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(-) Description

Title :  CRYSTAL STRUCTURE OF YFAU, A METAL ION DEPENDENT CLASS II ALDOLASE FROM ESCHERICHIA COLI K12
 
Authors :  D. Rea, J. F. Rakus, J. A. Gerlt, V. Fulop, T. D. H. Bugg, D. I. Roper
Date :  26 Jun 08  (Deposition) - 09 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.39
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Lyase, Escherichia Coli K-12 Protein Yfau, 2-Keto-3-Deoxy Sugar Aldolase, Degradation Of Homoprotocatechuate, Class Ii Aldolase, (Beta/Alpha)8 Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Rea, R. Hovington, J. F. Rakus, J. A. Gerlt, V. Fulop, T. D. H. Bugg, D. I. Roper
Crystal Structure And Functional Assignment Of Yfau, A Metal Ion Dependent Class Ii Aldolase From Escherichia Coli K12.
Biochemistry V. 47 9955 2008
PubMed-ID: 18754683  |  Reference-DOI: 10.1021/BI800943G

(-) Compounds

Molecule 1 - YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE
    Atcc: 27325
    Chains: A, B, C
    EC Number: 4.1.2.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7-YFAU
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector: PT7-7
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: UNCHARACTERIZED PROTEIN YFAU

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2PO48Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:27 , THR A:28 , ALA A:29 , ASP A:56 , HIS A:59 , HOH A:2316 , HOH A:2317 , HOH A:2319BINDING SITE FOR RESIDUE PO4 A1257
2AC2SOFTWARETHR B:27 , THR B:28 , ALA B:29 , ASP B:56 , HIS B:59 , HOH B:2320 , HOH B:2321BINDING SITE FOR RESIDUE PO4 B1257
3AC3SOFTWARELEU A:5 , SER A:6 , GLN A:92 , HOH A:2005 , HOH A:2193 , HOH A:2320BINDING SITE FOR RESIDUE PO4 A1258
4AC4SOFTWARETHR C:27 , THR C:28 , ALA C:29 , ASP C:56 , HIS C:59 , HOH C:2313 , HOH C:2315BINDING SITE FOR RESIDUE PO4 C1257
5AC5SOFTWAREGLY C:78 , SER C:79 , PRO C:97 , MET C:98 , GLN C:104BINDING SITE FOR RESIDUE GOL C1258
6AC6SOFTWAREVAL A:122 , ARG C:74 , GLN C:151 , ASP C:179 , HOH C:2316 , HOH C:2317 , HOH C:2318BINDING SITE FOR RESIDUE GOL C1259

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro A:115 -Pro A:116
2Pro B:115 -Pro B:116
3Pro C:115 -Pro C:116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VWS)

(-) 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:256
 aligned with RHMA_ECOLI | P76469 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:256
                                    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      
           RHMA_ECOLI     1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDALDQRLAMFKS 256
               SCOP domains d2vwsa_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh...eeeeee...hhhhhhhhhh....eeeee......hhhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhh..........hhhhhhhhhhhh..hhhhhhhhhheeeee..hhhhhhhhhhhhh.....eeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vws A   1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDALDQRLAMFKS 256
                                    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      


Chain B from PDB  Type:PROTEIN  Length:256
 aligned with RHMA_ECOLI | P76469 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:256
                                    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      
           RHMA_ECOLI     1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDALDQRLAMFKS 256
               SCOP domains d2vwsb_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh...eeeeee...hhhhhhhhhh....eeeee......hhhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhh..........hhhhhhhhhhhh..hhhhhhhhhheeeee..hhhhhhhhhhhhh.....eeeehhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vws B   1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDALDQRLAMFKS 256
                                    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      


Chain C from PDB  Type:PROTEIN  Length:256
 aligned with RHMA_ECOLI | P76469 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:256
                                    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      
           RHMA_ECOLI     1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDALDQRLAMFKS 256
               SCOP domains d2vwsc_ C: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------HpcH_HpaI-2vwsC01 C:19-246                                                                                                                                                                                                          ---------- Pfam domains (1)
           Pfam domains (2) ------------------HpcH_HpaI-2vwsC02 C:19-246                                                                                                                                                                                                          ---------- Pfam domains (2)
           Pfam domains (3) ------------------HpcH_HpaI-2vwsC03 C:19-246                                                                                                                                                                                                          ---------- Pfam domains (3)
         Sec.struct. author ......hhhhhhhhh...eeeeee...hhhhhhhhhh....eeeee......hhhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeee....hhhhhhhhhhhh..........hhhhhhhhhhhh..hhhhhhhhhheeeeee.hhhhhhhhhhhhh.....eeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vws C   1 MNALLSNPFKERLRKGEVQIGLWLSSTTAYMAEIAATSGYDWLLIDGEHAPNTIQDLYHQLQAVAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRYPPYGERGVGASVARAARWGRIENYMAQVNDSLCLLVQVESKTALDNLDEILDVEGIDGVFIGPADLSASLGYPDNAGHPEVQRIIETSIRRIRAAGKAAGFLAVAPDMAQQCLAWGANFVAVGVDTMLYSDALDQRLAMFKS 256
                                    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
   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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VWS)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: PK_TIM (63)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (RHMA_ECOLI | P76469)
molecular function
    GO:0016832    aldehyde-lyase activity    Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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: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.
    GO:0016151    nickel cation binding    Interacting selectively and non-covalently with nickel (Ni) cations.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  2vws
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 Related Entries

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

UniProtKB/Swiss-Prot
        RHMA_ECOLI | P76469: 2vwt

(-) Related Entries Specified in the PDB File

2vwt CRYSTAL STRUCTURE OF YFAU, A METAL ION DEPENDENT CLASS II ALDOLASE FROM ESCHERICHIA COLI K12 - MG-PYRUVATE PRODUCT COMPLEX