UBIQUITIN

Structure

Secondary structure:

 

(This is the local folding pattern of polypeptide chain)

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure 1. Wiring diagram of secondary structures for human ubiquitin (1ubq). Yellow are β-strands; Red are helices; Seablue characters are amino acids that make up β-turns; Red curves correspond to β-hairpins [33].

 

 

Sumary of secondary motifs present in human ubiquitin [33]:

 

a). 1 β-sheet:

 

- one sheet (A) consists of 5 β-strands; type: mixed; no barrel; topology[?]: -1 3X 1 –2X.

 

b). 5 β-strands (31,6%):

 

 

 

 

 

 

 

 

c). 3 Helices (15,8% of a-helix; 7,9% of 3,10 helix):

 

 

 

 

 

 

 

d). 6 β-turns:

 

 

 

 

 

 

 

e). 1 β-bulge:

 

- type: G1; antiparallel; residue X: T7; residue 1: G10; residue 2: K11.

 

f). 2 β-hairpins:

 

 

 

 

 

 

Primary structure

 

Tertiary structure

 

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Ubiquitilation

Structure

Number of stand

Start

End

Belongs to sheet

Edge

Number of residues

Sequence

1

2

7

A

-

6

QIFVKT

2

12

16

A

+

5

TITLE

3

41

45

A

-

5

QRLIF

4

48

49

A

+

2

KQ

5

66

71

A

-

6

TLHLVL

Helix no.

Start

End

Type

No. of residues

Lenght [Ǻ]

Unit rise

Residues per turn

Pitch [Ǻ]

Delia-tion [degrees]

Sequence

1

23

34

H

12

17,52

1,46

3,68

5,38

10,8

IENVKAKIQDKE

2

38

40

G

3

-

-

-

-

-

PDQ

3

56

59

G

4

6,77

1,69

3,45

5,82

40,1

LSDY

No. of turns

Start

End

Turn type

H - bond

Sequence

1

7

10

I

+

TLTG

2

18

21

I

+

EPSD

3

44

47

IV

-

IFAG

4

45

48

I’

+

FAGK

5

51

54

I

+

EDGR

6

62

65

II

+

QEKS

Strand 1

Strand 2

Class

Start

End

Lenght

Start

End

Lenght

2

7

8

12

16

5

3:5

41

45

5

48

49

2

2:2