3WAU - JenaLib

Title :   CRYSTAL STRUCTURE OF 4-O-BETA-D-MANNOSYL-D-GLUCOSE PHOSPHORYLASE MGP COMPLEXED WITH M1P

Authors :   S. Nakae, S. Ito, M. Higa, T. Senoura, J. Wasaki, A. Hijikata, M. Shionyu T. Shirai

Date :   08 May 13 (Deposition) - 04 Sep 13 (Release) - 20 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   5-Bladed Beta Propeller Fold, Phosphorylase, Mannan Biodegradation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Nakae, S. Ito, M. Higa, T. Senoura, J. Wasaki, A. Hijikata, M. Shionyu, S. Ito, T. Shirai
Structure Of Novel Enzyme In Mannan Biodegradation Process 4-O-Beta-D-Mannosyl-D-Glucose Phosphorylase Mgp
J. Mol. Biol. V. 425 4468 2013
PubMed-ID: 23954514 | Reference-DOI: 10.1016/J.JMB.2013.08.002

Compounds

Molecule 1 - 4-O-BETA-D-MANNOSYL-D-GLUCOSE PHOSPHORYLASE
	Chains	:	A, B
	EC Number	:	2.4.1.281
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-23A(+)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BF0772
	Organism Scientific	:	BACTEROIDES FRAGILIS
	Organism Taxid	:	272559
	Strain	:	NCTC 9343
	Synonym	:	MGP, MANNOSYLGLUCOSE PHOSPHORYLASE

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	M1P	2	Ligand/Ion	ALPHA-D-MANNOSE 1-PHOSPHATE
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 24)

No.	Name	Count	Type	Full Name
1	M1P	6	Ligand/Ion	ALPHA-D-MANNOSE 1-PHOSPHATE
2	MPD	6	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PO4	12	Ligand/Ion	PHOSPHATE ION

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:311 , GLY A:312 , ARG A:315 , HOH A:535 , HOH A:557 , HOH A:975 , HOH A:1061	BINDING SITE FOR RESIDUE PO4 A 401
2	AC2	SOFTWARE	HIS A:15 , GLU A:16 , LEU A:19 , PRO A:47 , PHE A:49 , ARG A:111 , HOH A:561 , HOH A:921	BINDING SITE FOR RESIDUE PO4 A 402
3	AC3	SOFTWARE	ARG A:88 , ARG A:94 , ARG A:276 , VAL A:319 , ASP A:344 , M1P A:404 , HOH A:610 , HOH A:974	BINDING SITE FOR RESIDUE MPD A 403
4	AC4	SOFTWARE	ASN A:73 , ARG A:88 , ASP A:131 , ARG A:191 , ASN A:192 , ARG A:209 , LYS A:254 , HIS A:273 , TYR A:284 , ASP A:344 , MPD A:403 , HOH A:895 , HOH A:896	BINDING SITE FOR RESIDUE M1P A 404
5	AC5	SOFTWARE	VAL B:311 , GLY B:312 , ARG B:315 , HOH B:562 , HOH B:592 , HOH B:769 , HOH B:898	BINDING SITE FOR RESIDUE PO4 B 401
6	AC6	SOFTWARE	HIS B:15 , GLU B:16 , LEU B:19 , PRO B:47 , PHE B:49 , ARG B:111 , HOH B:571 , HOH B:788 , HOH B:915	BINDING SITE FOR RESIDUE PO4 B 402
7	AC7	SOFTWARE	ARG B:88 , ARG B:94 , ARG B:276 , VAL B:319 , ASP B:344 , M1P B:404 , HOH B:581 , HOH B:969	BINDING SITE FOR RESIDUE MPD B 403
8	AC8	SOFTWARE	ASN B:73 , ARG B:88 , ASP B:131 , ARG B:191 , ASN B:192 , ARG B:209 , HIS B:273 , TYR B:284 , PHE B:324 , ASP B:344 , MPD B:403 , HOH B:816	BINDING SITE FOR RESIDUE M1P B 404

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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
	(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:387
 aligned with MGP_BACFN | Q5LH68 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:389
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
            MGP_BACFN     2 SLFNDKVAKLLAGHEALLMRKNEPVEEGNGVITRYRYPVLTAAHTPVFWRYDLNEETNPFLMERIGMNATLNAGAIKWDGKYLMLVRVEGADRKSFFAVAESPNGIDNFRFWEYPVTLPEDVVPATNVYDMRLTAHEDGWIYGIFCAERHDDNAPIGDLSSATATAGIARTKDLKNWERLPDLKTKSQQRNVVLHPEFVDGKYALYTRPQDGFIDTGSGGGIGWALIDDITHAEVGEEKIIDKRYYHTIKEVKNGEGPHPIKTPQGWLHLAHGVRNCAAGLRYVLYMYMTSLDDPTRLIASPAGYFMAPVGEERIGDVSNVLFSNGWIADDDGKVFIYYASSDTRMHVATSTIERLVDYCLHTPQDGFSSSASVEILKNLIERNLRLMK 390
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh............ee......hhhhhhhhhhh...............eeeeeeeeeeee..eeeeeeeeee....eeeeeeee.......ee...............eeeeeeeee.....eeeeeeeeee...........eeeeeeeeee......ee........ee...ee........eeeee.ee..--......eeeeeee.hhhhh....eeeeee.........eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eee.........hhhhhh......eeeeeeee....eeeeeeee...eeeeeeeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wau A   2 SLFNDKVAKLLAGHEALLMRKNEPVEEGNGVITRYRYPVLTAAHTPVFWRYDLNEETNPFLMERIGMNATLNAGAIKWDGKYLMLVRVEGADRKSFFAVAESPNGIDNFRFWEYPVTLPEDVVPATNVYDMRLTAHEDGWIYGIFCAERHDDNAPIGDLSSATATAGIARTKDLKNWERLPDLKTKSQQRNVVLHPEFVDGKYALYTRPQDG--DTGSGGGIGWALIDDITHAEVGEEKIIDKRYYHTIKEVKNGEGPHPIKTPQGWLHLAHGVRNCAAGLRYVLYMYMTSLDDPTRLIASPAGYFMAPVGEERIGDVSNVLFSNGWIADDDGKVFIYYASSDTRMHVATSTIERLVDYCLHTPQDGFSSSASVEILKNLIERNLRLMK 390
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 |  |  221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
                                                                                                                                                                                                                                             213  |                                                                                                                                                                              
                                                                                                                                                                                                                                                216

Chain B from PDB  Type:PROTEIN  Length:380
 aligned with MGP_BACFN | Q5LH68 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:389
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
            MGP_BACFN     2 SLFNDKVAKLLAGHEALLMRKNEPVEEGNGVITRYRYPVLTAAHTPVFWRYDLNEETNPFLMERIGMNATLNAGAIKWDGKYLMLVRVEGADRKSFFAVAESPNGIDNFRFWEYPVTLPEDVVPATNVYDMRLTAHEDGWIYGIFCAERHDDNAPIGDLSSATATAGIARTKDLKNWERLPDLKTKSQQRNVVLHPEFVDGKYALYTRPQDGFIDTGSGGGIGWALIDDITHAEVGEEKIIDKRYYHTIKEVKNGEGPHPIKTPQGWLHLAHGVRNCAAGLRYVLYMYMTSLDDPTRLIASPAGYFMAPVGEERIGDVSNVLFSNGWIADDDGKVFIYYASSDTRMHVATSTIERLVDYCLHTPQDGFSSSASVEILKNLIERNLRLMK 390
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh...............eeeeeeeeeeee..eeeeeeeeee....eeeeeeee.......ee...............eeeeeeeee.....eeeeeeeeee...........eeeeeeeeee......ee........ee...ee........eeeee.ee---------.eeeeeee.hhhhh.....eeeee.........eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eee.........hhhhhh......eeeeeeee....eeeeeeee...eeeeeeeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wau B   2 SLFNDKVAKLLAGHEALLMRKNEPVEEGNGVITRYRYPVLTAAHTPVFWRYDLNEETNPFLMERIGMNATLNAGAIKWDGKYLMLVRVEGADRKSFFAVAESPNGIDNFRFWEYPVTLPEDVVPATNVYDMRLTAHEDGWIYGIFCAERHDDNAPIGDLSSATATAGIARTKDLKNWERLPDLKTKSQQRNVVLHPEFVDGKYALYTRPQ---------GGIGWALIDDITHAEVGEEKIIDKRYYHTIKEVKNGEGPHPIKTPQGWLHLAHGVRNCAAGLRYVLYMYMTSLDDPTRLIASPAGYFMAPVGEERIGDVSNVLFSNGWIADDDGKVFIYYASSDTRMHVATSTIERLVDYCLHTPQDGFSSSASVEILKNLIERNLRLMK 390
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
                                                                                                                                                                                                                                           211       221

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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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

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Gene Ontology (5, 5)

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