3JUU - JenaLib

Title :   CRYSTAL STRUCTURE OF PORPHYRANASE B (PORB) FROM ZOBELLIA GALACTANIVORANS

Authors :   J. H. Hehemann, G. Correc, T. Barbeyron, G. Michel, M. Czjzek

Date :   15 Sep 09 (Deposition) - 07 Apr 10 (Release) - 27 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Glycoside Hydrolase Family Gh16, Beta-Sandwich Fold, Jelly Roll, Sugar Binding Protein, Hydrolase-Carbohydrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. H. Hehemann, G. Correc, T. Barbeyron, W. Helbert, M. Czjzek, G. Michel
Transfer Of Carbohydrate-Active Enzymes From Marine Bacteri To Japanese Gut Microbiota.
Nature V. 464 908 2010
PubMed-ID: 20376150 | Reference-DOI: 10.1038/NATURE08937

Compounds

Molecule 1 - PORPHYRANASE B
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PFO4
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ZG1017
	Organism Scientific	:	ZOBELLIA GALACTANIVORANS
	Organism Taxid	:	63186

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 14)

Asymmetric Unit (3, 14)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	SO4	4	Ligand/Ion	SULFATE ION

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SO4 A:7 , TRP A:67 , ARG A:70 , TRP A:139 , ILE A:141 , ARG A:252 , GOL A:295 , HOH A:387 , HOH A:410	BINDING SITE FOR RESIDUE MES A 1
02	AC2	SOFTWARE	HIS A:26 , TRP A:282 , ARG A:284 , HOH A:442 , HOH A:443	BINDING SITE FOR RESIDUE SO4 A 4
03	AC3	SOFTWARE	GLY A:52 , LYS A:53 , LYS A:54	BINDING SITE FOR RESIDUE SO4 A 5
04	AC4	SOFTWARE	THR A:90 , THR A:92 , LYS A:273 , ARG A:276 , HOH A:435	BINDING SITE FOR RESIDUE SO4 A 6
05	AC5	SOFTWARE	MES A:1 , ARG A:187 , ASN A:188 , HOH A:482	BINDING SITE FOR RESIDUE SO4 A 7
06	AC6	SOFTWARE	ARG A:70 , THR A:137 , TRP A:139 , GLU A:156 , ASP A:158 , GLU A:161 , GLU A:256 , HOH A:362	BINDING SITE FOR RESIDUE GOL A 294
07	AC7	SOFTWARE	MES A:1 , TRP A:67 , ARG A:70	BINDING SITE FOR RESIDUE GOL A 295
08	AC8	SOFTWARE	SO4 B:8 , TRP B:67 , ARG B:70 , TRP B:139 , ILE B:141 , ARG B:187 , ARG B:252 , GOL B:295 , GOL B:296 , HOH B:442 , HOH B:464	BINDING SITE FOR RESIDUE MES B 1
09	AC9	SOFTWARE	ARG B:187 , ASN B:188 , ILE B:189 , LYS B:197 , HOH B:353	BINDING SITE FOR RESIDUE SO4 B 294
10	BC1	SOFTWARE	ASN A:83 , ASN A:84 , HOH A:342 , GLN B:88 , LYS B:128 , GLU B:274 , THR B:279 , HOH B:366 , HOH B:391 , HOH B:452 , HOH B:487	BINDING SITE FOR RESIDUE SO4 B 2
11	BC2	SOFTWARE	HIS B:26 , TRP B:282 , ARG B:284	BINDING SITE FOR RESIDUE SO4 B 3
12	BC3	SOFTWARE	MES B:1 , ARG B:187 , ASN B:188 , HOH B:483	BINDING SITE FOR RESIDUE SO4 B 8
13	BC4	SOFTWARE	MES B:1 , TRP B:67 , ARG B:70 , THR B:137 , TRP B:139 , GLU B:156 , ASP B:158 , GLU B:161 , GLU B:256	BINDING SITE FOR RESIDUE GOL B 295
14	BC5	SOFTWARE	MES B:1 , TRP B:67 , ARG B:70 , HOH B:306 , HOH B:446	BINDING SITE FOR RESIDUE GOL B 296

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH16_2	PS51762	Glycosyl hydrolases family 16 (GH16) domain profile.	PORB_ZOBGA	38-291	2	A:38-290 B:38-291

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH16_2	PS51762	Glycosyl hydrolases family 16 (GH16) domain profile.	PORB_ZOBGA	38-291	1	A:38-290 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH16_2	PS51762	Glycosyl hydrolases family 16 (GH16) domain profile.	PORB_ZOBGA	38-291	1	- B:38-291

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
	(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:268
 aligned with PORB_ZOBGA | D7GXF9 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:268
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282        
           PORB_ZOBGA    23 EAPHFKPGEDPRQPHQEWKLIENMSDEFEGKKIDEKKWQISGQGWIGRAPGLFLAENISLNNGSLQITTTMLPEPIVKNNKTYTHGGGYVGSRNGMTYGYYECEMKANKTFMSSTFWLINEGKDRLGCDKRTTELDIQESVGQITNDADWMKYFDQTMNSNTHSRNIPEGCEYEKGSSKGKAELGGKAYEDFHVYGVWWKSKDEIIFFLDGKMQSKVTPPADFDIEMYLRMVVETYDWNPVPKDGGMTGSKEDRTTTYNWVRSWQLVD 290
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeee.hhhh............ee...........eee....eeee..eeeee.eeeeeeeee..eeeeeeeeeeee......eeeeeeee......eeeeeee.hhhhhhhhhhheeeeeeeeee......hhhhhhhh.eeeeeeeee..........ee..eeee.........eeeeeeeee..eeeeee..eeeeee..........eeeeee................hhhhheeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------GH16_2  PDB: A:38-290 UniProt: 38-291                                                                                                                                                                                                                         PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3juu A  23 EAPHFKPGEDPRQPHQEWKLIENMSDEFEGKKIDEKKWQISGQGWIGRAPGLFLAENISLNNGSLQITTTMLPEPIVKNNKTYTHGGGYVGSRNGMTYGYYECEMKANKTFMSSTFWLINEGKDRLGCDKRTTELDIQESVGQITNDADWMKYFDQTMNSNTHSRNIPEGCEYEKGSSKGKAELGGKAYEDFHVYGVWWKSKDEIIFFLDGKMQSKVTPPADFDIEMYLRMVVETYDWNPVPKDGGMTGSKEDRTTTYNWVRSWQLVD 290
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with PORB_ZOBGA | D7GXF9 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:269
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282         
           PORB_ZOBGA    23 EAPHFKPGEDPRQPHQEWKLIENMSDEFEGKKIDEKKWQISGQGWIGRAPGLFLAENISLNNGSLQITTTMLPEPIVKNNKTYTHGGGYVGSRNGMTYGYYECEMKANKTFMSSTFWLINEGKDRLGCDKRTTELDIQESVGQITNDADWMKYFDQTMNSNTHSRNIPEGCEYEKGSSKGKAELGGKAYEDFHVYGVWWKSKDEIIFFLDGKMQSKVTPPADFDIEMYLRMVVETYDWNPVPKDGGMTGSKEDRTTTYNWVRSWQLVDS 291
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeee.hhhh............ee...........eee....eeee..eeeee.eeeeeeeee..eeeeeeeeeeee......eeeeeeee......eeeeeee.......hhhhheeeeeeeeee......hhhhh....eeeeeeeee..........eeeeeeee.........eeeeeeeee..eeeeee..eeeeee..........eeeeee.....................eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------GH16_2  PDB: B:38-291 UniProt: 38-291                                                                                                                                                                                                                          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3juu B  23 EAPHFKPGEDPRQPHQEWKLIENMSDEFEGKKIDEKKWQISGQGWIGRAPGLFLAENISLNNGSLQITTTMLPEPIVKNNKTYTHGGGYVGSRNGMTYGYYECEMKANKTFMSSTFWLINEGKDRLGCDKRTTELDIQESVGQITNDADWMKYFDQTMNSNTHSRNIPEGCEYEKGSSKGKAELGGKAYEDFHVYGVWWKSKDEIIFFLDGKMQSKVTPPADFDIEMYLRMVVETYDWNPVPKDGGMTGSKEDRTTTYNWVRSWQLVDS 291
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282

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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 (6, 6)

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		Gly B:144 - Lys B:145	[ RasMol ]

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