1GQ8 - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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Title :   PECTIN METHYLESTERASE FROM CARROT

Authors :   K. Johansson, M. El-Ahmad, R. Friemann, H. Jornvall, O. Markovic, H. Eklund

Date :   20 Nov 01 (Deposition) - 18 Apr 02 (Release) - 14 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Carboxylic Ester Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Johansson, M. El-Ahmad, R. Friemann, H. Jornvall, O. Markovic, H. Eklund
Crystal Structure Of Plant Pectin Methylesterase
Febs Lett. V. 514 243 2002
PubMed-ID: 11943159 | Reference-DOI: 10.1016/S0014-5793(02)02372-4

Molecule 1 - PECTINESTERASE
	Chains	:	A
	EC Number	:	3.1.1.11
	Organ	:	RIPE ROOTS
	Organism Common	:	CARROT
	Organism Scientific	:	DAUCUS CAROTA
	Organism Taxid	:	4039
	Synonym	:	PECTIN METHYLESTERASE, PE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CAC	2	Ligand/Ion	CACODYLATE ION
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:135 , ASP A:136 , ASP A:157 , HOH A:2345	BINDING SITE FOR RESIDUE CAC A 501
2	AC2	SOFTWARE	SER A:217 , GLY A:299 , HOH A:2080 , HOH A:2179 , HOH A:2180	BINDING SITE FOR RESIDUE CAC A 502

(no "SS Bond" information available for 1GQ8)

(no "Cis Peptide Bond" information available for 1GQ8)

(no "SAP(SNP)/Variant" information available for 1GQ8)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PECTINESTERASE_1	PS00800	Pectinesterase signature 1.	PME_DAUCA	33-52	1	A:33-52
2	PECTINESTERASE_2	PS00503	Pectinesterase signature 2.	PME_DAUCA	152-161	1	A:152-161

(no "Exon" information available for 1GQ8)

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:319
 aligned with PME_DAUCA | P83218 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    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         
            PME_DAUCA     1 QSSTVTPNVVVAADGSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRTSTIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSAFYRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMVTAQGRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVINPAGWFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTPGSFIAGGSWLKATTFPFSLGL 319
               SCOP domains d1gq8a_ A: Pectin methylesterase PemA                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -1gq8A00 A:2-319 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.........hhhhhhhh......eeeeeee.eeee.eeeehhhheeeeeeeehhhheeeeee.......hhhhheeeee...eeeeeeeeeeee........eeeeee..eeeeeeeeeeee...eeeeeeeeeeeeeeeeee..eeee.eeeeeeeeeeee.......eeeeeeeeeehhhh.eeeeeeeeeee.hhhh.......eeeeee...eeeeeeeeeeeee......eee..........eeeeee.eeee...........eeeee.hhhhhhhhh.....hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------PECTINESTERASE_1    ---------------------------------------------------------------------------------------------------PECTINESTE-------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gq8 A   1 xSSTVGPNVVVAADGSGDYKTVSEAVAAAPEDSKTRYVIRIKAGVYRENVDVPKKKKNIMFLGDGRTSTIITASKNVQDGSTTFNSATVAAVGAGFLARDITFQNTAGAAKHQAVALRVGSDLSAFYRCDILAYQDSLYVHSNRQFFINCFIAGTVDFIFGNAAVVLQDCDIHARRPGSGQKNMVTAQGRTDPNQNTGIVIQKSRIGATSDLQPVQSSFPTYLGRPWKEYSRTVVMQSSITNVINPAGWFPWDGNFALDTLYYGEYQNTGAGAATSGRVTWKGFKVITSSTEAQGFTPGSFIAGGSWLKATTFPFSLGL 319
                            |       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         
                            |                                                                                                                                                                                                                                                                                                                              
                            1-PCA

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Single-stranded right-handed beta-helix (140)

Superfamily: Pectin lyase-like (89)

Family: Pectin methylesterase (10)

Protein domain: Pectin methylesterase PemA (2)

Carrot (Daucus carota) [TaxId: 4039] (1)

d1gq8a_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 3 Solenoid (196)

Topology: Pectate Lyase C-like (105)

Homologous Superfamily: Single-stranded right-handed beta-helix, Pectin lyase-like (73)

Carrot (Daucus carota) (1)

1gq8A00

A:2-319

(no "Pfam Domain" information available for 1GQ8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PME_DAUCA | P83218)

molecular function
	GO:0045330	aspartyl esterase activity	Catalysis of the hydrolysis of an ester bond by a mechanism involving a catalytically active aspartic acid residue.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0030599	pectinesterase activity	Catalysis of the reaction: pectin + n H2O = n methanol + pectate.
biological process
	GO:0042545	cell wall modification	The series of events leading to chemical and structural alterations of an existing cell wall that can result in loosening, increased extensibility or disassembly.
	GO:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0045490	pectin catabolic process	The chemical reactions and pathways resulting in the breakdown of pectin, a polymer containing a backbone of alpha-1,4-linked D-galacturonic acid residues.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	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.

Asymmetric/Biological Unit
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Description

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