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Table 1 PL genes in the C. rosea genome with assigned protein IDs, gene name, PL families, additional domains and subfamily identification, known activity based on Cazy database, list of crystal structures related to the PL families and organisms for which 3D structures are available in the PDB database

From: Evolution and functional characterization of pectate lyase PEL12, a member of a highly expanded Clonostachys rosea polysaccharide lyase 1 family

C. rosea protein ID

Gene name

CAZy module(s) and subfamilies

Known Activities

PDB/3D structure accession nr.

3D structure status

Organism with known 3D structure

PL1 genes identified in C. rosea

BN869_T00011408

pel1

PL1

pectate lyase (EC 4.2.2.2); exo-pectate lyase (EC 4.2.2.9); pectin lyase (EC 4.2.2.10)

1IDJ[A,B] 1IDK[A] 1QCX[A] 1PXZ[A,B]

parallel β-helix

Aspergillus niger, Juniperus ashei

BN869_T00008859

pel2

BN869_T00000002

pel3

CE8-PL1

BN869_T00000920

pel4

PL1_2

BN869_T00008472

pel5

PL1_4

BN869_T00010915

pel6

BN869_T00006080

pel7

BN869_T00010737

pel8

BN869_T00008735

pel9

BN869_T00007710

pel10

PL1_4-CBM1

BN869_T00005779

pel11

BN869_T00006915

pel12

PL1_7

BN869_T00007653

pel13

BN869_T00008627

pel14

BN869_T00002081

pel15

BN869_T00010228

pel16

BN869_T00007566

pel17

CBM1-PL1_9

    

Other PL gene families and PL subfamilies identified in C. rosea

BN869_T00011160

 

PL20

endo-β-1,4-glucuronan lyase A (GlA) (EC 4.2.2.14)

2ZZJ[A]

putative beta-jelly roll fold

Trichoderma reesei NBRC 31329

BN869_T00008392

 

PL3_2

pectate lyase (EC 4.2.2.2)

1EE6[A] 3B4N[A,B] 3B8Y[A,B] 3B90[A,B]

parallel β-helix

Bacillus sp. KSM-P15, Dickeya dadantii 3937

BN869_T00003737

 

BN869_T00012955

 

BN869_T00007220

 

BN869_T00010913

 

BN869_T00013332

 

BN869_T00000798

 

BN869_T00011510

 

BN869_T00010121

 

BN869_T00013099

 

BN869_T00002494

 

PL4_1

rhamnogalacturonan lyase (EC 4.2.2.23)

1NKG[A] 2XHN[A,B] 3NJV[A] 3NJX[A]

β-sandwich and β-sheet

Aspergillus aculeatus KSM 510

BN869_T00003115

 

BN869_T00009470

 

PL4_3

BN869_T00000818

 

PL9_3

pectate lyase (EC 4.2.2.2); exopolygalacturonate lyase (EC 4.2.2.9); thiopeptidoglycan lyase (EC 4.2.2.-)

1RU4[A]

parallel β-helix

Dickeya dadantii 3937

  1. List of polysaccharide lyase (PL) genes in the C. rosea genome
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BMC Microbiology

ISSN: 1471-2180

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