D1276
9AC9SOFTWAREGLU A:117 , HIS A:143 , PRO A:188 , GLY A:189 , HIS A:212 , TLA A:1275 , ZN A:1276 , HOH A:2164 , HOH A:2253 , GLU B:171 , PHE B:263BINDING SITE FOR RESIDUE TLA A1277

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2UYV)

(-) 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 d2uyva_ A: L-rhamnulose-1-phosphate aldolase                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2uyvA00 A:1-274 L-fuculose-1-phosphate Aldolase                                                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhh....eeee....hhhhh..eeeee....hhhhh..hhhhheeeeee.....eeeeeee.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhh.....hhhhhhhhhhhh..hhhhhh...eee.......hhhhhhhhhhhhh...eeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyv A   1 MQNITYSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDAIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 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 d2uyvb_ B: L-rhamnulose-1-phosphate aldolase                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2uyvB00 B:1-274 L-fuculose-1-phosphate Aldolase                                                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhh....eeee....hhhhh..eeeee....hhhhhhhhhhhheeeeee.....eeeeeee.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhh.....hhhhhhhhhhhh..hhhhhh...eee.......hhhhhhhhhhhhh...eeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyv B   1 MQNITYSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDAIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 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 C 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 d2uyvc_ C: L-rhamnulose-1-phosphate aldolase                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2uyvC00 C:1-274 L-fuculose-1-phosphate Aldolase                                                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhh....eeee....hhhhh..eeeee....hhhhhhhhhhhheeeeee.....eeeeeee.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhh.....hhhhhhhhhhhh..hhhhhh...eee.......hhhhhhhhhhhhh...eeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyv C   1 MQNITYSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDAIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 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 D 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 d2uyvd_ D: L-rhamnulose-1-phosphate aldolase                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2uyvD00 D:1-274 L-fuculose-1-phosphate Aldolase                                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) ----------Aldolase_II-2uyvD01 D:11-239                                                                                                                                                                                                         ----------------------------------- Pfam domains (1)
           Pfam domains (2) ----------Aldolase_II-2uyvD02 D:11-239                                                                                                                                                                                                         ----------------------------------- Pfam domains (2)
           Pfam domains (3) ----------Aldolase_II-2uyvD03 D:11-239                                                                                                                                                                                                         ----------------------------------- Pfam domains (3)
           Pfam domains (4) ----------Aldolase_II-2uyvD04 D:11-239                                                                                                                                                                                                         ----------------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhh....eeee....hhhhh..eeeee....hhhhh..hhhhheeeeee.....eeeeeee.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhh.....hhhhhhhhhhhh..hhhhhh...eee.......hhhhhhhhhhhhhhh.eeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyv D   1 MQNITYSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDAIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 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)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  2uyv
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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 2v29 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)
2uyu L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT A88F-E192A)