2DKC - JenaLib

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Title :   CRYSTAL STRUCTURE OF N-ACETYLGLUCOSAMINE-PHOSPHATE MUTASE, A MEMBER OF THE ALPHA-D-PHOSPHOHEXOMUTASE SUPERFAMILY, IN THE SUBSTRATE COMPLEX

Authors :   Y. Nishitani, D. Maruyama, T. Nonaka, A. Kita, T. A. Fukami, T. Mio, H. Yamada-Okabe, T. Yamada-Okabe, K. Miki

Date :   07 Apr 06 (Deposition) - 16 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Mutase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Nishitani, D. Maruyama, T. Nonaka, A. Kita, T. A. Fukami, T. Mio, H. Yamada-Okabe, T. Yamada-Okabe, K. Miki
Crystal Structures Of N-Acetylglucosamine-Phosphate Mutase, A Member Of The {Alpha}-D-Phosphohexomutase Superfamily, And Its Substrate And Product Complexes.
J. Biol. Chem. V. 281 19740 2006
PubMed-ID: 16651269 | Reference-DOI: 10.1074/JBC.M600801200
(for further references see the PDB file header)

Molecule 1 - PHOSPHOACETYLGLUCOSAMINE MUTASE
	Chains	:	A, B
	EC Number	:	5.4.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2T
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	CANDIDA ALBICANS
	Organism Taxid	:	5476
	Synonym	:	PAGM, ACETYLGLUCOSAMINE PHOSPHOMUTASE, N- ACETYLGLUCOSAMINE-PHOSPHATE MUTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	16G	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
2	PO4	2	Ligand/Ion	PHOSPHATE ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	16G	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
2	PO4	1	Ligand/Ion	PHOSPHATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	16G	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
2	PO4	1	Ligand/Ion	PHOSPHATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:368 , GLY A:369 , VAL A:370 , GLU A:387 , ASN A:389 , HIS A:391 , ARG A:512 , SER A:514 , GLY A:515 , THR A:516 , ARG A:521 , PO4 A:802 , HOH A:974 , HOH A:1057 , HOH A:1102 , HOH A:1108	BINDING SITE FOR RESIDUE 16G A 701
2	AC2	SOFTWARE	THR B:26 , THR B:368 , GLY B:369 , VAL B:370 , GLU B:387 , HIS B:391 , ARG B:512 , SER B:514 , GLY B:515 , THR B:516 , ARG B:521 , PO4 B:801 , HOH B:1162 , HOH B:1165	BINDING SITE FOR RESIDUE 16G B 702
3	AC3	SOFTWARE	ARG B:30 , SER B:66 , HIS B:67 , ASP B:290 , ASP B:294 , ARG B:295 , HIS B:391 , 16G B:702 , ZN B:902	BINDING SITE FOR RESIDUE PO4 B 801
4	AC4	SOFTWARE	ARG A:30 , SER A:66 , HIS A:67 , ASP A:290 , ARG A:295 , HIS A:391 , 16G A:701 , ZN A:901	BINDING SITE FOR RESIDUE PO4 A 802
5	AC5	SOFTWARE	SER A:66 , ASP A:290 , ASP A:292 , ASP A:294 , PO4 A:802	BINDING SITE FOR RESIDUE ZN A 901
6	AC6	SOFTWARE	SER B:66 , ASP B:290 , ASP B:292 , ASP B:294 , PO4 B:801	BINDING SITE FOR RESIDUE ZN B 902

(no "SS Bond" information available for 2DKC)

Asymmetric Unit

No.	Residues
1	Glu A:489	-	Pro A:490
2	Glu B:489	-	Pro B:490

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGM_PMM	PS00710	Phosphoglucomutase and phosphomannomutase phosphoserine signature.	AGM1_CANAX	60-69	2	A:60-69 B:60-69

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGM_PMM	PS00710	Phosphoglucomutase and phosphomannomutase phosphoserine signature.	AGM1_CANAX	60-69	1	A:60-69 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGM_PMM	PS00710	Phosphoglucomutase and phosphomannomutase phosphoserine signature.	AGM1_CANAX	60-69	1	- B:60-69

(no "Exon" information available for 2DKC)

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:536
 aligned with AGM1_CANAX | Q9P4V2 from UniProtKB/Swiss-Prot  Length:544

    Alignment length:544
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540    
           AGM1_CANAX     1 MSIEQTLSQYLPSHPKPQGVTFTYGTAGFRMKADKLDYVTFTVGIIASLRSKYLQGKTVGVMITASHNPPEDNGVKVVDPLGSMLESSWEKYATDLANASPSPSNDSEGEKNSLVEVIKNLVSDLKIDLSIPANVVIARDSRESSPALSMATIDGFQSVPNTKYQDFGLFTTPELHYVTRTLNDPDFGKPTEDGYYSKLAKSFQEIYTICESNNEKIDITIDAANGVGAPKIQELLEKYLHKEISFTVVNGDYKQPNLLNFDCGADYVKTNQKLPKNVKPVNNKLYASFDGDADRLICYYQNNDNKFKLLDGDKLSTLFALFLQQLFKQIDPTKISLNIGVVQTAYANGSSTKYVEDVLKIPVRCTPTGVKHLHHEAENFDIGVYFEANGHGTVIFNPEAEKKIFDYKPNNDNEAKAIKVLQNFSQLINQTVGDAISDLLAVLIVVHYLKLSPSDWDNEYTDLPNKLVKVIVPDRSIFKTTNAERTLVEPKGMQDEIDKLVAQYPNGRSFVRASGTEDAVRVYAEADTQNNVEELSKAVSELVK 544
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..............eeee...hhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee.......hhhhhhhhhhhhh.....--------.hhhhhhhhhhhhhh......eeeeeee....hhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhh...eeeeee.....hhhhh....hhhhhhhhh.............eeee......eeeeee.....eeeehhhhhhhhhhhhhhhhhh..........eeeee....hhhhhhhhhhh....eee...hhhhhhhhhh...eeeee.....eeeeehhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhh......eeeeee...hhhhheee....eeee..hhhhhhhhhhhh....eeeeee......eeeeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------PGM_PMM   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dkc A   1 MSIEQTLSQYLPSHPKPQGVTFTYGTAGFRMKADKLDYVTFTVGIIASLRSKYLQGKTVGVMITASHNPPEDNGVKVVDPLGSMLESSWEKYATDLANASPSP--------NSLVEVIKNLVSDLKIDLSIPANVVIARDSRESSPALSMATIDGFQSVPNTKYQDFGLFTTPELHYVTRTLNDPDFGKPTEDGYYSKLAKSFQEIYTICESNNEKIDITIDAANGVGAPKIQELLEKYLHKEISFTVVNGDYKQPNLLNFDCGADYVKTNQKLPKNVKPVNNKLYASFDGDADRLICYYQNNDNKFKLLDGDKLSTLFALFLQQLFKQIDPTKISLNIGVVQTAYANGSSTKYVEDVLKIPVRCTPTGVKHLHHEAENFDIGVYFEANGHGTVIFNPEAEKKIFDYKPNNDNEAKAIKVLQNFSQLINQTVGDAISDLLAVLIVVHYLKLSPSDWDNEYTDLPNKLVKVIVPDRSIFKTTNAERTLVEPKGMQDEIDKLVAQYPNGRSFVRASGTEDAVRVYAEADTQNNVEELSKAVSELVK 544
                                    10        20        30        40        50        60        70        80        90       100  |      - |     120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540    
                                                                                                                                103      112

Chain B from PDB  Type:PROTEIN  Length:535
 aligned with AGM1_CANAX | Q9P4V2 from UniProtKB/Swiss-Prot  Length:544

    Alignment length:544
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540    
           AGM1_CANAX     1 MSIEQTLSQYLPSHPKPQGVTFTYGTAGFRMKADKLDYVTFTVGIIASLRSKYLQGKTVGVMITASHNPPEDNGVKVVDPLGSMLESSWEKYATDLANASPSPSNDSEGEKNSLVEVIKNLVSDLKIDLSIPANVVIARDSRESSPALSMATIDGFQSVPNTKYQDFGLFTTPELHYVTRTLNDPDFGKPTEDGYYSKLAKSFQEIYTICESNNEKIDITIDAANGVGAPKIQELLEKYLHKEISFTVVNGDYKQPNLLNFDCGADYVKTNQKLPKNVKPVNNKLYASFDGDADRLICYYQNNDNKFKLLDGDKLSTLFALFLQQLFKQIDPTKISLNIGVVQTAYANGSSTKYVEDVLKIPVRCTPTGVKHLHHEAENFDIGVYFEANGHGTVIFNPEAEKKIFDYKPNNDNEAKAIKVLQNFSQLINQTVGDAISDLLAVLIVVHYLKLSPSDWDNEYTDLPNKLVKVIVPDRSIFKTTNAERTLVEPKGMQDEIDKLVAQYPNGRSFVRASGTEDAVRVYAEADTQNNVEELSKAVSELVK 544
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..............eeee...hhhhhhhhhhhhhhhhhhh....eeeee........eeeeeee.......hhhhhhhhhhhhh.....-------..hhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.--...eeeeee....hhhhhhhhhhhhhh...eeeeee.....hhhhh....hhhhhhhhh.............eeee......eeeeee.....eeeehhhhhhhhhhhhhhhhhh..........eeeee....hhhhhhhhhhh....eee...hhhhhhhhhh...eeeee.....eeeeehhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhh......eeeeee...hhhhheee....eeee..hhhhhhhhhhhh....eeeeee......eeeeee..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------PGM_PMM   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dkc B   1 MSIEQTLSQYLPSHPKPQGVTFTYGTAGFRMKADKLDYVTFTVGIIASLRSKYLQGKTVGVMITASHNPPEDNGVKVVDPLGSMLESSWEKYATDLANASPSP-------KNSLVEVIKNLVSDLKIDLSIPANVVIARDSRESSPALSMATIDGFQSVPNTKYQDFGLFTTPELHYVTRTLNDPDFGKPTEDGYYSKLAKSFQEIYTICE--NEKIDITIDAANGVGAPKIQELLEKYLHKEISFTVVNGDYKQPNLLNFDCGADYVKTNQKLPKNVKPVNNKLYASFDGDADRLICYYQNNDNKFKLLDGDKLSTLFALFLQQLFKQIDPTKISLNIGVVQTAYANGSSTKYVEDVLKIPVRCTPTGVKHLHHEAENFDIGVYFEANGHGTVIFNPEAEKKIFDYKPNNDNEAKAIKVLQNFSQLINQTVGDAISDLLAVLIVVHYLKLSPSDWDNEYTDLPNKLVKVIVPDRSIFKTTNAERTLVEPKGMQDEIDKLVAQYPNGRSFVRASGTEDAVRVYAEADTQNNVEELSKAVSELVK 544
                                    10        20        30        40        50        60        70        80        90       100  |      -|      120       130       140       150       160       170       180       190       200       210|  |   220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540    
                                                                                                                                103     111                                                                                                 211  |                                                                                                                                                                                                                                                                                                                                          
                                                                                                                                                                                                                                               214

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

(no "SCOP Domain" information available for 2DKC)

(no "CATH Domain" information available for 2DKC)

(no "Pfam Domain" information available for 2DKC)

Asymmetric Unit(hide GO term definitions)

Chain A,B (AGM1_CANAX | Q9P4V2)

molecular function
	GO:0016868	intramolecular transferase activity, phosphotransferases	Catalysis of the transfer of a phosphate group from one position to another within a single molecule.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004610	phosphoacetylglucosamine mutase activity	Catalysis of the reaction: N-acetyl-alpha-D-glucosamine 1-phosphate = N-acetyl-D-glucosamine 6-phosphate.
biological process
	GO:0006048	UDP-N-acetylglucosamine biosynthetic process	The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	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:0071704	organic substance metabolic process	The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:489 - Pro A:490	[ RasMol ]
		Glu B:489 - Pro B:490	[ RasMol ]

Biological Units
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	2dkc
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	5.4.2.3
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	AGM1_CANAX \| Q9P4V2	:	2dka 2dkd

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Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

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Cis Peptide Bonds (2, 2)

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