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(-) Description

Title :  THE CRYSTAL STRUCTURE OF MANNONATE DEHYDRATASE FROM STREPTOCOCCUS SUIS SEROTYPE2
 
Authors :  H. Peng, Q. M. Zhang, F. Gao, Y. W. Liu, J. X. Qi, G. F. Gao
Date :  08 Nov 07  (Deposition) - 11 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Xylose-Like Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Peng, Q. M. Zhang, F. Gao, Y. W. Liu, J. X. Qi, G. F. Gao
The Crystal Structure Of Mannonate Dehydratase From Streptococcus Suis Serotype2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-MANNONATE DEHYDRATASE
    Chains: A, B
    EC Number: 4.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UXUA
    Organism Scientific: STREPTOCOCCUS SUIS
    Organism Taxid: 1307
    Strain: SEROTYPE 2, STRAIN 05ZYH33

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3BAN)

(-) Sites  (0, 0)

(no "Site" information available for 3BAN)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BAN)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:222 -Pro A:223
2Asp B:222 -Pro B:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BAN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BAN)

(-) Exons   (0, 0)

(no "Exon" information available for 3BAN)

(-) Sequences/Alignments

Asymmetric/Biological 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:349
 aligned with UXUA_STRSY | A4VVI4 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:363
                              1                                                                                                                                                                                                                                                                                                                                                                        
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358   
           UXUA_STRSY     - --MKMSFRWYGKKDPVTLEEIKAIPGMQGIVTAVYDVPVGQAWPLENILELKKMVEEAGLEITVIESIPVHEDIKQGKPNRDALIENYKTSIRNVGAAGIPVVCYNFMPVFDWTRSDLHHPLPDGSTSLAFLKSDLAGVDPVADDLNLPGWDSSYSKEEMKAIIENYRQNISEEDLWANLEYFIKAILPTAEEAGVKMAIHPDDPPYGIFGLPRIITGQEAVERFLNLYDSEHNGITMCVGSYASDPKNDVLAMTEYALKRNRINFMHTRNVTAGAWGFQETAHLSQAGDIDMNAVVKLLVDYDWQGSLRPDHGRRIWGDQTKTPGYGLYDRALGATYFNGLYEANMRAAGKTPDFGIKAKTV 361
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee........hhhhhhh.....eeee...........hhhhhhhhhhhhhh...eeeeee....hhhhhh...hhhhhhhhhhhhhhhhhh....eeee...........eeeee.....eeeeeehhhhh....--------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.................hhhhhhhhhhh.....eeeeeehhhhhh....hhhhhhhhhhhh..eeeee..eeeee..eeeee..hhhhh..hhhhhhhhhhhh.....ee..................hhhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ban A  19 SHMKMSFRWYGKKDPVTLEEIKAIPGMQGIVTAVYDVPVGQAWPLENILELKKMVEEAGLEITVIESIPVHEDIKQGKPNRDALIENYKTSIRNVGAAGIPVVCYNFMPVFDWTRSDLHHPLPDGSTSLAFLKSDLAGVDP--------------SKEEMKAIIENYRQNISEEDLWANLEYFIKAILPTAEEAGVKMAIHPDDPPYGIFGLPRIITGQEAVERFLNLYDSEHNGITMCVGSYASDPKNDVLAMTEYALKRNRINFMHTRNVTAGAWGFQETAHLSQAGDIDMNAVVKLLVDYDWQGSLRPDHGRRIWGDQTKTPGYGLYDRALGATYFNGLYEANMRAAGKTPDFGIKAKTV 381
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158|        -     | 178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378   
                                                                                                                                                                      159            174                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:349
 aligned with UXUA_STRSY | A4VVI4 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:368
                               1                                                                                                                                                                                                                                                                                                                                                                            
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357        
           UXUA_STRSY     - ---MKMSFRWYGKKDPVTLEEIKAIPGMQGIVTAVYDVPVGQAWPLENILELKKMVEEAGLEITVIESIPVHEDIKQGKPNRDALIENYKTSIRNVGAAGIPVVCYNFMPVFDWTRSDLHHPLPDGSTSLAFLKSDLAGVDPVADDLNLPGWDSSYSKEEMKAIIENYRQNISEEDLWANLEYFIKAILPTAEEAGVKMAIHPDDPPYGIFGLPRIITGQEAVERFLNLYDSEHNGITMCVGSYASDPKNDVLAMTEYALKRNRINFMHTRNVTAGAWGFQETAHLSQAGDIDMNAVVKLLVDYDWQGSLRPDHGRRIWGDQTKTPGYGLYDRALGATYFNGLYEANMRAAGKTPDFGIKAKTVGTKE 365
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee........hhhhhhh.....eeee...........hhhhhhhhhhhhhhh..eeeeee....hhhhhhh..hhhhhhhhhhhhhhhhhhh...eeee........................ee...........-------------------hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeee.................hhhhhhhhhhh.....eeeeeehhhhh.....hhhhhhhhhhhh..eeeee..eeeee..eeeee..hhhhh..hhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ban B  18 GSHMKMSFRWYGKKDPVTLEEIKAIPGMQGIVTAVYDVPVGQAWPLENILELKKMVEEAGLEITVIESIPVHEDIKQGKPNRDALIENYKTSIRNVGAAGIPVVCYNFMPVFDWTRSDLHHPLPDGSTSLAFLKSDLAGVDPV-------------------AIIENYRQNISEEDLWANLEYFIKAILPTAEEAGVKMAIHPDDPPYGIFGLPRIITGQEAVERFLNLYDSEHNGITMCVGSYASDPKNDVLAMTEYALKRNRINFMHTRNVTAGAWGFQETAHLSQAGDIDMNAVVKLLVDYDWQGSLRPDHGRRIWGDQTKTPGYGLYDRALGATYFNGLYEANMRAAGKTPDFGIKAKTVGTKE 385
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157  |      -         -  |    187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377        
                                                                                                                                                                        160                 180
   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  (0, 0)

(no "SCOP Domain" information available for 3BAN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3BAN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BAN)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (UXUA_STRSY | A4VVI4)
molecular function
    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:0008927    mannonate dehydratase activity    Catalysis of the reaction: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H(2)O.
biological process
    GO:0006064    glucuronate catabolic process    The chemical reactions and pathways resulting in the breakdown of glucuronate, any salt or ester of glucuronic acid.

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  Sites
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  Cis Peptide Bonds
    Asp A:222 - Pro A:223   [ RasMol ]  
    Asp B:222 - Pro B:223   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        UXUA_STRSY | A4VVI4: 3bdk 3dbn 3fvm

(-) Related Entries Specified in the PDB File

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