3FF1 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF GLUCOSE 6-PHOSPHATE ISOMERASE FROM STAPHYLOCOCCUS AUREUS

Authors :   S. M. Anderson, J. S. Brunzelle, O. Onopriyenko, S. Peterson, W. F. Ande A. Savchenko, Center For Structural Genomics Of Infectious Di (Csgid)

Date :   01 Dec 08 (Deposition) - 03 Feb 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (2x)
Biol. Unit 2: A (2x),B (2x)
Biol. Unit 3: B  (2x)

Keywords :   Alpha Beta, Rossmann Fold, Glucose-6-Phosphate Isomerase Like Protein, Gluconeogenesis, Glycolysis, Isomerase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Anderson, J. S. Brunzelle, O. Onopriyenko, S. Peterson, W. F. Anderson, A. Savchenko
Structure Of Glucose 6-Phosphate Isomerase From Staphylococcus Aureus
To Be Published
PubMed: search

Molecule 1 - GLUCOSE-6-PHOSPHATE ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.1.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PGI, SACOL0966
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
	Organism Taxid	:	93062
	Strain	:	COL
	Synonym	:	GPI, PHOSPHOGLUCOSE ISOMERASE, PGI, PHOSPHOHEXOSE ISOMERASE, PHI

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A
Biological Unit 2 (2x)	:	A (2x)	B (2x)
Biological Unit 3 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 23)

No.	Name	Count	Type	Full Name
1	G6Q	1	Ligand/Ion	GLUCOSE-6-PHOSPHATE
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
3	NA	4	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 18)

No.	Name	Count	Type	Full Name
1	G6Q	-1	Ligand/Ion	GLUCOSE-6-PHOSPHATE
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 18)

No.	Name	Count	Type	Full Name
1	G6Q	-1	Ligand/Ion	GLUCOSE-6-PHOSPHATE
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (2, 20)

No.	Name	Count	Type	Full Name
1	G6Q	2	Ligand/Ion	GLUCOSE-6-PHOSPHATE
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:104 , LYS B:70 , GLU B:71 , SER B:73 , ASP B:74 , ASN B:103 , GLU B:104 , HOH B:453 , HOH B:713 , HOH B:724 , HOH B:780 , HOH B:1196 , HOH B:1356	BINDING SITE FOR RESIDUE G6Q B 444
2	AC2	SOFTWARE	ASN A:101 , HOH A:1298 , GLU B:104 , TYR B:105 , HOH B:750 , HOH B:878	BINDING SITE FOR RESIDUE NA B 445
3	AC3	SOFTWARE	HOH A:1197 , SER B:60 , HOH B:452 , HOH B:565 , HOH B:1198	BINDING SITE FOR RESIDUE NA B 446
4	AC4	SOFTWARE	LYS A:70 , SER A:73 , HOH A:1076 , HOH A:1193 , HOH A:1194 , HOH A:1195	BINDING SITE FOR RESIDUE NA A 444
5	AC5	SOFTWARE	HOH A:1402 , ASN B:327 , HOH B:771 , HOH B:787 , HOH B:978 , HOH B:980	BINDING SITE FOR RESIDUE NA B 447

(no "SS Bond" information available for 3FF1)

Asymmetric Unit

No.	Residues
1	Tyr A:301	-	Thr A:302
2	Tyr B:301	-	Thr B:302

(no "SAP(SNP)/Variant" information available for 3FF1)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	P_GLUCOSE_ISOMERASE_3	PS51463	Glucose-6-phosphate isomerase family profile.	G6PI_STAAC	1-443	2	A:1-443 B:1-443
2	P_GLUCOSE_ISOMERASE_1	PS00765	Phosphoglucose isomerase signature 1.	G6PI_STAAC	197-210	2	A:197-210 B:197-210
3	P_GLUCOSE_ISOMERASE_2	PS00174	Phosphoglucose isomerase signature 2.	G6PI_STAAC	403-420	2	A:403-420 B:403-420

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	P_GLUCOSE_ISOMERASE_3	PS51463	Glucose-6-phosphate isomerase family profile.	G6PI_STAAC	1-443	2	A:1-443 -
2	P_GLUCOSE_ISOMERASE_1	PS00765	Phosphoglucose isomerase signature 1.	G6PI_STAAC	197-210	2	A:197-210 -
3	P_GLUCOSE_ISOMERASE_2	PS00174	Phosphoglucose isomerase signature 2.	G6PI_STAAC	403-420	2	A:403-420 -

Biological Unit 2 (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	P_GLUCOSE_ISOMERASE_3	PS51463	Glucose-6-phosphate isomerase family profile.	G6PI_STAAC	1-443	4	A:1-443 B:1-443
2	P_GLUCOSE_ISOMERASE_1	PS00765	Phosphoglucose isomerase signature 1.	G6PI_STAAC	197-210	4	A:197-210 B:197-210
3	P_GLUCOSE_ISOMERASE_2	PS00174	Phosphoglucose isomerase signature 2.	G6PI_STAAC	403-420	4	A:403-420 B:403-420

Biological Unit 3 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	P_GLUCOSE_ISOMERASE_3	PS51463	Glucose-6-phosphate isomerase family profile.	G6PI_STAAC	1-443	2	- B:1-443
2	P_GLUCOSE_ISOMERASE_1	PS00765	Phosphoglucose isomerase signature 1.	G6PI_STAAC	197-210	2	- B:197-210
3	P_GLUCOSE_ISOMERASE_2	PS00174	Phosphoglucose isomerase signature 2.	G6PI_STAAC	403-420	2	- B:403-420

(no "Exon" information available for 3FF1)

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:444
 aligned with G6PI_STAAC | Q5HHC2 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:444
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439    
           G6PI_STAAC     - -MTHIQLDFSKTLEFFGEHELKQQQEIVKSIHKTIHEGTGAGSDFLGWVDLPVDYDKEEFSRIVEASKRIKENSDVLVVIGIGGSYLGARAAIEMLTSSFRNSNEYPEIVFVGNHLSSTYTKELVDYLADKDFSVNVISKSGTTTEPAVAFRLFKQLVEERYGKEEAQKRIFATTDKEKGALKQLATNEGYETFIVPDDVGGRYSVLTAVGLLPIATAGINIEAMMIGAAKAREELSSDKLEENIAYQYATIRNILYAKGYTTEMLINYEPSMQYFNEWWKQLFGESEGKDFKGIYPSSANYTTDLHSLGQYVQEGRRFLFETVVKVNHPKYDITIEKDSDDLDGLNYLAGKTIDEVNTKAFEGTLLAHTDGGVPNMVVNIPQLDEETFGYVVYFFELACAMSGYQLGVNPFNQPGVEAYKQNMFALLGKPGFEDLKKELEERL 443
               SCOP domains d3ff1a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3ff1A01 A:0-38,A:222-412               3ff1A02 A:39-221 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                  3ff1A01 A:0-38,A:222-412 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                  ------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee..hhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh..........eeeee....hhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhheeeee....hhhhhhhhhhh.eeee.....hhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhh...eeeeeeee.................hhhhhh..hhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -P_GLUCOSE_ISOMERASE_3  PDB: A:1-443 UniProt: 1-443                                                                                                                                                                                                                                                                                                                                                                                                          PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P_GLUCOSE_ISOM------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P_GLUCOSE_ISOMERAS----------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ff1 A   0 AmTHIQLDFSKTLEFFGEHELKQQQEIVKSIHKTIHEGTGAGSDFLGWVDLPVDYDKEEFSRIVEASKRIKENSDVLVVIGIGGSYLGARAAIEmLTSSFRNSNEYPEIVFVGNHLSSTYTKELVDYLADKDFSVNVISKSGTTTEPAVAFRLFKQLVEERYGKEEAQKRIFATTDKEKGALKQLATNEGYETFIVPDDVGGRYSVLTAVGLLPIATAGINIEAmmIGAAKAREELSSDKLEENIAYQYATIRNILYAKGYTTEmLINYEPSmQYFNEWWKQLFGESEGKDFKGIYPSSANYTTDLHSLGQYVQEGRRFLFETVVKVNHPKYDITIEKDSDDLDGLNYLAGKTIDEVNTKAFEGTLLAHTDGGVPNmVVNIPQLDEETFGYVVYFFELACAmSGYQLGVNPFNQPGVEAYKQNmFALLGKPGFEDLKKELEERL 443
                             |       9        19        29        39        49        59        69        79        89    |   99       109       119       129       139       149       159       169       179       189       199       209       219    || 229       239       249       259    |  269  |    279       289       299       309       319       329       339       349       359       369      |379       389       399 |     409       419   |   429       439    
                             |                                                                                           94-MSE                                                                                                                           224-MSE                                 264-MSE 272-MSE                                                                                                 376-MSE                  401-MSE               423-MSE                
                             1-MSE                                                                                                                                                                                                                         225-MSE

Chain B from PDB  Type:PROTEIN  Length:444
 aligned with G6PI_STAAC | Q5HHC2 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:444
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439    
           G6PI_STAAC     - -MTHIQLDFSKTLEFFGEHELKQQQEIVKSIHKTIHEGTGAGSDFLGWVDLPVDYDKEEFSRIVEASKRIKENSDVLVVIGIGGSYLGARAAIEMLTSSFRNSNEYPEIVFVGNHLSSTYTKELVDYLADKDFSVNVISKSGTTTEPAVAFRLFKQLVEERYGKEEAQKRIFATTDKEKGALKQLATNEGYETFIVPDDVGGRYSVLTAVGLLPIATAGINIEAMMIGAAKAREELSSDKLEENIAYQYATIRNILYAKGYTTEMLINYEPSMQYFNEWWKQLFGESEGKDFKGIYPSSANYTTDLHSLGQYVQEGRRFLFETVVKVNHPKYDITIEKDSDDLDGLNYLAGKTIDEVNTKAFEGTLLAHTDGGVPNMVVNIPQLDEETFGYVVYFFELACAMSGYQLGVNPFNQPGVEAYKQNMFALLGKPGFEDLKKELEERL 443
               SCOP domains d3ff1b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3ff1B01 B:0-38,B:223-412               3ff1B02 B:39-222 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                   3ff1B01 B:0-38,B:223-412 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                 ------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee..hhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh..........eeeee....hhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhheeeee....hhhhhhhhhhh.eeee.....hhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhh...eeeeeeee.................hhhhhh..hhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -P_GLUCOSE_ISOMERASE_3  PDB: B:1-443 UniProt: 1-443                                                                                                                                                                                                                                                                                                                                                                                                          PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P_GLUCOSE_ISOM------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P_GLUCOSE_ISOMERAS----------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ff1 B   0 AmTHIQLDFSKTLEFFGEHELKQQQEIVKSIHKTIHEGTGAGSDFLGWVDLPVDYDKEEFSRIVEASKRIKENSDVLVVIGIGGSYLGARAAIEmLTSSFRNSNEYPEIVFVGNHLSSTYTKELVDYLADKDFSVNVISKSGTTTEPAVAFRLFKQLVEERYGKEEAQKRIFATTDKEKGALKQLATNEGYETFIVPDDVGGRYSVLTAVGLLPIATAGINIEAmmIGAAKAREELSSDKLEENIAYQYATIRNILYAKGYTTEmLINYEPSmQYFNEWWKQLFGESEGKDFKGIYPSSANYTTDLHSLGQYVQEGRRFLFETVVKVNHPKYDITIEKDSDDLDGLNYLAGKTIDEVNTKAFEGTLLAHTDGGVPNmVVNIPQLDEETFGYVVYFFELACAmSGYQLGVNPFNQPGVEAYKQNmFALLGKPGFEDLKKELEERL 443
                             |       9        19        29        39        49        59        69        79        89    |   99       109       119       129       139       149       159       169       179       189       199       209       219    || 229       239       249       259    |  269  |    279       289       299       309       319       329       339       349       359       369      |379       389       399 |     409       419   |   429       439    
                             1-MSE                                                                                       94-MSE                                                                                                                           224-MSE                                 264-MSE 272-MSE                                                                                                 376-MSE                  401-MSE               423-MSE                
                                                                                                                                                                                                                                                           225-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: Alpha and beta proteins (a/b) (23833)

Fold: SIS domain (85)

Superfamily: SIS domain (85)

Family: Phosphoglucose isomerase, PGI (37)

Protein domain: automated matches (13)

Staphylococcus aureus [TaxId: 93062] (1)

1a	d3ff1a_	A:
1b	d3ff1b_	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: Glucose-6-phosphate isomerase like protein; domain 1 (105)

Aureus col (Staphylococcus aureus subsp) (1)

1a	3ff1B01	B:0-38,B:223-412
1b	3ff1A01	A:0-38,A:222-412
1c	3ff1B02	B:39-222
1d	3ff1A02	A:39-221

(no "Pfam Domain" information available for 3FF1)

Asymmetric Unit(hide GO term definitions)

Chain A,B (G6PI_STAAC | Q5HHC2)

molecular function
	GO:0004347	glucose-6-phosphate isomerase activity	Catalysis of the reaction: D-glucose 6-phosphate = D-fructose 6-phosphate.
	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.
biological process
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	GO:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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