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(-) Description

Title :  CRYSTAL STRUCTURE OF GMHA FROM BURKHOLDERIA PSEUDOMALLEI IN COMPLEX WITH PRODUCT
 
Authors :  N. J. Harmer
Date :  13 Apr 10  (Deposition) - 19 May 10  (Release) - 21 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Capsule, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. J. Harmer
The Structure Of Sedoheptulose-7-Phosphate Isomerase From Burkholderia Pseudomallei Reveals A Zinc Binding Site At The Heart Of The Active Site.
J. Mol. Biol. V. 400 379 2010
PubMed-ID: 20447408  |  Reference-DOI: 10.1016/J.JMB.2010.04.058

(-) Compounds

Molecule 1 - PHOSPHOHEPTOSE ISOMERASE
    Chains: A, B, C, D
    EC Number: 5.3.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 272560
    Strain: K96243
    Synonym: GMHA, SEDOHEPTULOSE 7-PHOSPHATE ISOMERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
1M7P4Ligand/IonD-GLYCERO-D-MANNOPYRANOSE-7-PHOSPHATE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4PGE1Ligand/IonTRIETHYLENE GLYCOL
5ZN4Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:64 , GLU A:68 , HIS A:183 , GLN D:175 , M7P D:1199BINDING SITE FOR RESIDUE ZN A1197
02AC2SOFTWAREGLN B:175 , M7P B:1197 , HIS C:64 , GLU C:68 , HIS C:183BINDING SITE FOR RESIDUE ZN C1196
03AC3SOFTWAREHIS B:64 , GLU B:68 , HIS B:183 , GLN C:175 , M7P C:1197BINDING SITE FOR RESIDUE ZN B1196
04AC4SOFTWAREGLN A:175 , M7P A:1198 , HIS D:64 , GLU D:68 , HIS D:183BINDING SITE FOR RESIDUE ZN D1198
05AC5SOFTWAREGLU A:68 , ARG A:72 , ZN A:1197 , ASN C:97 , ASP C:98 , HOH C:2126 , ASN D:55 , GLY D:56 , GLY D:57 , SER D:123 , THR D:124 , SER D:125 , SER D:128 , THR D:171 , GLN D:175 , HOH D:2205 , HOH D:2206 , HOH D:2207 , HOH D:2208 , HOH D:2209 , HOH D:2210BINDING SITE FOR RESIDUE M7P D1199
06AC6SOFTWAREASN A:97 , ASP A:98 , ASN B:55 , GLY B:56 , GLY B:57 , SER B:123 , THR B:124 , SER B:125 , SER B:128 , THR B:171 , GLN B:175 , HOH B:2113 , HOH B:2179 , HOH B:2245 , HOH B:2246 , HOH B:2247 , HOH B:2248 , HOH B:2249 , GLU C:68 , ARG C:72 , ZN C:1196 , HOH C:2108 , HOH C:2110BINDING SITE FOR RESIDUE M7P B1197
07AC7SOFTWAREASN A:55 , GLY A:56 , GLY A:57 , SER A:123 , THR A:124 , SER A:125 , SER A:128 , THR A:171 , GLN A:175 , HOH A:2188 , HOH A:2260 , HOH A:2261 , HOH A:2262 , HOH A:2263 , HOH A:2264 , ALA B:94 , ASN B:97 , ASP B:98 , HOH B:2146 , GLU D:68 , ARG D:72 , ZN D:1198 , HOH D:2088BINDING SITE FOR RESIDUE M7P A1198
08AC8SOFTWAREGLU B:68 , ARG B:72 , ZN B:1196 , ASN C:55 , GLY C:56 , GLY C:57 , SER C:123 , THR C:124 , SER C:125 , SER C:128 , THR C:171 , GLN C:175 , HOH C:2096 , HOH C:2213 , HOH C:2214 , HOH C:2215 , HOH C:2216 , HOH C:2217 , HOH C:2218 , ASN D:97 , ASP D:98 , HOH D:2109BINDING SITE FOR RESIDUE M7P C1197
09AC9SOFTWAREALA D:31 , THR D:32 , LYS D:35BINDING SITE FOR RESIDUE PEG D1200
10BC1SOFTWAREALA C:31 , THR C:32 , LYS C:35BINDING SITE FOR RESIDUE PGE C1198
11BC2SOFTWAREALA A:31 , THR A:32 , LYS A:35 , LEU A:162BINDING SITE FOR RESIDUE PG4 A1199

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SISPS51464 SIS domain profile.GMHA_BURPS40-197
 
 
 		  4A:40-196
B:40-195
C:40-195
D:40-197

(-) Exons   (0, 0)

(no "Exon" information available for 2XBL)

(-) 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:194
 aligned with GMHA_BURPS | Q93UJ2 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:194
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192    
           GMHA_BURPS     3 NRELTYITNSIAEAQRVMAAMLADERLLATVRKVADACIASIAQGGKVLLAGNGGSAADAQHIAGEFVSRFAFDRPGLPAVALTTDTSILTAIGNDYGYEKLFSRQVQALGNEGDVLIGYSTSGKSPNILAAFREAKAKGMTCVGFTGNRGGEMRELCDLLLEVPSADTPKIQEGHLVLGHIVCGLVEHSIFGK 196
               SCOP domains d2xbla_ A: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh..........eee...hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh..eeeeee.....hhhhhh.eeee....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------SIS  PDB: A:40-196 UniProt: 40-197                                                                                                                            PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xbl A   3 NRELTYITNSIAEAQRVMAAMLADERLLATVRKVADACIASIAQGGKVLLAGNGGSAADAQHIAGEFVSRFAFDRPGLPAVALTTDTSILTAIGNDYGYEKLFSRQVQALGNEGDVLIGYSTSGKSPNILAAFREAKAKGMTCVGFTGNRGGEMRELCDLLLEVPSADTPKIQEGHLVLGHIVCGLVEHSIFGK 196
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192    


Chain B from PDB  Type:PROTEIN  Length:193
 aligned with GMHA_BURPS | Q93UJ2 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   
           GMHA_BURPS     3 NRELTYITNSIAEAQRVMAAMLADERLLATVRKVADACIASIAQGGKVLLAGNGGSAADAQHIAGEFVSRFAFDRPGLPAVALTTDTSILTAIGNDYGYEKLFSRQVQALGNEGDVLIGYSTSGKSPNILAAFREAKAKGMTCVGFTGNRGGEMRELCDLLLEVPSADTPKIQEGHLVLGHIVCGLVEHSIFG 195
               SCOP domains d2xblb_ B: automated matches                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh..........eee...hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh.eeeeee.....hhhhhh.eeee....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------SIS  PDB: B:40-195 UniProt: 40-197                                                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xbl B   3 NRELTYITNSIAEAQRVMAAMLADERLLATVRKVADACIASIAQGGKVLLAGNGGSAADAQHIAGEFVSRFAFDRPGLPAVALTTDTSILTAIGNDYGYEKLFSRQVQALGNEGDVLIGYSTSGKSPNILAAFREAKAKGMTCVGFTGNRGGEMRELCDLLLEVPSADTPKIQEGHLVLGHIVCGLVEHSIFG 195
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   


Chain C from PDB  Type:PROTEIN  Length:193
 aligned with GMHA_BURPS | Q93UJ2 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   
           GMHA_BURPS     3 NRELTYITNSIAEAQRVMAAMLADERLLATVRKVADACIASIAQGGKVLLAGNGGSAADAQHIAGEFVSRFAFDRPGLPAVALTTDTSILTAIGNDYGYEKLFSRQVQALGNEGDVLIGYSTSGKSPNILAAFREAKAKGMTCVGFTGNRGGEMRELCDLLLEVPSADTPKIQEGHLVLGHIVCGLVEHSIFG 195
               SCOP domains d2xblc_ C: automated matches                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh..........eee...hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh..eeeeee.....hhhhhh.eeee....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------SIS  PDB: C:40-195 UniProt: 40-197                                                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xbl C   3 NRELTYITNSIAEAQRVMAAMLADERLLATVRKVADACIASIAQGGKVLLAGNGGSAADAQHIAGEFVSRFAFDRPGLPAVALTTDTSILTAIGNDYGYEKLFSRQVQALGNEGDVLIGYSTSGKSPNILAAFREAKAKGMTCVGFTGNRGGEMRELCDLLLEVPSADTPKIQEGHLVLGHIVCGLVEHSIFG 195
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   


Chain D from PDB  Type:PROTEIN  Length:195
 aligned with GMHA_BURPS | Q93UJ2 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:195
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     
           GMHA_BURPS     3 NRELTYITNSIAEAQRVMAAMLADERLLATVRKVADACIASIAQGGKVLLAGNGGSAADAQHIAGEFVSRFAFDRPGLPAVALTTDTSILTAIGNDYGYEKLFSRQVQALGNEGDVLIGYSTSGKSPNILAAFREAKAKGMTCVGFTGNRGGEMRELCDLLLEVPSADTPKIQEGHLVLGHIVCGLVEHSIFGKQ 197
               SCOP domains d2xbld_ D: automated matches                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----SIS_2-2xblD01 D:7-150                                                                                                                           ----------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----SIS_2-2xblD02 D:7-150                                                                                                                           ----------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----SIS_2-2xblD03 D:7-150                                                                                                                           ----------------------------------------------- Pfam domains (3)
           Pfam domains (4) ----SIS_2-2xblD04 D:7-150                                                                                                                           ----------------------------------------------- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh..........eee...hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh..eeeeee.....hhhhhh.eeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------SIS  PDB: D:40-197 UniProt: 40-197                                                                                                                             PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xbl D   3 NRELTYITNSIAEAQRVMAAMLADERLLATVRKVADACIASIAQGGKVLLAGNGGSAADAQHIAGEFVSRFAFDRPGLPAVALTTDTSILTAIGNDYGYEKLFSRQVQALGNEGDVLIGYSTSGKSPNILAAFREAKAKGMTCVGFTGNRGGEMRELCDLLLEVPSADTPKIQEGHLVLGHIVCGLVEHSIFGKQ 197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: SIS (53)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (GMHA_BURPS | Q93UJ2)
molecular function
    GO:0008968    D-sedoheptulose 7-phosphate isomerase activity    Catalysis of the reaction: D-sedoheptulose-7-phosphate = D-alpha,beta-D-heptose 7-phosphate.
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:2001061    D-glycero-D-manno-heptose 7-phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a D-glycero-D-manno-heptose 7-phosphate.
    GO:0045227    capsule polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of polysaccharides that make up the capsule, a protective structure surrounding some species of bacteria and fungi.
    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.
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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  2xbl
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 Related Entries

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

UniProtKB/Swiss-Prot
        GMHA_BURPS | Q93UJ2: 2x3y

(-) Related Entries Specified in the PDB File

2x3y CRYSTAL STRUCTURE OF GMHA FROM BURKHOLDERIA PSEUDOMALLEI