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24  structures 1488  species 0  interactions 14934  sequences 366  architectures

Family: Pectinesterase (PF01095)

Summary: Pectinesterase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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Pectinesterase Edit Wikipedia article

pectinesterase
2ntb.png
pectin methylesterase from Dickeya dadantii in complex with hexasaccharide. PDB 2ntb [1]
Identifiers
EC number3.1.1.11
CAS number9025-98-3
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO

Pectinesterase (PE) (EC 3.1.1.11) is a ubiquitous cell-wall-associated enzyme that presents several isoforms that facilitate plant cell wall modification and subsequent breakdown. It is found in all higher plants as well as in some bacteria and fungi. Pectinesterase functions primarily by altering the localised pH of the cell wall resulting in alterations in cell wall integrity.

Pectinesterase catalyses the de-esterification of pectin into pectate and methanol. Pectin is one of the main components of the plant cell wall. In plants, pectinesterase plays an important role in cell wall metabolism during fruit ripening. In plant bacterial pathogens such as Erwinia carotovora and in fungal pathogens such as Aspergillus niger, pectinesterase is involved in maceration and soft-rotting of plant tissue. Plant pectinesterases are regulated by pectinesterase inhibitors, which are ineffective against microbial enzymes.[2]

Function

Recent studies[citation needed] have shown that the manipulation of pectinesterase expression can influence numerous physiological processes. In plants, pectinesterase plays a role in the modulation of cell wall mechanical stability during fruit ripening, cell wall extension during pollen germination and pollen tube growth, abscission, stem elongation, tuber yield and root development. Pectinesterase has also been shown to play a role in a plants response to pathogen attack. A cell wall-associated pectinesterase of Nicotiana tabacum is involved in host cell receptor recognition for the tobacco mosaic virus movement protein and it has been shown that this interaction is required for cell-to-cell translocation of the virus.

Pectinesterase action on the components of the plant cell wall can produce two diametrically opposite effects. The first being a contribution to the stiffening of the cell wall by producing blocks of unesterified carboxyl groups that can interact with calcium ions forming a pectate gel. The other being that proton release may stimulate the activity of cell wall hydrolases contributing to cell wall loosening.

Esterification of pectin

Pectins form approximately 35% of the dry weight of dicot cell walls. They are polymerised in the cis Golgi, methylesterified in the medial Golgi and substituted with side chains in the trans Golgi cisternae. Pectin biochemistry can be rather complicated but put simply, the pectin backbone comprises 3 types of polymer: homogalacturonan (HGA); rhamnogalacturonan I (RGI); rhamnogalacturonan II (RGII).

Homogalacturonan is highly methyl-esterified when exported into cell walls and is subsequently de-esterified by the action of pectinesterase and other pectic enzymes. Pectinesterase catalyses the de-esterification of methyl-esterified D-galactosiduronic acid units in pectic compounds yielding substrates for depolymerising enzymes, particularly acidic pectins and methanol.

Most of the purified plant pectinesterases have neutral or alkaline isoelectric points and are bound to the cell wall via electrostatic interactions. Pectinesterases can however display acidic isoelectric points as detected in soluble fractions of plant tissues. Until recently, it was generally assumed that plant pectinesterases remove methyl esters in a progressive block-wise fashion, giving rise to long contiguous stretches of un-esterified GalA residues in homogalacturonan domains of pectin. Alternatively it was thought that fungal pectinesterases had a random activity resulting in the de-esterification of single GalA residues per enzyme/substrate interactions. It has now been shown that some plant pectinesterase isoforms may exhibit both mechanisms and that such mechanisms are driven by alterations in pH. The optimal pH of higher plants is usually between pH 7 and pH 8 although the pH of pectinesterase from fungi and bacteria is usually much lower than this.

Molecular biology and biochemistry

PE proteins are synthesised as pre-proteins of 540-580 amino acids possessing a signal sequence and a large amino-terminal extension of around 22 kDa. This terminal extension is eventually removed to yield a mature protein of 34-37 kDa. Most PEs lack consensus sequences for N-glycosylation in the mature protein, although at least one site is present in the amino-terminal extension region.

Spatial and temporal regulation of pectinesterase activity during plant development is based on a large family of isoforms. Recently, the systematic sequencing of the Arabidopsis thaliana genome has led to the identification of 66 open reading frames that are annotated as pectinesterases, most of which are encoded as large pre-proproteins. The signal peptide pre-region is required for targeting the enzyme to the endoplasmic reticulum and consists of about 25 amino acid residues. These N-terminal regions contain several glycosylation sites and it is thought that these sites also play a role in targeting.

Pectinesterase is thought to be secreted to the apoplasm with highly methylated pectin although at some point along this secretory pathway the N-terminal pro-peptide is cleaved off. Currently, the role of the pro-region is unknown although it has been hypothesised that it may act as an intramolecular chaperone, ensuring correct folding or deactivating activity until PE insertion in the cell wall is complete.

Recently, particular attention has been devoted to molecular studies of pectinesterase leading to the characterisation of several related isoforms in various higher plant species. Some of these pectinesterases were shown to be ubiquitously expressed, whereas others are specifically expressed during fruit ripening, germination of the pollen grain, or stem elongation. Such data suggests that pectinesterses are encoded by a family of genes that are differentially regulated in cell type in response to specific developmental or environmental cues.

Plant isoforms

Several pectinesterase isoforms differing in molecular weight, isoelectric point and biochemical activity have been identified in dicotyledonous plants. Pectinesterase isoforms are encoded by a family of genes, some of which are constitutively expressed throughout the plant, whereas others are differentially expressed in specific tissues and at different developmental stages. Isoforms of pectinesterase differ in various biochemical parameters such as relative molecular mass, isoelectric point, optimum pH, substrate affinity, ion-requirement and location.

Structure

Pectinesterase, catalytic
Identifiers
SymbolPectinesterase_cat
PfamPF01095
InterProIPR000070
PROSITEPDOC00413

The N-terminal pro-peptides of pectinesterase are variable in size and sequence and show a low level of amino acid identity. Alternatively the C-terminal catalytic region is highly conserved and constitutes the mature enzyme. The first three-dimensional structure solved for a plant pectinesterase was for an isoform from carrot (Daucus carota) root and consists of a right-handed parallel β-helix as seen in all the carbohydrate esterase family CE-8, a transmembrane domain and a pectin binding cleft.[3] Similarly several pectinesterase structures have been elucidated in fungi and E.coli and share most of the structural motifs seen in plants.

Prokaryotic and eukaryotic pectinesterases share a few regions of sequence similarity. The crystal structure of pectinesterase from Erwinia chrysanthemi revealed a beta-helix structure similar to that found in pectinolytic enzymes, though it is different from most structures of esterases.[4] The putative catalytic residues are in a similar location to those of the active site and substrate-binding cleft of pectate lyase.

References

  1. ^ Fries, M.; Ihrig, J.; Brocklehurst, K.; Shevchik, V. E.; Pickersgill, R. W. (2007). "Molecular basis of the activity of the phytopathogen pectin methylesterase". The EMBO Journal. 26 (17): 3879–3887. doi:10.1038/sj.emboj.7601816. PMC 2000356. PMID 17717531.
  2. ^ Giovane A, Tsernoglou D, Camardella L, Di Matteo A, Raiola A, Bonivento D, De Lorenzo G, Cervone F, Bellincampi D (2005). "Structural basis for the interaction between pectin methylesterase and a specific inhibitor protein". Plant Cell. 17 (3): 849–858. doi:10.1105/tpc.104.028886. PMC 1069703. PMID 15722470.
  3. ^ PDB: 1GQ8​; Johansson K, El-Ahmad M, Friemann R, Jörnvall H, Markovic O, Eklund H (March 2002). "Crystal structure of plant pectin methylesterase". FEBS Lett. 514 (2–3): 243–9. doi:10.1016/S0014-5793(02)02372-4. PMID 11943159.
  4. ^ PDB: 1QJV​; Pickersgill RW, Smith D, Jenkins J, Mayans O, Worboys K (2001). "Three-dimensional structure of Erwinia chrysanthemi pectin methylesterase reveals a novel esterase active site". J. Mol. Biol. 305 (4): 951–960. doi:10.1006/jmbi.2000.4324. PMID 11162105.

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Pectinesterase Provide feedback

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Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000070

Pectinesterase EC (pectin methylesterase) catalyses the de-esterification of pectin into pectate and methanol. Pectin is one of the main components of the plant cell wall. In plants, pectinesterase plays an important role in cell wall metabolism during fruit ripening. In plant bacterial pathogens such as Erwinia carotovora and in fungal pathogens such as Aspergillus niger, pectinesterase is involved in maceration and soft-rotting of plant tissue. Plant pectinesterases are regulated by pectinesterase inhibitors, which are ineffective against microbial enzymes [ PUBMED:15722470 ].

Prokaryotic and eukaryotic pectinesterases share a few regions of sequence similarity. The crystal structure of pectinesterase from Erwinia chrysanthemi revealed a beta-helix structure similar to that found in pectinolytic enzymes, though it is different from most structures of esterases [ PUBMED:11162105 ]. The putative catalytic residues are in a similar location to those of the active site and substrate-binding cleft of pectate lyase.

Gene Ontology

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Domain organisation

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Alignments

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(1516)
RP35
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RP55
(12519)
RP75
(17937)
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  Seed
(26)
Full
(14934)
Representative proteomes UniProt
(28650)
RP15
(1516)
RP35
(7642)
RP55
(12519)
RP75
(17937)
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Curation and family details

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Seed source: Prosite
Previous IDs: none
Type: Repeat
Sequence Ontology: SO:0001068
Author: Finn RD , Bateman A
Number in seed: 26
Number in full: 14934
Average length of the domain: 246.80 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 58.02 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 21.3 21.3
Model length: 298
Family (HMM) version: 21
Download: download the raw HMM for this family

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Pectinesterase domain has been found. There are 24 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0N7KTB2 View 3D Structure Click here
A0A0P0V0P1 View 3D Structure Click here
A0A0P0V0X2 View 3D Structure Click here
A0A0P0V1X3 View 3D Structure Click here
A0A0P0V238 View 3D Structure Click here
A0A0P0VNG3 View 3D Structure Click here
A0A0P0VNG3 View 3D Structure Click here
A0A0P0WCC6 View 3D Structure Click here
A0A0P0WCC6 View 3D Structure Click here
A0A0P0WDD7 View 3D Structure Click here
A0A0P0WJ77 View 3D Structure Click here
A0A0P0WLF6 View 3D Structure Click here
A0A0P0XD60 View 3D Structure Click here
A0A0P0XPW3 View 3D Structure Click here
A0A0P0XPW4 View 3D Structure Click here
A0A0P0XZT1 View 3D Structure Click here
A0A0P0XZW0 View 3D Structure Click here
A0A0P0Y3P2 View 3D Structure Click here
A0A0P0Y3Z7 View 3D Structure Click here
A0A0R0ERS6 View 3D Structure Click here
A0A0R0ERW6 View 3D Structure Click here
A0A0R0FCT0 View 3D Structure Click here
A0A0R0FJV6 View 3D Structure Click here
A0A0R0G2T3 View 3D Structure Click here
A0A0R0GDU9 View 3D Structure Click here
A0A0R0GEZ6 View 3D Structure Click here
A0A0R0GJA3 View 3D Structure Click here
A0A0R0GYI7 View 3D Structure Click here
A0A0R0HMQ9 View 3D Structure Click here
A0A0R0HMZ4 View 3D Structure Click here
A0A0R0HMZ4 View 3D Structure Click here
A0A0R0I8Z3 View 3D Structure Click here
A0A0R0I8Z3 View 3D Structure Click here
A0A0R0ICF9 View 3D Structure Click here
A0A0R0J590 View 3D Structure Click here
A0A0R0J6Y3 View 3D Structure Click here
A0A0R0J7M3 View 3D Structure Click here
A0A0R0JDA6 View 3D Structure Click here
A0A0R0JNR4 View 3D Structure Click here
A0A0R0K4H7 View 3D Structure Click here
A0A0R0K4H7 View 3D Structure Click here
A0A0R0KE56 View 3D Structure Click here
A0A0R0KGZ7 View 3D Structure Click here
A0A0R0KN67 View 3D Structure Click here
A0A0R0KWN5 View 3D Structure Click here
A0A0R0KWN5 View 3D Structure Click here
A0A0R0L355 View 3D Structure Click here
A0A0R0L355 View 3D Structure Click here
A0A0R4J2J3 View 3D Structure Click here
A0A0R4J2K9 View 3D Structure Click here
A0A1D6DWT9 View 3D Structure Click here
A0A1D6DWT9 View 3D Structure Click here
A0A1D6E3U8 View 3D Structure Click here
A0A1D6E3U8 View 3D Structure Click here
A0A1D6E3U8 View 3D Structure Click here
A0A1D6E975 View 3D Structure Click here
A0A1D6EQT6 View 3D Structure Click here
A0A1D6F4U1 View 3D Structure Click here
A0A1D6F4U3 View 3D Structure Click here
A0A1D6FHT9 View 3D Structure Click here
A0A1D6FHT9 View 3D Structure Click here
A0A1D6FU22 View 3D Structure Click here
A0A1D6G099 View 3D Structure Click here
A0A1D6GCB2 View 3D Structure Click here
A0A1D6H4M1 View 3D Structure Click here
A0A1D6H4M1 View 3D Structure Click here
A0A1D6HB34 View 3D Structure Click here
A0A1D6I082 View 3D Structure Click here
A0A1D6I4U1 View 3D Structure Click here
A0A1D6I4U1 View 3D Structure Click here
A0A1D6I4Y9 View 3D Structure Click here
A0A1D6I4Y9 View 3D Structure Click here
A0A1D6I4Y9 View 3D Structure Click here
A0A1D6IJ74 View 3D Structure Click here
A0A1D6IN03 View 3D Structure Click here
A0A1D6IP48 View 3D Structure Click here
A0A1D6IYN8 View 3D Structure Click here
A0A1D6IYN8 View 3D Structure Click here
A0A1D6JFJ4 View 3D Structure Click here
A0A1D6JFJ4 View 3D Structure Click here
A0A1D6JVC7 View 3D Structure Click here
A0A1D6JZZ9 View 3D Structure Click here
A0A1D6K584 View 3D Structure Click here
A0A1D6KDB9 View 3D Structure Click here
A0A1D6KDB9 View 3D Structure Click here
A0A1D6KE17 View 3D Structure Click here
A0A1D6KE17 View 3D Structure Click here
A0A1D6KNK0 View 3D Structure Click here
A0A1D6KNZ1 View 3D Structure Click here
A0A1D6MAL2 View 3D Structure Click here
A0A1D6MRY9 View 3D Structure Click here
A0A1D6N5J3 View 3D Structure Click here
A0A1D6N5J4 View 3D Structure Click here
A0A1D6N7W7 View 3D Structure Click here
A0A1D6N7W7 View 3D Structure Click here
A0A1D6NCW4 View 3D Structure Click here
A0A1D6P829 View 3D Structure Click here
A0A1D6PJ96 View 3D Structure Click here
A0A1D6PN94 View 3D Structure Click here
A0A1D6PZP0 View 3D Structure Click here
A0A368UH87 View 3D Structure Click here
A0A368UJK3 View 3D Structure Click here
B4F9U3 View 3D Structure Click here
B4FCY2 View 3D Structure Click here
B4FRR6 View 3D Structure Click here
B6SZL3 View 3D Structure Click here
B6TZE6 View 3D Structure Click here
B8A1C3 View 3D Structure Click here
B8A2X5 View 3D Structure Click here
I1J4H5 View 3D Structure Click here
I1J658 View 3D Structure Click here
I1J659 View 3D Structure Click here
I1J676 View 3D Structure Click here
I1J771 View 3D Structure Click here
I1J7T0 View 3D Structure Click here
I1J7T2 View 3D Structure Click here
I1JAV9 View 3D Structure Click here
I1JBB4 View 3D Structure Click here
I1JBB5 View 3D Structure Click here
I1JBK1 View 3D Structure Click here
I1JEL9 View 3D Structure Click here
I1JJI8 View 3D Structure Click here
I1JKR6 View 3D Structure Click here
I1JKR7 View 3D Structure Click here
I1JKR8 View 3D Structure Click here
I1JKR9 View 3D Structure Click here
I1JQN6 View 3D Structure Click here
I1JQN7 View 3D Structure Click here
I1JR84 View 3D Structure Click here
I1JVR8 View 3D Structure Click here
I1K4X9 View 3D Structure Click here
I1K5N0 View 3D Structure Click here
I1K5N1 View 3D Structure Click here
I1K5Z7 View 3D Structure Click here
I1KAS1 View 3D Structure Click here
I1KFM7 View 3D Structure Click here
I1KFS6 View 3D Structure Click here
I1KFS7 View 3D Structure Click here
I1KGU8 View 3D Structure Click here
I1KGU9 View 3D Structure Click here
I1KGW7 View 3D Structure Click here
I1KMW7 View 3D Structure Click here
I1KPW3 View 3D Structure Click here
I1KTG6 View 3D Structure Click here
I1L0Q4 View 3D Structure Click here
I1L0X0 View 3D Structure Click here
I1L0X1 View 3D Structure Click here
I1L1W5 View 3D Structure Click here
I1L1W7 View 3D Structure Click here
I1L1X0 View 3D Structure Click here
I1L7K4 View 3D Structure Click here
I1L7T9 View 3D Structure Click here
I1LAS9 View 3D Structure Click here
I1LAT0 View 3D Structure Click here
I1LB84 View 3D Structure Click here
I1LB85 View 3D Structure Click here
I1LGQ0 View 3D Structure Click here
I1LNR8 View 3D Structure Click here
I1LWM4 View 3D Structure Click here
I1LYB7 View 3D Structure Click here
I1M0H1 View 3D Structure Click here
I1M6H2 View 3D Structure Click here
I1MHL2 View 3D Structure Click here
I1MHL4 View 3D Structure Click here
I1MHL7 View 3D Structure Click here
I1MII6 View 3D Structure Click here
I1MK76 View 3D Structure Click here
I1MRL0 View 3D Structure Click here
I1MS29 View 3D Structure Click here
I1MS31 View 3D Structure Click here
I1N4G3 View 3D Structure Click here
I1N7G8 View 3D Structure Click here
I1N963 View 3D Structure Click here
I1NAE9 View 3D Structure Click here
I1NB83 View 3D Structure Click here
I1NB85 View 3D Structure Click here
I1NBN0 View 3D Structure Click here
I1NBU8 View 3D Structure Click here
I1NBU9 View 3D Structure Click here
K7K5X8 View 3D Structure Click here
K7K766 View 3D Structure Click here
K7KBH8 View 3D Structure Click here
K7KBL9 View 3D Structure Click here
K7KBL9 View 3D Structure Click here
K7KGC5 View 3D Structure Click here
K7KGG2 View 3D Structure Click here
K7KJK7 View 3D Structure Click here
K7KJK8 View 3D Structure Click here
K7KJK8 View 3D Structure Click here
K7KJK8 View 3D Structure Click here
K7KV70 View 3D Structure Click here
K7KZN7 View 3D Structure Click here
K7KZN7 View 3D Structure Click here
K7L4Y5 View 3D Structure Click here
K7LCD5 View 3D Structure Click here
K7LCD6 View 3D Structure Click here
K7LFL7 View 3D Structure Click here
K7LJG3 View 3D Structure Click here
K7LZ36 View 3D Structure Click here
K7LZ49 View 3D Structure Click here
K7M4G5 View 3D Structure Click here
K7M8N6 View 3D Structure Click here
K7MBF9 View 3D Structure Click here
K7MC88 View 3D Structure Click here
K7MC88 View 3D Structure Click here
K7MD49 View 3D Structure Click here
K7MFK8 View 3D Structure Click here
K7MFK8 View 3D Structure Click here
K7MFK8 View 3D Structure Click here
K7MFX9 View 3D Structure Click here
K7MJY0 View 3D Structure Click here
K7MJY0 View 3D Structure Click here
K7MZI7 View 3D Structure Click here
K7MZI8 View 3D Structure Click here
K7N5A6 View 3D Structure Click here
K7UUE2 View 3D Structure Click here
K7W5K6 View 3D Structure Click here
O04953 View 3D Structure Click here
O22149 View 3D Structure Click here
O22256 View 3D Structure Click here
O23038 View 3D Structure Click here
O23447 View 3D Structure Click here
O48711 View 3D Structure Click here
O49006 View 3D Structure Click here
O49298 View 3D Structure Click here
O64479 View 3D Structure Click here
O80722 View 3D Structure Click here
O81301 View 3D Structure Click here
O81320 View 3D Structure Click here
O81415 View 3D Structure Click here
P46130 View 3D Structure Click here
Q0D411 View 3D Structure Click here
Q0DX02 View 3D Structure Click here
Q0JB65 View 3D Structure Click here
Q0JD10 View 3D Structure Click here
Q0JL04 View 3D Structure Click here
Q10MG7 View 3D Structure Click here
Q10MP6 View 3D Structure Click here
Q1JPL7 View 3D Structure Click here
Q1PEC0 View 3D Structure Click here
Q2QNI9 View 3D Structure Click here
Q2QZJ9 View 3D Structure Click here
Q2QZK1 View 3D Structure Click here
Q2R044 View 3D Structure Click here
Q3E8Z8 View 3D Structure Click here
Q3E989 View 3D Structure Click here
Q3E9D3 View 3D Structure Click here
Q3EAY9 View 3D Structure Click here
Q42534 View 3D Structure Click here
Q43867 View 3D Structure Click here
Q4PSN0 View 3D Structure Click here
Q4PSQ5 View 3D Structure Click here
Q4PT34 View 3D Structure Click here
Q53NH8 View 3D Structure Click here
Q53P90 View 3D Structure Click here
Q53P90 View 3D Structure Click here
Q53WM8 View 3D Structure Click here
Q5MFV6 View 3D Structure Click here
Q5MFV8 View 3D Structure Click here
Q5ZAW1 View 3D Structure Click here
Q651B2 View 3D Structure Click here
Q69J29 View 3D Structure Click here
Q69PI0 View 3D Structure Click here
Q69Y54 View 3D Structure Click here
Q6K8B0 View 3D Structure Click here
Q6Z2E1 View 3D Structure Click here
Q6ZDX2 View 3D Structure Click here
Q6ZLF5 View 3D Structure Click here
Q6ZLF6 View 3D Structure Click here
Q7F0H7 View 3D Structure Click here
Q7X6L1 View 3D Structure Click here
Q7XEU2 View 3D Structure Click here
Q7XUZ9 View 3D Structure Click here
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