2NT9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF PECTIN METHYLESTERASE D178A MUTANT IN COMPLEX WITH HEXASACCHARIDE IV

Authors :   M. Fries, K. Brocklehurst, V. E. Shevchik, R. W. Pickersgill

Date :   07 Nov 06 (Deposition) - 18 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C^#,D^#
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Keywords :   Michaelis Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Fries, J. Ihrig, K. Brocklehurst, V. E. Shevchik, R. W. Pickersgill
Molecular Basis Of The Activity Of The Phytopathogen Pectin Methylesterase.
Embo J. V. 26 3879 2007
PubMed-ID: 17717531 | Reference-DOI: 10.1038/SJ.EMBOJ.7601816

Molecule 1 - PECTINESTERASE A
	Chains	:	A, B
	EC Number	:	3.1.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBCKS/PEMA
	Expression System Strain	:	NM522
	Expression System Taxid	:	562
	Expression System Vector	:	PBCKS
	Expression System Vector Type	:	PLASMID
	Gene	:	PEMA, PEM
	Mutation	:	YES
	Organism Scientific	:	ERWINIA CHRYSANTHEMI
	Organism Taxid	:	198628
	Strain	:	3937
	Synonym	:	PECTIN METHYLESTERASE A, PE A

		1	2	3	4
Asymmetric Unit	:	A	B	C^#	D^#
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	ADA	4	Ligand/Ion	ALPHA-D-GALACTOPYRANURONIC ACID
2	M8C	8	Ligand/Ion	METHYL ALPHA-D-GALACTOPYRANURONATE

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ADA	-1	Ligand/Ion	ALPHA-D-GALACTOPYRANURONIC ACID
2	M8C	-1	Ligand/Ion	METHYL ALPHA-D-GALACTOPYRANURONATE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ADA	-1	Ligand/Ion	ALPHA-D-GALACTOPYRANURONIC ACID
2	M8C	-1	Ligand/Ion	METHYL ALPHA-D-GALACTOPYRANURONATE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:223 , ASN A:226 , M8C C:2 , HOH C:262 , HOH C:634 , HOH C:700	BINDING SITE FOR RESIDUE ADA C 1
02	AC2	SOFTWARE	ADA C:1 , M8C C:3 , HOH C:74 , HOH C:102 , HOH C:355 , HOH C:568 , HOH C:634	BINDING SITE FOR RESIDUE M8C C 2
03	AC3	SOFTWARE	VAL A:198 , ARG A:219 , VAL A:227 , SER A:228 , TYR A:230 , M8C C:2 , M8C C:4 , HOH C:214 , HOH C:320 , HOH C:568	BINDING SITE FOR RESIDUE M8C C 3
04	AC4	SOFTWARE	GLN A:177 , ARG A:267 , SER A:307 , M8C C:3 , M8C C:5 , HOH C:21 , HOH C:72 , HOH C:339 , HOH C:619	BINDING SITE FOR RESIDUE M8C C 4
05	AC5	SOFTWARE	GLN A:153 , GLN A:177 , ASP A:199 , PHE A:202 , MET A:306 , HOH A:492 , M8C C:4 , ADA C:6 , HOH C:359	BINDING SITE FOR RESIDUE M8C C 5
06	AC6	SOFTWARE	THR A:109 , GLN A:153 , TRP A:269 , PRO A:271 , THR A:272 , HOH A:396 , M8C C:5 , HOH C:150 , HOH C:259 , HOH C:431 , HOH C:738	BINDING SITE FOR RESIDUE ADA C 6
07	AC7	SOFTWARE	LYS B:223 , ASN B:226 , M8C D:2 , HOH D:515 , HOH D:722 , HOH D:797 , HOH D:814	BINDING SITE FOR RESIDUE ADA D 1
08	AC8	SOFTWARE	HOH B:396 , HOH B:521 , ADA D:1 , M8C D:3 , HOH D:398	BINDING SITE FOR RESIDUE M8C D 2
09	AC9	SOFTWARE	ARG B:219 , VAL B:227 , SER B:228 , TYR B:230 , M8C D:2 , M8C D:4 , HOH D:398 , HOH D:514 , HOH D:544	BINDING SITE FOR RESIDUE M8C D 3
10	BC1	SOFTWARE	GLN B:177 , ARG B:267 , SER B:307 , HOH B:511 , HOH B:517 , M8C D:3 , M8C D:5 , HOH D:407	BINDING SITE FOR RESIDUE M8C D 4
11	BC2	SOFTWARE	GLN B:153 , GLN B:177 , ASP B:199 , PHE B:202 , MET B:306 , HOH B:466 , M8C D:4 , ADA D:6 , HOH D:436	BINDING SITE FOR RESIDUE M8C D 5
12	BC3	SOFTWARE	THR B:109 , GLN B:153 , TRP B:269 , PRO B:271 , THR B:272 , HOH B:410 , HOH B:603 , M8C D:5 , HOH D:297 , HOH D:479 , HOH D:699	BINDING SITE FOR RESIDUE ADA D 6

Asymmetric Unit

No.	Residues
1	A:192	-	A:212
2	B:192	-	B:212

(no "Cis Peptide Bond" information available for 2NT9)

(no "SAP(SNP)/Variant" information available for 2NT9)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PECTINESTERASE_2	PS00503	Pectinesterase signature 2.	PMEA_DICD3	194-203	2	A:194-203 B:194-203

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PECTINESTERASE_2	PS00503	Pectinesterase signature 2.	PMEA_DICD3	194-203	1	A:194-203 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PECTINESTERASE_2	PS00503	Pectinesterase signature 2.	PMEA_DICD3	194-203	1	- B:194-203

(no "Exon" information available for 2NT9)

Asymmetric 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:342
 aligned with PMEA_DICD3 | P0C1A9 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:342
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364  
           PMEA_DICD3    25 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIYGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATVSKDRRQLTDAQAAEYTQSKVLGDWTPTLP 366
               SCOP domains d2nt9a_ A: automated matches                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2nt9A00 A:25-366 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...........hhhhhhhh.......eeeee..eeee..eee....eeeee.....eeeee.............hhhhhh..eee.....eeeeeeeee..hhhhhhhh...............eee......eeeeeeeee.....eee...eeeee..eeee.eeeeee..eeeee..eeee............eeeeee.........eeee..eeee.........eeee.....eeee..eeee......eeeee..ee...eee...eeee.....eeeehhhhheeeee................hhhhhh..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------PECTINESTE------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nt9 A  25 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIYGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATVSKDRRQLTDAQAAEYTQSKVLGDWTPTLP 366
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364

Chain B from PDB  Type:PROTEIN  Length:342
 aligned with PMEA_DICD3 | P0C1A9 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:342
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364  
           PMEA_DICD3    25 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQDTLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIYGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATVSKDRRQLTDAQAAEYTQSKVLGDWTPTLP 366
               SCOP domains d2nt9b_ B: automated matches                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2nt9B00 B:25-366 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                            CATH domains
           Pfam domains (1) ----Pectinesterase-2nt9B01 B:29-360                                                                                                                                                                                                                                                                                                             ------ Pfam domains (1)
           Pfam domains (2) ----Pectinesterase-2nt9B02 B:29-360                                                                                                                                                                                                                                                                                                             ------ Pfam domains (2)
         Sec.struct. author .....eee...........hhhhhhhh.......eeeee..eeee..eee....eeeee.....eeeee.............hhhhhh..eee.....eeeeeeeee..hhhhhhh................eee......eeeeeeeee.....eee...eeeee..eeee.eeeeee..eeeee..eeee............eeeeee.........eeee..eeee.........eeee.....eeee..eeee......eeeee..ee...eee...eeee.....eeeehhhhheeeee................hhhhhh..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------PECTINESTE------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nt9 B  25 ATTYNAVVSKSSSDGKTFKTIADAIASAPAGSTPFVILIKNGVYNERLTITRNNLHLKGESRNGAVIAAATAAGTLKSDGSKWGTAGSSTITISAKDFSAQSLTIRNDFDFPANQAKSDSDSSKIKDTQAVALYVTKSGDRAYFKDVSLVGYQATLYVSGGRSFFSDCRISGTVDFIFGDGTALFNNCDLVSRYRADVKSGNVSGYLTAPSTNINQKYGLVITNSRVIRESDSVPAKSYGLGRPWHPTTTFSDGRYADPNAIGQTVFLNTSMDNHIYGWDKMSGKDKNGNTIWFNPEDSRFFEYKSYGAGATVSKDRRQLTDAQAAEYTQSKVLGDWTPTLP 366
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364

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 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: automated matches (8)

Erwinia chrysanthemi [TaxId: 198628] (7)

1a	d2nt9a_	A:
1b	d2nt9b_	B:

Asymmetric 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)

3937 (Erwinia chrysanthemi str) (7)

1a	2nt9A00	A:25-366
1b	2nt9B00	B:25-366

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Pec_lyase (42)

Family: Pectinesterase (8)

Dickeya dadantii (strain 3937) (Erwinia chrysanthemi (strain 3937)) (7)

1a	Pectinesterase-2nt9B01	B:29-360
1b	Pectinesterase-2nt9B02	B:29-360

Asymmetric Unit(hide GO term definitions)

Chain A,B (PMEA_DICD3 | P0C1A9)

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.

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	2nt9
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	PMEA_DICD3 \| P0C1A9	:	1qjv 2nsp 2nst 2nt6 2ntb 2ntp 2ntq

1qjv	CRYSTAL STRUCTURE OF PECTIN METHYLESTERASE APO-ENZYME
2nsp	CRYSTAL STRUCTURE OF PECTIN METHYLESTERASE D178A MUTANT IN COMPLEX WITH HEXASACCHARIDE I
2nst	CRYSTAL STRUCTURE OF PECTIN METHYLESTERASE D178A MUTANT IN COMPLEX WITH HEXASACCHARIDE II
2nt6	CRYSTAL STRUCTURE OF PECTIN METHYLESTERASE D178A MUTANT IN COMPLEX WITH HEXASACCHARIDE III
2ntb	CRYSTAL STRUCTURE OF PECTIN METHYLESTERASE IN COMPLEX WITH HEXASACCHARIDE V
2ntp	CRYSTAL STRUCTURE OF PECTIN METHYLESTERASE IN COMPLEX WITH HEXASACCHARIDE VI
2ntq	CRYSTAL STRUCTURE OF PECTIN METHYLESTERASE IN COMPLEX WITH HEXASACCHARIDE VII

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Ligands, Modified Residues, Ions (2, 12)

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SS Bonds (2, 2)

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