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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE/PHOSPHOMANNOSE ISOMERASE FROM PYROBACULUM AEROPHILUM IN COMPLEX WITH FRUCTOSE 6-PHOSPHATE
 
Authors :  M. K. Swan, T Hansen, P. Schoenheit, C. Davies
Date :  21 Aug 04  (Deposition) - 07 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enzyme, Crenarchaeon, Hyperthermophile, Pgi Superfamily, Fructose 6- Phosphate, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Swan, T. Hansen, P. Schoenheit, C. Davies
Structural Basis For Phosphomannose Isomerase Activity In Phosphoglucose Isomerase From Pyrobaculum Aerophilum: A Subtle Difference Between Distantly Related Enzymes.
Biochemistry V. 43 14088 2004
PubMed-ID: 15518558  |  Reference-DOI: 10.1021/BI048608Y
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOSE-6-PHOSPHATE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.9, 5.3.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PAE1610
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 13773

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1F6R2Ligand/IonFRUCTOSE -6-PHOSPHATE
2GOL4Ligand/IonGLYCEROL
3SO45Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:104 , ARG B:105BINDING SITE FOR RESIDUE SO4 B 501
02AC2SOFTWAREARG A:299 , ARG A:300BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWAREARG A:104 , ARG A:105BINDING SITE FOR RESIDUE SO4 A 503
04AC4SOFTWAREGLN A:179 , ARG A:181 , ARG A:284 , HOH A:846 , ARG B:79BINDING SITE FOR RESIDUE SO4 A 504
05AC5SOFTWAREGLN B:179 , ARG B:181 , ARG B:284 , HOH B:780 , HOH B:878 , HOH B:894BINDING SITE FOR RESIDUE SO4 B 505
06AC6SOFTWAREHIS A:219 , MET B:45 , GLY B:46 , GLY B:47 , SER B:48 , SER B:87 , TYR B:88 , SER B:89 , THR B:92 , PRO B:134 , ARG B:135 , GLU B:203 , LYS B:298 , HOH B:723 , HOH B:887 , HOH B:888BINDING SITE FOR RESIDUE F6R B 700
07AC7SOFTWAREMET A:45 , GLY A:46 , GLY A:47 , SER A:48 , SER A:87 , TYR A:88 , SER A:89 , THR A:92 , PRO A:134 , ARG A:135 , GLU A:203 , LYS A:298 , HOH A:723 , HOH A:760 , HIS B:219BINDING SITE FOR RESIDUE F6R A 701
08AC8SOFTWAREASP A:53 , LYS A:72 , ARG A:191 , TYR A:195 , HOH A:739 , HOH A:757 , HOH A:784 , HOH A:909BINDING SITE FOR RESIDUE GOL A 601
09AC9SOFTWARETHR A:233 , GLN A:242 , HOH A:893 , HOH A:898BINDING SITE FOR RESIDUE GOL A 602
10BC1SOFTWARESER A:89 , ASN A:91 , THR A:92 , ILE A:93 , LYS A:298 , HOH A:720 , HOH A:751 , HOH A:814 , ARG B:117BINDING SITE FOR RESIDUE GOL A 603
11BC2SOFTWAREVAL B:27 , GLU B:28 , GLU B:30 , LYS B:103 , ARG B:104 , ARG B:106BINDING SITE FOR RESIDUE GOL B 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X9H)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:214 -Pro A:215
2Leu B:214 -Pro B:215

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X9H)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SISPS51464 SIS domain profile.PGMI_PYRAE27-160
 		  2A:27-160
B:27-160

(-) Exons   (0, 0)

(no "Exon" information available for 1X9H)

(-) 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:301
 aligned with PGMI_PYRAE | Q8ZWV0 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:301
                                    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       281       291       301 
           PGMI_PYRAE     2 SQLLQDYLNWENYILRRVDFPTSYVVEGEVVRIEAMPRLYISGMGGSGVVADLIRDFSLTWNWEVEVIAVKDYFLKARDGLLIAVSYSGNTIETLYTVEYAKRRRIPAVAITTGGRLAQMGVPTVIVPKASAPRAALPQLLTAALHVVAKVYGIDVKIPEGLEPPNEALIHKLVEEFQKRPTIIAAESMRGVAYRVKNEFNENAKIEPSVEILPEAHHNWIEGSERAVVALTSPHIPKEHQERVKATVEIVGGSIYAVEMHPKGVLSFLRDVGIASVKLAEIRGVNPLATPRIDALKRRLQ 302
               SCOP domains d1x9ha_ A: Glucose-6-phosphate isomerase, conjectural                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1x9hA01 A:2-163 Glucose-6-phosphate isomerase like protein; domain 1                                                                                              1x9hA02 A:164-302 Glucose-6-phosphate isomerase like protein; domain 1                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh........eeee..eeee.....eeeee.hhhhhhhhhhhhhhhhhh....eeeee..........eeeee.....hhhhhhhhhhhhhh...eeeee...hhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------SIS  PDB: A:27-160 UniProt: 27-160                                                                                                    ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x9h A   2 SQLLQDYLNWENYILRRVDFPTSYVVEGEVVRIEAMPRLYISGMGGSGVVADLIRDFSLTWNWEVEVIAVKDYFLKARDGLLIAVSYSGNTIETLYTVEYAKRRRIPAVAITTGGRLAQMGVPTVIVPKASAPRAALPQLLTAALHVVAKVYGIDVKIPEGLEPPNEALIHKLVEEFQKRPTIIAAESMRGVAYRVKNEFNENAKIEPSVEILPEAHHNWIEGSERAVVALTSPHIPKEHQERVKATVEIVGGSIYAVEMHPKGVLSFLRDVGIASVKLAEIRGVNPLATPRIDALKRRLQ 302
                                    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       281       291       301 


Chain B from PDB  Type:PROTEIN  Length:301
 aligned with PGMI_PYRAE | Q8ZWV0 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:301
                                    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       281       291       301 
           PGMI_PYRAE     2 SQLLQDYLNWENYILRRVDFPTSYVVEGEVVRIEAMPRLYISGMGGSGVVADLIRDFSLTWNWEVEVIAVKDYFLKARDGLLIAVSYSGNTIETLYTVEYAKRRRIPAVAITTGGRLAQMGVPTVIVPKASAPRAALPQLLTAALHVVAKVYGIDVKIPEGLEPPNEALIHKLVEEFQKRPTIIAAESMRGVAYRVKNEFNENAKIEPSVEILPEAHHNWIEGSERAVVALTSPHIPKEHQERVKATVEIVGGSIYAVEMHPKGVLSFLRDVGIASVKLAEIRGVNPLATPRIDALKRRLQ 302
               SCOP domains d1x9hb_ B: Glucose-6-phosphate isomerase, conjectural                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1x9hB01 B:2-163 Glucose-6-phosphate isomerase like protein; domain 1                                                                                              1x9hB02 B:164-302 Glucose-6-phosphate isomerase like protein; domain 1                                                                      CATH domains
           Pfam domains (1) --------------------------------SIS-1x9hB01 B:34-149                                                                                                --------------bact-PGI_C-1x9hB03 B:164-302                                                                                                                Pfam domains (1)
           Pfam domains (2) --------------------------------SIS-1x9hB02 B:34-149                                                                                                --------------bact-PGI_C-1x9hB04 B:164-302                                                                                                                Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh........eeee..eeee.....eeeee.hhhhhhhhhhhhhhhhhh....eeeee..........eeeeee....hhhhhhhhhhhhhh...eeeee...hhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------SIS  PDB: B:27-160 UniProt: 27-160                                                                                                    ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x9h B   2 SQLLQDYLNWENYILRRVDFPTSYVVEGEVVRIEAMPRLYISGMGGSGVVADLIRDFSLTWNWEVEVIAVKDYFLKARDGLLIAVSYSGNTIETLYTVEYAKRRRIPAVAITTGGRLAQMGVPTVIVPKASAPRAALPQLLTAALHVVAKVYGIDVKIPEGLEPPNEALIHKLVEEFQKRPTIIAAESMRGVAYRVKNEFNENAKIEPSVEILPEAHHNWIEGSERAVVALTSPHIPKEHQERVKATVEIVGGSIYAVEMHPKGVLSFLRDVGIASVKLAEIRGVNPLATPRIDALKRRLQ 302
                                    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       281       291       301
   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, 2)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: SIS (53)
(-)
Clan: no clan defined [family: bact-PGI_C] (4)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PGMI_PYRAE | Q8ZWV0)
molecular function
    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: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:0004347    glucose-6-phosphate isomerase activity    Catalysis of the reaction: D-glucose 6-phosphate = D-fructose 6-phosphate.
    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:0004476    mannose-6-phosphate isomerase activity    Catalysis of the reaction: D-mannose 6-phosphate = D-fructose 6-phosphate.
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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PGMI_PYRAE | Q8ZWV0: 1tzb 1tzc 1x9i

(-) Related Entries Specified in the PDB File

1tzb NATIVE STRUCTURE
1tzc IN COMPLEX WITH 5-PHOSPHOARABINONATE
1x9i