Introduction to Structural Bioinformatics

3PSG: Pepsinogen

By: Elaine Lee

 

 

 

General Information

A protein precursor to pepsin, Pepsinogen I or Pepsinogen A is secreted exclusively by the chief cells of gastric corpus.  The levels of Pepsinogen I correlate directly with the active number of chief cells in this area.  In cases of severe atrophic gastritis of the corpus region, the chief cells will be destroyed and the levels of Pepsinogen I will fall.

 

                                            

CATH Hierarchy (Class Architecture Topology Homologous Superfamily)

SCOP (Structure Classification of Proteins)

 

 

Structure and Sequence Alignments

Example:

Structural alignments with neighbors 2PSG and 3PEP:

3PSG:_ 1/2P LVKVPLVRKKSLRQNLIKDGKLKDFLKTHKHNPASKYFPEAAALIGDEPLENYLDTEYFG
2PSG:_ 1/2P LVKVPLVRKKSLRQNLIKDGKLKDFLKTHKHNPASKYFPEAAALIGDEPLENYLDTEYFG
3PEP:_ 13/14 --------------------------------------------------------EYFG

3PSG:_ 61/18 TIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQFNPDDSSTFEATSQELSITYG
2PSG:_ 61/18 TIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQFNPDDSSTFEATSQELSITYG
3PEP:_ 17/18 TIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQFNPDDSSTFEATSQELSITYG

3PSG:_ 121/78 TGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISASGATPV
2PSG:_ 121/78 TGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISASGATPV
3PEP:_ 77/78 TGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISASGATPV

3PSG:_ 181/138 FDNLWDQGLVSQDLFSVYLSSNDDSGSVVLLGGIDSSYYTGSLNWVPVSVEGYWQITLDS
2PSG:_ 181/138 FDNLWDQGLVSQDLFSVYLSSNDDSGSVVLLGGIDSSYYTGSLNWVPVSVEGYWQITLDS
3PEP:_ 137/138 FDNLWDQGLVSQDLFSVYLSSNDDSGSVVLLGGIDSSYYTGSLNWVPVSVEGYWQITLDS

3PSG:_ 241/198 ITMDGETIACSGGCQAIVDTGTSLLTGPTSAIANIQSDIGASENSDGEMVISCSSIDSLP
2PSG:_ 241/198 ITMDGETIACSGGCQAIVDTGTSLLTGPTSAIANIQSDIGASENSDGEMVISCSSIDSLP
3PEP:_ 197/198 ITMDGETIACSGGCQAIVDTGTSLLTGPTSAIANIQSDIGASENSDGEMVISCSSIDSLP

3PSG:_ 301/258 DIVFTIDGVQYPLSPSAYILQDDDSCTSGFEGMD------VPTSSGELWILGDVFIRQYY
2PSG:_ 301/258 DIVFTIDGVQYPLSPSAYILQDDDSCTSGFEGMD------VPTSSGELWILGDVFIRQYY
3PEP:_ 257/258 DIVFTIDGVQYPLSPSAYILQDDDSCTSGFEGMDVPTSSGE------LWILGDVFIRQYY

3PSG:_ 355/312 TVFDRANNKVGLAPVA
2PSG:_ 355/312 TVFDRANNKVGLAPVA
3PEP:_ 311/312 TVFDRANNKVGLAPVA



Clusta1W based sequence alignment with neighbors 2PSG and 3PEP:

 

>3PSG:_ PEPSINOGEN - CHAIN _
LVKVPLVRKKSLRQNLIKDGKLKDFLKTHKHNPASKYFPEAAALIGDEPLENYLDTEYFG
TIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQFNPDDSSTFEATSQELSITYG
TGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISASGATPV
FDNLWDQGLVSQDLFSVYLSSNDDSGSVVLLGGIDSSYYTGSLNWVPVSVEGYWQITLDS
ITMDGETIACSGGCQAIVDTGTSLLTGPTSAIANIQSDIGASENSDGEMVISCSSIDSLP
DIVFTIDGVQYPLSPSAYILQDDDSCTSGFEGMDVPTSSGELWILGDVFIRQYYTVFDRA
NNKVGLAPVA
>3PEP:_ PEPSIN (E.C.3.4.23.1) - CHAIN _
IGDEPLENYLDTEYFGTIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQFNPDD
SSTFEATSQELSITYGTGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGI
LGLAYPSISASGATPVFDNLWDQGLVSQDLFSVYLSSNDDSGSVVLLGGIDSSYYTGSLN
WVPVSVEGYWQITLDSITMDGETIACSGGCQAIVDTGTSLLTGPTSAIANIQSDIGASEN
SDGEMVISCSSIDSLPDIVFTIDGVQYPLSPSAYILQDDDSCTSGFEGMDVPTSSGELWI
LGDVFIRQYYTVFDRANNKVGLAPV
 Comment: The two proteins are monomeric, so there are no extraneous sequences.
 

                                                                   Experimental Detail                                        

Resolution [Å]:

1.65

R-Value:

0.173

Space Group:

C 2

 

Unit Cell:

dim [Å]:

a

106.10

b

43.70

c

88.90

angles [°]:

alpha

90.00

beta

91.40

gamma

90.00

 

Polymer Chains:

3PSG

Residues:

370

Atoms:

2872

HET groups:

HOH

 

 

 

 

                                               

                                                                                                H bonds on

 

 

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