4XPR - JenaLib

Title :   CRYSTAL STRUCTURE OF THE MUTANT D365A OF PEDOBACTER SALTANS GH31 ALPHA-GALACTOSIDASE

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 :   2.01

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

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 6)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	EDO	12	Ligand/Ion	1,2-ETHANEDIOL

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:100 , VAL A:109 , PHE A:450 , GLY A:533 , MET A:534 , ILE A:567	binding site for residue EDO A 1001
2	AC2	SOFTWARE	TYR A:515 , ALA A:519 , ARG A:522 , ASP A:575 , ASP A:576 , PHE A:662 , HOH A:1168	binding site for residue EDO A 1002
3	AC3	SOFTWARE	TYR A:373 , ARG A:418 , ASP A:434 , EDO A:1006 , HOH A:1204	binding site for residue EDO A 1003
4	AC4	SOFTWARE	PHE A:601 , ARG A:653 , TYR A:655 , HOH A:1340	binding site for residue EDO A 1004
5	AC5	SOFTWARE	GLU A:266 , TRP A:305 , LYS A:363 , ASP A:434 , ASN A:484 , TRP A:486 , HOH A:1151 , HOH A:1189	binding site for residue EDO A 1005
6	AC6	SOFTWARE	TYR A:370 , ASP A:434 , TYR A:435 , EDO A:1003 , HOH A:1230 , HOH A:1412	binding site for residue EDO A 1006

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)
	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
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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...eeeeee....eeeee..............................eeeeee...eeeeeee...hhhhhhhhhhhhh......hhhhh.eeee.....hhhhhhhhhhhhhhhh....eeeehhhhh................hhhhhhhhhhhh..eeeeee.........hhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh..eeee.....................hhhhhhhhhhhhhhhhhhhhhhh......eee...........eee.....hhhhhhhhhhhhh....ee........hhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee............eee...eee.........eeeeeeeeeeee.....eeeeeeeeee........eeee...eeee.............eeeeeee.....eeeeeee.....hhhhhh..eeeeeeeee.....eeeee..........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xpr A  29 NWTEIYPGVWKATVGKPESYDLLKAAGAQPNKDALSKTEKVSFPFANGGVSLEVSGGKTYLRFPLQKEEQLYGFGLNFQTVHQRGKILELHVDHYGGKDSGRTHAPTPFYVSSNGYGVFINSARYIKVWAGTGVRKDSENFPTPKDRNTDKTWSSRPYSDAVEILVPAEGVEVYVFGGPKPIDAVKRYNLLNGGGYLPPRWGLGFTQRVMTRYTDKDVEKEVNDFKEKGYPLDFVGLEPGWQSKAYPGTFSWDKSRYPDPTSFVKKMKDQGIRLNLWINPYISPDAPFYKEIKPYTGSHTVWLGLVPDFTMAEARKPFFNQLLKDQIERGVSGYKIAEVDGYDYYLWPDAAKFPSGLSAEQMRQTYGLLVQRYSAELYKQRNERTFGLVRASNGGGTSFPYVIYNDYYNHQDFITALINSGFAGVLWTPEVRASKSGEEWLRRFQSNVFSPMAMINAWASGTKPWSYPEVEADVKKFALLRMQMMPYWYSAFARYHFEGMPPFRGMGLEEKEIKDQYMAGDDLLVAPMFAGEKSRKVVLPKGKWYDFYTGEYAGDGEVLDVTPGLDKIPVYVRDGGIVPMMPALLNSPKSNQKVDLEIRYYGNKPGEFKLYDDDGETFNYEKGDFSWRTIRVEKDKSGKVKGSISAAVKGKVNTVGKVTFTAMTK 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       538|      574       584       594       604       614       624       634       644       654       664       674       684       694       704       714     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       538|                                                                                                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        565

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

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 ]
		Gly A:369 - Tyr A:370	[ RasMol ]
		Tyr A:274 - Pro A:275	[ RasMol ]

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	4xpr
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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
4xps	THE MUTANT D365A COMPLEXED WITH P-NITROPHENYL-ALPHA-D- GALACTOPYRANOSIDE

Description