4XPS - JenaLib

Title :   CRYSTAL STRUCTURE OF THE MUTANT D365A OF PEDOBACTER SALTANS GH31 ALPHA-GALACTOSIDASE COMPLEXED WITH P-NITROPHENYL-ALPHA-GALACTOPYRANOSIDE

Authors :   T. Miyazaki, Y. Ishizaki, M. Ichikawa, A. Nishikawa, T. Tonozuka

Date :   17 Jan 15 (Deposition) - 20 May 15 (Release) - 09 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Hydrolase, Tim-Barrel, Gh31 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Miyazaki, Y. Ishizaki, M. Ichikawa, A. Nishikawa, T. Tonozuka
Structural And Biochemical Characterization Of Novel Bacterial Alpha-Galactosidases Belonging To Glycoside Hydrolase Family 31
Biochem. J. V. 469 145 2015
PubMed-ID: 25942325 | Reference-DOI: 10.1042/BJ20150261

Compounds

Molecule 1 - ALPHA-GLUCOSIDASE
	Chains	:	A
	EC Number	:	3.2.1.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	PEDOBACTER SALTANS
	Organism Taxid	:	151895
	Strain	:	NBRC 100064

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	GLA	1	Ligand/Ion	ALPHA D-GALACTOSE
3	NPO	1	Ligand/Ion	P-NITROPHENOL

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	GLA	2	Ligand/Ion	ALPHA D-GALACTOSE
3	NPO	2	Ligand/Ion	P-NITROPHENOL

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:370 , ARG A:418 , ASP A:434	binding site for residue EDO A 1003
2	AC2	SOFTWARE	TYR A:515 , ALA A:519 , ARG A:522 , GLY A:574 , ASP A:575 , ASP A:576 , PHE A:662 , HOH A:1238	binding site for residue EDO A 1004
3	AC3	SOFTWARE	VAL A:109 , PHE A:450 , GLY A:533 , MET A:534 , LEU A:536 , ILE A:567 , HOH A:1179	binding site for residue EDO A 1005
4	AC4	SOFTWARE	ARG A:175 , GLU A:266 , PRO A:267 , TYR A:274 , TRP A:305 , LYS A:363 , GLU A:366 , ARG A:418 , TYR A:432 , ASP A:434 , ASN A:484 , TRP A:486 , HOH A:1164 , HOH A:1263	binding site for Poly-Saccharide residues GLA A 1001 through NPO A 1002

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:665
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeeeee.....hhhhhhh...hhhhhhh.............eeeee..eeeeeee......eee.............eeeeee.........ee.....eeee....eeeee....eeeee..............................eeeeee...eeeeeee...hhhhhhhhhhhhh......hhhhh.eeee.....hhhhhhhhhhhhhhhh....eeeehhhhh................hhhhhhhhhhhh..eeeeee.........hhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh..eeee.....................hhhhhhhhhhhhhhhhhhhhhhhh.....eee...........eee.....hhhhhhhhhhhhh....ee........hhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee............eee...eee.........eeee....eeee.....eeee..eeee........eeee...eeee.............eeeeeee.....eeeeeee.....hhhhhh..eeeeeeeee.....eeeee..........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xps A  29 NWTEIYPGVWKATVGKPESYDLLKAAGAQPNKDALSKTEKVSFPFANGGVSLEVSGGKTYLRFPLQKEEQLYGFGLNFQTVHQRGKILELHVDHYGGKDSGRTHAPTPFYVSSNGYGVFINSARYIKVWAGTGVRKDSENFPTPKDRNTDKTWSSRPYSDAVEILVPAEGVEVYVFGGPKPIDAVKRYNLLNGGGYLPPRWGLGFTQRVMTRYTDKDVEKEVNDFKEKGYPLDFVGLEPGWQSKAYPGTFSWDKSRYPDPTSFVKKMKDQGIRLNLWINPYISPDAPFYKEIKPYTGSHTVWLGLVPDFTMAEARKPFFNQLLKDQIERGVSGYKIAEVDGYDYYLWPDAAKFPSGLSAEQMRQTYGLLVQRYSAELYKQRNERTFGLVRASNGGGTSFPYVIYNDYYNHQDFITALINSGFAGVLWTPEVRASKSGEEWLRRFQSNVFSPMAMINAWASGTKPWSYPEVEADVKKFALLRMQMMPYWYSAFARYHFEGMPPFRGMGLESKEIKDQYMAGDDLLVAPMFAGEKSRKVVLPKGKWYDFYTGEYAGDGEVLDVTPGLDKIPVYVRDGGIVPMMPALLNSPKSNQKVDLEIRYYGNKPGEFKLYDDDGETFNYEKGDFSWRTIRVEKDKSGKVKGSISAAVKGKVNTVGKVTFTAMTK 719
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      537|                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       564

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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	Cis Peptide Bonds
		Gly A:206 - Pro A:207	[ RasMol ]
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	4xps
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

4xpo	THE WILD-TYPE PROTEIN
4xpp	THE WILD-TYPE PROTEIN COMPLEXED WITH D-GALACTOSE
4xpq	THE WILD-TYPE PROTEIN COMPLEXED WITH L-FUCOSE
4xpr	THE MUTANT D365A WITHOUT LIGAND

Description