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(-) Description

Title :  E COLI GDP-4-KETO-6-DEOXY-D-MANNOSE-3-DEHYDRATASE WITH BOUND HYDRATED PLP
 
Authors :  P. D. Cook, J. B. Thoden, H. M. Holden
Date :  07 Apr 06  (Deposition) - 05 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Colitose, 0-Antigen, Aspartate Aminotransferase, Plp, Deoxysugar (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. D. Cook, J. B. Thoden, H. M. Holden
The Structure Of Gdp-4-Keto-6-Deoxy-D-Mannose-3-Dehydratase: A Unique Coenzyme B6-Dependent Enzyme.
Protein Sci. V. 15 2093 2006
PubMed-ID: 16943443  |  Reference-DOI: 10.1110/PS.062328306
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE PYRIDOXAMINE 5-PHOSPHATE-DEPENDENT DEHYDRASE, WBDK
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: WBDK
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2P0P2Ligand/Ion[4-(DIHYDROXYMETHYL)-5-HYDROXY-6-METHYLPYRIDIN-3-YL]METHYL DIHYDROGEN PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:375 , ASP A:378BINDING SITE FOR RESIDUE MG A 403
2AC2SOFTWARESER A:55 , GLY A:56 , SER A:57 , SER A:87 , TRP A:88 , THR A:91 , ASP A:159 , CYS A:161 , GLU A:162 , SER A:183 , PHE A:185 , HIS A:188 , HOH A:548 , HOH A:549 , HOH A:551 , ASN B:248BINDING SITE FOR RESIDUE P0P A 400
3AC3SOFTWAREASN A:248 , SER B:55 , GLY B:56 , SER B:57 , ASN B:60 , SER B:87 , TRP B:88 , THR B:90 , THR B:91 , ASP B:159 , CYS B:161 , GLU B:162 , SER B:183 , PHE B:185 , HIS B:188 , HOH B:545 , HOH B:546 , HOH B:547BINDING SITE FOR RESIDUE P0P B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GMS)

(-) 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:390
 aligned with COLD_ECOCB | D3QY10 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:390
                              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       368       378       388
           COLD_ECOCB     - --MINYPLASSTWDDLEYKAIQSVLDSKMFTMGEYVKQYETQFAKTFGSKYAVMVSSGSTANLLMIAALFFTKKPRLKKGDEIIVPAVSWSTTYYPLQQYGLRVKFVDIDINTLNIDIESLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGRDIILLEDNCESMGATFNNKCAGTFGLMGTFSSFYSHHIATMEGGCIVTDDEEIYHILLCIRAHGWTRNLPKKNKVTGVKSDDQFEESFKFVLPGYNVRPLEMSGAIGIEQLKKLPRFISVRRKNAEYFLDKFKDHPYLDVQQETGESSWFGFSFIIKKDSGVIRKQLVENLNSAGIECRPIVTGNFLKNTDVLKYFDYTVHNNVDNAEYLDKNGLFVGNHQIELFDEIDYLREVLK 388
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2gmsA01 A:-1-264 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                      2gmsA02 A:265-388 Aspartate Aminotransferase, domain 1                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh............eeeee...hhhhhhhhhhh..eeeee.........hhhhhhhhh...eeeeeee.hhhh..hhhhhhhhhh....eeeee.......ee..ee......eeeee............eeeee.hhhhhhhhhhhh..........ee...ee...hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee...........eeeeee......hhhhhhhhhhhh..........hhhhhhhhhh...eee...hhhhhhhhhheeeee.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gms A  -1 GHMINYPLASSTWDDLEYKAIQSVLDSKMFTMGEYVKQYETQFAKTFGSKYAVMVSSGSTANLLMIAALFFTKKPRLKKGDEIIVPAVSWSTTYYPLQQYGLRVKFVDIDINTLNIDIESLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGRDIILLEDNCESMGATFNNKCAGTFGLMGTFSSFYSHHIATMEGGCIVTDDEEIYHILLCIRAHGWTRNLPKKNKVTGVKSDDQFEESFKFVLPGYNVRPLEMSGAIGIEQLKKLPRFISVRRKNAEYFLDKFKDHPYLDVQQETGESSWFGFSFIIKKDSGVIRKQLVENLNSAGIECRPIVTGNFLKNTDVLKYFDYTVHNNVDNAEYLDKNGLFVGNHQIELFDEIDYLREVLK 388
                                     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       368       378       388


Chain A from PDB  Type:PROTEIN  Length:390
 aligned with Q9F118_ECOLX | Q9F118 from UniProtKB/TrEMBL  Length:388

    Alignment length:390
                              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       368       378       388
         Q9F118_ECOLX     - --MINYPLASSTWDDLEYKAIQSVLDSKMFTMGEYVKQYETQFAKTFGSKYAVMVSSGSTANLLMIAALFFTKKPRLKKGDEIIVPAVSWSTTYYPLQQYGLRVKFVDIDINTLNIDIESLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGRDIILLEDNCESMGATFNNKCAGTFGLMGTFSSFYSHHIATMEGGCIVTDDEEIYHILLCIRAHGWTRNLPKKNKVTGVKSDDQFEESFKFVLPGYNVRPLEMSGAIGIEQLKKLPRFISVRRKNAEYFLDKFKDHPYLDVQQETGESSWFGFSFIIKKDSGVIRKQLVENLNSAGIECRPIVTGNFLKNTDVLKYFDYTVHNNVDNAEYLDKNGLFVGNHQIELFDEIDYLREVLK 388
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2gmsA01 A:-1-264 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                      2gmsA02 A:265-388 Aspartate Aminotransferase, domain 1                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh............eeeee...hhhhhhhhhhh..eeeee.........hhhhhhhhh...eeeeeee.hhhh..hhhhhhhhhh....eeeee.......ee..ee......eeeee............eeeee.hhhhhhhhhhhh..........ee...ee...hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee...........eeeeee......hhhhhhhhhhhh..........hhhhhhhhhh...eee...hhhhhhhhhheeeee.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gms A  -1 GHMINYPLASSTWDDLEYKAIQSVLDSKMFTMGEYVKQYETQFAKTFGSKYAVMVSSGSTANLLMIAALFFTKKPRLKKGDEIIVPAVSWSTTYYPLQQYGLRVKFVDIDINTLNIDIESLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGRDIILLEDNCESMGATFNNKCAGTFGLMGTFSSFYSHHIATMEGGCIVTDDEEIYHILLCIRAHGWTRNLPKKNKVTGVKSDDQFEESFKFVLPGYNVRPLEMSGAIGIEQLKKLPRFISVRRKNAEYFLDKFKDHPYLDVQQETGESSWFGFSFIIKKDSGVIRKQLVENLNSAGIECRPIVTGNFLKNTDVLKYFDYTVHNNVDNAEYLDKNGLFVGNHQIELFDEIDYLREVLK 388
                                     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       368       378       388


Chain B from PDB  Type:PROTEIN  Length:389
 aligned with COLD_ECOCB | D3QY10 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:389
                             1                                                                                                                                                                                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379         
           COLD_ECOCB     - -MINYPLASSTWDDLEYKAIQSVLDSKMFTMGEYVKQYETQFAKTFGSKYAVMVSSGSTANLLMIAALFFTKKPRLKKGDEIIVPAVSWSTTYYPLQQYGLRVKFVDIDINTLNIDIESLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGRDIILLEDNCESMGATFNNKCAGTFGLMGTFSSFYSHHIATMEGGCIVTDDEEIYHILLCIRAHGWTRNLPKKNKVTGVKSDDQFEESFKFVLPGYNVRPLEMSGAIGIEQLKKLPRFISVRRKNAEYFLDKFKDHPYLDVQQETGESSWFGFSFIIKKDSGVIRKQLVENLNSAGIECRPIVTGNFLKNTDVLKYFDYTVHNNVDNAEYLDKNGLFVGNHQIELFDEIDYLREVLK 388
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2gmsB01 B:0-264 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                      2gmsB02 B:265-388 Aspartate Aminotransferase, domain 1                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh............eeeee...hhhhhhhhhhh..eeeee.........hhhhhhhhh...eeeeeee.hhhh..hhhhhhhhhh....eeeee.......ee..ee......eeeee............eeeee.hhhhhhhhhhhh..........ee...ee...hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee..........eeeeee......hhhhhhhhhhhh..........hhhhhhhhhh...eee...hhhhhhhhhheeeee.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gms B   0 HMINYPLASSTWDDLEYKAIQSVLDSKMFTMGEYVKQYETQFAKTFGSKYAVMVSSGSTANLLMIAALFFTKKPRLKKGDEIIVPAVSWSTTYYPLQQYGLRVKFVDIDINTLNIDIESLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGRDIILLEDNCESMGATFNNKCAGTFGLMGTFSSFYSHHIATMEGGCIVTDDEEIYHILLCIRAHGWTRNLPKKNKVTGVKSDDQFEESFKFVLPGYNVRPLEMSGAIGIEQLKKLPRFISVRRKNAEYFLDKFKDHPYLDVQQETGESSWFGFSFIIKKDSGVIRKQLVENLNSAGIECRPIVTGNFLKNTDVLKYFDYTVHNNVDNAEYLDKNGLFVGNHQIELFDEIDYLREVLK 388
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379         


Chain B from PDB  Type:PROTEIN  Length:389
 aligned with Q9F118_ECOLX | Q9F118 from UniProtKB/TrEMBL  Length:388

    Alignment length:389
                             1                                                                                                                                                                                                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379         
         Q9F118_ECOLX     - -MINYPLASSTWDDLEYKAIQSVLDSKMFTMGEYVKQYETQFAKTFGSKYAVMVSSGSTANLLMIAALFFTKKPRLKKGDEIIVPAVSWSTTYYPLQQYGLRVKFVDIDINTLNIDIESLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGRDIILLEDNCESMGATFNNKCAGTFGLMGTFSSFYSHHIATMEGGCIVTDDEEIYHILLCIRAHGWTRNLPKKNKVTGVKSDDQFEESFKFVLPGYNVRPLEMSGAIGIEQLKKLPRFISVRRKNAEYFLDKFKDHPYLDVQQETGESSWFGFSFIIKKDSGVIRKQLVENLNSAGIECRPIVTGNFLKNTDVLKYFDYTVHNNVDNAEYLDKNGLFVGNHQIELFDEIDYLREVLK 388
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2gmsB01 B:0-264 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                      2gmsB02 B:265-388 Aspartate Aminotransferase, domain 1                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh............eeeee...hhhhhhhhhhh..eeeee.........hhhhhhhhh...eeeeeee.hhhh..hhhhhhhhhh....eeeee.......ee..ee......eeeee............eeeee.hhhhhhhhhhhh..........ee...ee...hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee..........eeeeee......hhhhhhhhhhhh..........hhhhhhhhhh...eee...hhhhhhhhhheeeee.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gms B   0 HMINYPLASSTWDDLEYKAIQSVLDSKMFTMGEYVKQYETQFAKTFGSKYAVMVSSGSTANLLMIAALFFTKKPRLKKGDEIIVPAVSWSTTYYPLQQYGLRVKFVDIDINTLNIDIESLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGRDIILLEDNCESMGATFNNKCAGTFGLMGTFSSFYSHHIATMEGGCIVTDDEEIYHILLCIRAHGWTRNLPKKNKVTGVKSDDQFEESFKFVLPGYNVRPLEMSGAIGIEQLKKLPRFISVRRKNAEYFLDKFKDHPYLDVQQETGESSWFGFSFIIKKDSGVIRKQLVENLNSAGIECRPIVTGNFLKNTDVLKYFDYTVHNNVDNAEYLDKNGLFVGNHQIELFDEIDYLREVLK 388
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379
   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  (0, 0)

(no "SCOP Domain" information available for 2GMS)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GMS)

(-) Gene Ontology  (3, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9F118_ECOLX | Q9F118)
molecular function
    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:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.

Chain A,B   (COLD_ECOCB | D3QY10)
molecular function
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        COLD_ECOCB | D3QY10: 2gmu 2r0t 3b8x
        Q9F118_ECOLX | Q9F118: 3gr9
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        Q9F118_ECOLX | Q9F118: 2gmu 2r0t 3b8x

(-) Related Entries Specified in the PDB File

2gmu CRYSTAL STRUCTURE OF E COLI GDP-4-KETO-6-DEOXY-D-MANNOSE-3- DEHYDRATASE COMPLEXED WITH PLP-GLUTAMATE KETIMINE INTERMEDIATE