1Z4O - JenaLib

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Title :   STRUCTURE OF BETA-PHOSPHOGLUCOMUTASE WITH INHIBITOR BOUND ALPHA-GALACTOSE 1-PHOSPHATE

Authors :   L. W. Tremblay, G. Zhang, J. Dai, D. Dunaway-Mariano, K. N. Allen

Date :   16 Mar 05 (Deposition) - 19 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Isomerase, Beta-Phosphoglucomutase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. W. Tremblay, G. Zhang, J. Dai, D. Dunaway-Mariano, K. N. Allen
Chemical Confirmation Of A Pentavalent Phosphorane In Complex With Beta-Phosphoglucomutase
J. Am. Chem. Soc. V. 127 5298 2005
PubMed-ID: 15826149 | Reference-DOI: 10.1021/JA0509073
(for further references see the PDB file header)

Molecule 1 - BETA-PHOSPHOGLUCOMUTASE
	Chains	:	A, B
	EC Number	:	5.4.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	ISOMERASE, BETA-PHOSPHOGLUCOMUTASE
	Gene	:	PGMB
	Organism Scientific	:	LACTOCOCCUS LACTIS
	Organism Taxid	:	1358
	Synonym	:	BETA-PGM

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	GL1	2	Ligand/Ion	1-O-PHOSPHONO-ALPHA-D-GALACTOPYRANOSE
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GL1	1	Ligand/Ion	1-O-PHOSPHONO-ALPHA-D-GALACTOPYRANOSE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GL1	1	Ligand/Ion	1-O-PHOSPHONO-ALPHA-D-GALACTOPYRANOSE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:8 , ASP A:10 , ASP A:170 , HOH A:1250 , HOH A:1332 , HOH A:1476	BINDING SITE FOR RESIDUE MG A 800
2	AC2	SOFTWARE	ASP B:8 , ASP B:10 , GLU B:169 , ASP B:170 , HOH B:1326	BINDING SITE FOR RESIDUE MG B 801
3	AC3	SOFTWARE	ASP A:10 , HIS A:20 , TRP A:24 , LEU A:44 , GLY A:46 , VAL A:47 , ARG A:49 , LYS A:76 , SER A:116 , LYS A:117 , ASN A:118 , HOH A:1222 , HOH A:1235 , HOH A:1250 , HOH A:1264 , HOH A:1280	BINDING SITE FOR RESIDUE GL1 A 1220
4	AC4	SOFTWARE	HIS B:20 , TRP B:24 , LEU B:44 , GLY B:46 , VAL B:47 , ARG B:49 , LYS B:76 , SER B:114 , ALA B:115 , SER B:116 , LYS B:117 , ASN B:118 , HOH B:1235 , HOH B:1236 , HOH B:1237 , HOH B:1245 , HOH B:1247 , HOH B:1250	BINDING SITE FOR RESIDUE GL1 B 1221

(no "SS Bond" information available for 1Z4O)

Asymmetric Unit

No.	Residues
1	Lys A:145	-	Pro A:146
2	Lys B:145	-	Pro B:146

(no "SAP(SNP)/Variant" information available for 1Z4O)

(no "PROSITE Motif" information available for 1Z4O)

(no "Exon" information available for 1Z4O)

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:219
 aligned with PGMB_LACLA | P71447 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
           PGMB_LACLA     1 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLEKMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSYYTLEFLKEVWLQKQ 220
               SCOP domains d1z4oa_ A: beta-Phosphoglucomutase                                                                                                                                                                                           SCOP domains
               CATH domains 1z4oA01       1z4oA02 A:15-92 Putative phosphatase; domain 2                                1z4oA01 A:1-14,A:93-220  [code=3.40.50.1000, no  name defined]                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhh..eeee.....hhhhhhhhh.hhhhh.ee....-.......hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh.eeeee.hhhhhh...eee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z4o A   1 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLERMNLTGYFDAIADPA-VAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSHYTLEFLKEVWLQKQ 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |-|      150       160       170       180       190       200       210       220
                                                                                                                                                                    139 |                                                                               
                                                                                                                                                                      141

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with PGMB_LACLA | P71447 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           PGMB_LACLA     1 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLEKMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSYYTLEFLKEVWLQK 219
               SCOP domains d1z4ob_ B: beta-Phosphoglucomutase                                                                                                                                                                                          SCOP domains
               CATH domains 1z4oB01       1z4oB02 B:15-92 Putative phosphatase; domain 2                                1z4oB01 B:1-14,B:93-219  [code=3.40.50.1000, no name defined]                                                                   CATH domains
           Pfam domains (1) -Hydrolase-1z4oB01 B:2-182                                                                                                                                                            ------------------------------------- Pfam domains (1)
           Pfam domains (2) -Hydrolase-1z4oB02 B:2-182                                                                                                                                                            ------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeee........hhhhhhhhhhhhhhhh.......hhhhhh...hhhhhhhhhhhh...----.hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh..eeee.....hhhhhhhhh.hhhhh.ee.hhhhh......hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh.eeeee.hhhhhh...eee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z4o B   1 MFKAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADK----EEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGRPEDLGDDIVIVPDTSHYTLEFLKEVWLQK 219
                                    10        20        30        40        50        60 |    | 70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
                                                                                        62   67

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: beta-Phosphoglucomutase-like (27)

Protein domain: beta-Phosphoglucomutase (15)

Lactococcus lactis [TaxId: 1358] (14)

1a	d1z4oa_	A:
1b	d1z4ob_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1000, no name defined] (211)

Lactococcus lactis. Organism_taxid: 1358. (4)

1a	1z4oA01	A:1-14,A:93-220
1b	1z4oB01	B:1-14,B:93-219

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: Putative phosphatase; domain 2 (65)

Lactococcus lactis. Organism_taxid: 1358. (4)

2a	1z4oB02	B:15-92
2b	1z4oA02	A:15-92

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: Hydrolase (64)

Lactococcus lactis subsp. lactis (Streptococcus lactis) (13)

1a	Hydrolase-1z4oB01	B:2-182
1b	Hydrolase-1z4oB02	B:2-182

Asymmetric Unit(hide GO term definitions)

Chain A,B (PGMB_LACLA | P71447)

molecular function
	GO:0008801	beta-phosphoglucomutase activity	Catalysis of the reaction: beta-D-glucose 1-phosphate = beta-D-glucose 6-phosphate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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.
biological process
	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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
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1z4n	STRUCTURE OF SAME PROTEIN WITH INHIBITOR BOUND ALPHA- GALACTOSE 1-PHOSPHATE COCRYSTALLIZED WITH FLUORIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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Exons (0, 0)

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