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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF RABBIT PHOSPHOGLUCOSE ISOMERASE COMPLEXED WITH 5-PHOSPHOARABINONATE, A TRANSITION STATE ANALOGUE
 
Authors :  C. J. Jeffery, R. Hardre, L. Salmon
Date :  22 Nov 00  (Deposition) - 01 Jun 01  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphoglucose Isomerase, 5-Phosphoarabinonate, Transition State Analogue, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Jeffery, R. Hardre, L. Salmon
Crystal Structure Of Rabbit Phosphoglucose Isomerase Complexed With 5-Phospho-D-Arabinonate Identifies The Role Of Glu357 In Catalysis.
Biochemistry V. 40 1560 2001
PubMed-ID: 11327814  |  Reference-DOI: 10.1021/BI0018483

(-) Compounds

Molecule 1 - PHOSPHOGLUCOSE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.9
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Other Details: RABBIT SKELETAL MUSCLE TISSUE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PA52Ligand/Ion5-PHOSPHOARABINONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:156 , GLY A:157 , GLY A:158 , SER A:159 , SER A:209 , LYS A:210 , THR A:211 , THR A:214 , GLN A:353 , GLU A:357 , LYS A:518 , HOH A:926 , HOH A:929 , HOH A:930 , HOH A:931 , HOH A:932 , HOH A:935 , HIS B:388BINDING SITE FOR RESIDUE PA5 A 558
2AC2SOFTWAREHIS A:388 , ILE B:156 , GLY B:157 , GLY B:158 , SER B:159 , SER B:209 , LYS B:210 , THR B:211 , THR B:214 , GLN B:353 , GLU B:357 , LYS B:518 , HOH B:926 , HOH B:966 , HOH B:967 , HOH B:969 , HOH B:973 , HOH B:974BINDING SITE FOR RESIDUE PA5 B 558

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G98)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:383 -Thr A:384
2Gly B:383 -Thr B:384

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G98)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1P_GLUCOSE_ISOMERASE_3PS51463 Glucose-6-phosphate isomerase family profile.G6PI_RABIT7-553
 		  2A:6-552
B:6-552
2P_GLUCOSE_ISOMERASE_1PS00765 Phosphoglucose isomerase signature 1.G6PI_RABIT268-281
 		  2A:267-280
B:267-280
3P_GLUCOSE_ISOMERASE_2PS00174 Phosphoglucose isomerase signature 2.G6PI_RABIT502-519
 		  2A:501-518
B:501-518

(-) Exons   (0, 0)

(no "Exon" information available for 1G98)

(-) 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:555
 aligned with G6PI_RABIT | Q9N1E2 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:555
                                    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       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551     
           G6PI_RABIT     2 AALTRNPQFQKLQQWHREHGSELNLRHLFDTDKERFNHFSLTLNTNHGHILLDYSKNLVTEEVMHMLLDLAKSRGVEAARESMFNGEKINSTEDRAVLHVALRNRSNTPIVVDGKDVMPEVNKVLDKMKAFCQRVRSGDWKGYTGKTITDVINIGIGGSDLGPLMVTEALKPYSSGGPRVWFVSNIDGTHIAKTLACLNPESSLFIIASKTFTTQETITNAETAKDWFLLSAKDPSTVAKHFVALSTNTAKVKEFGIDPQNMFEFWDWVGGRYSLWSAIGLSIALHVGFDNFEQLLSGAHWMDQHFRTTPLEKNAPVLLAMLGIWYINCFGCETQAVLPYDQYLHRFAAYFQQGDMESNGKYITKSGARVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRKGLHHKILLANFLAQTEALMKGKSTEEARKELQAAGKSPEDLMKLLPHKVFEGNRPTNSIVFTKLTPFILGALIAMYEHKIFVQGVVWDINSFDQWGVELGKQLAKKIEPELDGSSPVTSHDSSTNGLINFIKQQREAK 556
               SCOP domains d1g98a_ A: Phosphoglucose isomerase, PGI                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1g98A01 A:1-98,A:294-514 Glucose-6-phosphate isomerase like protein; domain 1                     1g98A02 A:99-293 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                              1g98A01 A:1-98,A:294-514 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                                                1g98A03 A:515-555                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhheeeee....eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh.............hhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhh....hhhh.eeeee.hhhhhhhh..hhh.eee.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhh................eee....hhhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.....hhhhhhhhhhh......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----P_GLUCOSE_ISOMERASE_3  PDB: A:6-552 UniProt: 7-553                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P_GLUCOSE_ISOM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P_GLUCOSE_ISOMERAS------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g98 A   1 AALTRNPQFQKLQQWHREHGSELNLRHLFDTDKERFNHFSLTLNTNHGHILLDYSKNLVTEEVMHMLLDLAKSRGVEAARESMFNGEKINSTEDRAVLHVALRNRSNTPIVVDGKDVMPEVNKVLDKMKAFCQRVRSGDWKGYTGKTITDVINIGIGGSDLGPLMVTEALKPYSSGGPRVWFVSNIDGTHIAKTLACLNPESSLFIIASKTFTTQETITNAKTAKDWFLLSAKDPSTVAKHFVALSTNTAKVKEFGIDPQNMFEFWDWVGGRYSLWSAIGLSIALHVGFDNFEQLLSGAHWMDQHFRTTPLEKNAPVLLAMLGIWYINCFGCETQAVLPYDQYLHRFAAYFQQGDMESNGKYITKSGARVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRKGLHHKILLANFLAQTEALMKGKSTEEARKELQAAGKSPEDLMKLLPHKVFEGNRPTNSIVFTKLTPFILGALIAMYEHKIFVQGVVWDINSFDQWGVELGKQLAKKIEPELDGSSPVTSHDSSTNGLINFIKQQREAK 555
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550     


Chain B from PDB  Type:PROTEIN  Length:555
 aligned with G6PI_RABIT | Q9N1E2 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:555
                                    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       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551     
           G6PI_RABIT     2 AALTRNPQFQKLQQWHREHGSELNLRHLFDTDKERFNHFSLTLNTNHGHILLDYSKNLVTEEVMHMLLDLAKSRGVEAARESMFNGEKINSTEDRAVLHVALRNRSNTPIVVDGKDVMPEVNKVLDKMKAFCQRVRSGDWKGYTGKTITDVINIGIGGSDLGPLMVTEALKPYSSGGPRVWFVSNIDGTHIAKTLACLNPESSLFIIASKTFTTQETITNAETAKDWFLLSAKDPSTVAKHFVALSTNTAKVKEFGIDPQNMFEFWDWVGGRYSLWSAIGLSIALHVGFDNFEQLLSGAHWMDQHFRTTPLEKNAPVLLAMLGIWYINCFGCETQAVLPYDQYLHRFAAYFQQGDMESNGKYITKSGARVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRKGLHHKILLANFLAQTEALMKGKSTEEARKELQAAGKSPEDLMKLLPHKVFEGNRPTNSIVFTKLTPFILGALIAMYEHKIFVQGVVWDINSFDQWGVELGKQLAKKIEPELDGSSPVTSHDSSTNGLINFIKQQREAK 556
               SCOP domains d1g98b_ B: Phosphoglucose isomerase, PGI                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1g98B01 B:1-98,B:294-514 Glucose-6-phosphate isomerase like protein; domain 1                     1g98B02 B:99-293 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                              1g98B01 B:1-98,B:294-514 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                                                1g98B03 B:515-555                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhheeeee....eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh.......ee..eehhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhh.hhh.eee.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhh................eee....hhhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhh......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----P_GLUCOSE_ISOMERASE_3  PDB: B:6-552 UniProt: 7-553                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P_GLUCOSE_ISOM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P_GLUCOSE_ISOMERAS------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g98 B   1 AALTRNPQFQKLQQWHREHGSELNLRHLFDTDKERFNHFSLTLNTNHGHILLDYSKNLVTEEVMHMLLDLAKSRGVEAARESMFNGEKINSTEDRAVLHVALRNRSNTPIVVDGKDVMPEVNKVLDKMKAFCQRVRSGDWKGYTGKTITDVINIGIGGSDLGPLMVTEALKPYSSGGPRVWFVSNIDGTHIAKTLACLNPESSLFIIASKTFTTQETITNAKTAKDWFLLSAKDPSTVAKHFVALSTNTAKVKEFGIDPQNMFEFWDWVGGRYSLWSAIGLSIALHVGFDNFEQLLSGAHWMDQHFRTTPLEKNAPVLLAMLGIWYINCFGCETQAVLPYDQYLHRFAAYFQQGDMESNGKYITKSGARVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRKGLHHKILLANFLAQTEALMKGKSTEEARKELQAAGKSPEDLMKLLPHKVFEGNRPTNSIVFTKLTPFILGALIAMYEHKIFVQGVVWDINSFDQWGVELGKQLAKKIEPELDGSSPVTSHDSSTNGLINFIKQQREAK 555
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550
   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  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G98)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (G6PI_RABIT | Q9N1E2)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    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.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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  1g98
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  5.3.1.9
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 Related Entries

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

UniProtKB/Swiss-Prot
        G6PI_RABIT | Q9N1E2: 1dqr 1hm5 1hox 1koj 1n8t 1xtb

(-) Related Entries Specified in the PDB File

1dqr RABBIT PHOSPHOGLUCOSE ISOMERASE COMPLEXED WITH 6- PHOSPHOGLUCONATE, A COMPETITIVE INHIBITOR OF ISOMERASE CATALYTIC ACTIVITY