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Title :   CRYSTAL STRUCTURE ANALYSIS OF THE MANNOSE 6-PHOSPHATE ISOMERASE FROM BACILLUS SUBTILIS

Authors :   Y. Kim, L. Lezondra, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)

Date :   03 Sep 03 (Deposition) - 02 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Structural Genomics, D-Mannose 6-Phosphate, Isomerase, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, L. Lezondra, A. Joachimiak
Crystal Structure Analysis Of The Mannose 6-Phosphate Isomerase From Bacillus Subtilis
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - MANNOSE-6-PHOSPHATE ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PMI OR BSU35790
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	PHOSPHOMANNOSE ISOMERASE, PMI, PHOSPHOHEXOMUTASE

		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 (5, 13)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	FMT	1	Ligand/Ion	FORMIC ACID
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	3	Ligand/Ion	SULFATE ION
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 7)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	FMT	1	Ligand/Ion	FORMIC ACID
3	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	2	Ligand/Ion	SULFATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	FMT	-1	Ligand/Ion	FORMIC ACID
3	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	1	Ligand/Ion	SULFATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:15 , TRP A:17 , THR A:93 , SER A:94 , LYS A:96 , ARG A:193 , ARG A:207 , HOH A:708	BINDING SITE FOR RESIDUE SO4 A 601
2	AC2	SOFTWARE	LYS B:15 , TRP B:17 , THR B:93 , SER B:94 , LYS B:96 , ARG B:193 , ARG B:207 , HOH B:716	BINDING SITE FOR RESIDUE SO4 B 602
3	AC3	SOFTWARE	ARG A:234 , ILE A:239 , TRP A:253 , MSE A:261 , ALA A:262 , HOH A:823	BINDING SITE FOR RESIDUE SO4 A 603
4	AC4	SOFTWARE	LYS A:96 , HIS A:98 , GLU A:116 , HIS A:173 , HOH A:737	BINDING SITE FOR RESIDUE ZN A 604
5	AC5	SOFTWARE	LYS B:96 , HIS B:98 , GLU B:116 , HIS B:173 , HOH B:720	BINDING SITE FOR RESIDUE ZN B 605
6	AC6	SOFTWARE	ARG A:23 , SER A:29 , ILE A:30 , GLY B:54 , HOH B:821	BINDING SITE FOR RESIDUE ACT A 607
7	AC7	SOFTWARE	ARG A:25 , HOH A:731 , HOH A:857	BINDING SITE FOR RESIDUE FMT A 606

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

Asymmetric Unit

No.	Residues
1	Val A:220	-	Pro A:221
2	Val B:220	-	Pro B:221

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

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

(no "Exon" information available for 1QWR)

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:315
 aligned with MANA3_BACSU | P39841 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:315
                                    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     
          MANA3_BACSU     2 TQSPIFLTPVFKEKIWGGTALRDRFGYSIPSESTGECWAISAHPKGPSTVANGPYKGKTLIELWEEHREVFGGVEGDRFPLLTKLLDVKEDTSIKVHPDDYYAGENEEGELGKTECWYIIDCKENAEIIYGHTARSKTELVTMINSGDWEGLLRRIKIKPGDFYYVPSGTLHALCKGALVLETQQNSDATYRVYDYDRLDSNGSPRELHFAKAVNAATVPHVDGYIDESTESRKGITIKTFVQGEYFSVYKWDINGEAEMAQDESFLICSVIEGSGLLKYEDKTCPLKKGDHFILPAQMPDFTIKGTCTLIVSHI 316
               SCOP domains d1qwra_ A: Mannose-6-phosphate isomerase ManA                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1qwrA01 A:2-227 Jelly Rolls                                                                                                                                                                                                       1qwrA02 A:228-316 Jelly Rolls                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.eeee.....hhhhhhhh.......eeeeeee........ee........hhhhhhhhhhhhhh........eeeeeeee.....eee..hhhhhhhhh.......eeeeeeee....eeeeee...hhhhhhhhhhh.hhhhheeeee.....eeee.....eee...eeeeeeee.....eeee..............hhhhhhhhh...........eeeee..eeeeeeee....eeeeeeeeeeeee......eeeeeeeeeeeeee..eeeeee...eeee......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qwr A   2 TQSPIFLTPVFKEKIWGGTALRDRFGYSIPSESTGECWAISAHPKGPSTVANGPYKGKTLIELWEEHREVFGGVEGDRFPLLTKLLDVKEDTSIKVHPDDYYAGENEEGELGKTECWYIIDCKENAEIIYGHTARSKTELVTmINSGDWEGLLRRIKIKPGDFYYVPSGTLHALCKGALVLETQQNSDATYRVYDYDRLDSNGSPRELHFAKAVNAATVPHVDGYIDESTESRKGITIKTFVQGEYFSVYKWDINGEAEmAQDESFLICSVIEGSGLLKYEDKTCPLKKGDHFILPAQmPDFTIKGTCTLIVSHI 316
                                    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     
                                                                                                                                                                        144-MSE                                                                                                              261-MSE                                300-MSE

Chain B from PDB  Type:PROTEIN  Length:314
 aligned with MANA3_BACSU | P39841 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:314
                                    12        22        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       292       302       312    
          MANA3_BACSU     3 QSPIFLTPVFKEKIWGGTALRDRFGYSIPSESTGECWAISAHPKGPSTVANGPYKGKTLIELWEEHREVFGGVEGDRFPLLTKLLDVKEDTSIKVHPDDYYAGENEEGELGKTECWYIIDCKENAEIIYGHTARSKTELVTMINSGDWEGLLRRIKIKPGDFYYVPSGTLHALCKGALVLETQQNSDATYRVYDYDRLDSNGSPRELHFAKAVNAATVPHVDGYIDESTESRKGITIKTFVQGEYFSVYKWDINGEAEMAQDESFLICSVIEGSGLLKYEDKTCPLKKGDHFILPAQMPDFTIKGTCTLIVSHI 316
               SCOP domains d1qwrb_ B: Mannose-6-phosphate isomerase ManA                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1qwrB01 B:3-227 Jelly Rolls                                                                                                                                                                                                      1qwrB02 B:228-316 Jelly Rolls                                                             CATH domains
           Pfam domains (1) ---PMI_typeI-1qwrB01 B:6-316                                                                                                                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) ---PMI_typeI-1qwrB02 B:6-316                                                                                                                                                                                                                                                                                               Pfam domains (2)
         Sec.struct. author ...eeee.eeee.....hhhhhhhh.......eeeeeee........ee........hhhhhhhhhhhhhh........eeeeeeee.....eee..hhhhhhh.........eeeeeeee....eeeeee...hhhhhhhhhhh.hhhhheeeee.....eeee.....eee...eeeeeeee.....eeee..............hhhhhhhhh...........eeeee..eeeeeeee....eeeeeeeeeeeee......eeeeeeeeeeeeee..eeeeee...eeee......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qwr B   3 QSPIFLTPVFKEKIWGGTALRDRFGYSIPSESTGECWAISAHPKGPSTVANGPYKGKTLIELWEEHREVFGGVEGDRFPLLTKLLDVKEDTSIKVHPDDYYAGENEEGELGKTECWYIIDCKENAEIIYGHTARSKTELVTmINSGDWEGLLRRIKIKPGDFYYVPSGTLHALCKGALVLETQQNSDATYRVYDYDRLDSNGSPRELHFAKAVNAATVPHVDGYIDESTESRKGITIKTFVQGEYFSVYKWDINGEAEmAQDESFLICSVIEGSGLLKYEDKTCPLKKGDHFILPAQmPDFTIKGTCTLIVSHI 316
                                    12        22        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       292       302       312    
                                                                                                                                                                       144-MSE                                                                                                              261-MSE                                300-MSE

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: RmlC-like cupins (220)

Family: Type I phosphomannose isomerase (3)

Protein domain: Mannose-6-phosphate isomerase ManA (1)

Bacillus subtilis [TaxId: 1423] (1)

1a	d1qwra_	A:
1b	d1qwrb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Jelly Rolls (177)

Bacillus subtilis. Organism_taxid: 1423. (2)

1a	1qwrA02	A:228-316
1b	1qwrB02	B:228-316
1c	1qwrB01	B:3-227
1d	1qwrA01	A:2-227

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cupin (179)

Family: PMI_typeI (4)

Bacillus subtilis (1)

1a	PMI_typeI-1qwrB01	B:6-316
1b	PMI_typeI-1qwrB02	B:6-316

Asymmetric Unit(hide GO term definitions)

Chain A,B (MANA3_BACSU | P39841)

molecular function
	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:0004476	mannose-6-phosphate isomerase activity	Catalysis of the reaction: D-mannose 6-phosphate = D-fructose 6-phosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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