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(-) Description

Title :  L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI ( MUTANT Q6Y-L84W-E192A)
 
Authors :  D. Grueninger, G. E. Schulz
Date :  23 Aug 07  (Deposition) - 22 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Zinc, Lyase, Aldolase, Class Ii, Cytoplasm, Protein Engineering, 2-Ketose Degradation, Cleavage Of L-Rhamnulose-1-Phosphate To Dihydroxyacetoneph Bacterial L-Rhamnose Metabolism, Metal-Binding, Oligomerization, Interface Design, Protein-Protein Interface, Rare Sugar, Aggregation, Zinc Enzyme, Fibrillation, Surface Mutation, Rhamnose Metabolism (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 B:29 , GLY B:31 , ASN B:32 , SER B:75 , GLY B:76 , THR B:115 , SER B:116 , GLU B:117 , HIS B:141 , ZN B:1277 , GLU C:171BINDING SITE FOR RESIDUE TLA B1275
2AC2SOFTWAREASN C:29 , GLY C:31 , ASN C:32 , GLY C:76 , THR C:115 , GLU C:117 , ZN C:1276 , HOH C:2015 , HOH C:2036 , GLU D:171BINDING SITE FOR RESIDUE TLA C1275
3AC3SOFTWAREASN A:29 , GLY A:30 , GLY A:31 , ASN A:32 , GLU A:117 , HIS A:141 , HIS A:143 , HIS A:212 , ZN A:1276 , HOH A:2019 , HOH A:2020BINDING SITE FOR RESIDUE TLA A1275
4AC4SOFTWARESER B:75 , SER B:116BINDING SITE FOR RESIDUE TLA B1276
5AC5SOFTWAREASN D:29 , GLY D:31 , ASN D:32 , THR D:115 , SER D:116 , GLU D:117 , HIS D:141 , HIS D:143 , ZN D:1276 , HOH D:2015 , HOH D:2027 , HOH D:2028BINDING SITE FOR RESIDUE TLA D1275
6AC6SOFTWAREHIS A:141 , HIS A:143 , HIS A:212 , TLA A:1275 , HOH A:2020BINDING SITE FOR RESIDUE ZN A1276
7AC7SOFTWAREHIS B:141 , HIS B:143 , HIS B:212 , TLA B:1275 , GLU C:171BINDING SITE FOR RESIDUE ZN B1277
8AC8SOFTWAREHIS C:141 , HIS C:143 , HIS C:212 , TLA C:1275 , GLU D:171BINDING SITE FOR RESIDUE ZN C1276
9AC9SOFTWAREHIS D:141 , HIS D:143 , HIS D:212 , TLA D:1275 , HOH D:2015BINDING SITE FOR RESIDUE ZN D1276

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V9G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V9G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V9G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V9G)

(-) Exons   (0, 0)

(no "Exon" information available for 2V9G)

(-) 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:273
 aligned with RHAD_ECOLI | P32169 from UniProtKB/Swiss-Prot  Length:274

    Alignment length: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   
           RHAD_ECOLI     2 QNITQSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQLDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDEIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 274
               SCOP domains d2v9ga_ A: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2v9gA00 A:2-274 L-fuculose-1-phosphate Aldolase                                                                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh........eeeee.hhhhhhhhh.......eeee....hhhhh..eeeee....hhhhhh.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
                 2v9g A   2 QNITYSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQWDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDAIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 274
                                    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   


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 d2v9gb_ B: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2v9gB00 B:1-274 L-fuculose-1-phosphate Aldolase                                                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhh.......eeee....hhhhh..eeeee....hhhhh..hhhhheeeeee.....eeeeeee.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhh..hhhhhhhhhhhh..hhhhhh...eee.......hhhhhhhhhhhhh...eeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v9g B   1 MQNITYSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQWDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDAIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 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 d2v9gc_ C: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2v9gC00 C:1-274 L-fuculose-1-phosphate Aldolase                                                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhh....eeee...........eeeee....hhhhh..hhhhheeeeee.....eeeeeee.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhh.....hhhhhhhhhhhh..hhhhhh....ee.......hhhhhhhhhhhhh...eeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v9g C   1 MQNITYSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQWDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDAIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 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 d2v9gd_ D: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2v9gD00 D:1-274 L-fuculose-1-phosphate Aldolase                                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) ----------Aldolase_II-2v9gD01 D:11-239                                                                                                                                                                                                         ----------------------------------- Pfam domains (1)
           Pfam domains (2) ----------Aldolase_II-2v9gD02 D:11-239                                                                                                                                                                                                         ----------------------------------- Pfam domains (2)
           Pfam domains (3) ----------Aldolase_II-2v9gD03 D:11-239                                                                                                                                                                                                         ----------------------------------- Pfam domains (3)
           Pfam domains (4) ----------Aldolase_II-2v9gD04 D:11-239                                                                                                                                                                                                         ----------------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhh....eeee....hhhhh..eeeee....hhhhh..hhhhheeeeee.....eeeeeee.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhh.....hhhhhhhhhhhh..hhhhhh....ee........hhhhhhhhhhhh...eeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v9g D   1 MQNITYSWFVQGMIKATTDAWLKGWDERNGGNLTLRLDDADIAPYHDNFHQQPRYIPLSQPMPLLANTPFIVTGSGKFFRNVQWDPAANLGIVKVDSDGAGYHILWGLTNEAVPTSELPAHFLSHCERIKATNGKDRVIMHCHATNLIALTYVLENDTAVFTRQLWEGSTECLVVFPDGVGILPWMVPGTDAIGQATAQEMQKHSLVLWPFHGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFGVTPLASALAL 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)
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  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, 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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  2v9g
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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 2v29 2v2a 2v2b 2v9e 2v9f 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)
2v2b L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E117S-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)
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)