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Title :   CRYSTAL STRUCTURE OF A D-RIBULOSE-5-PHOSPHATE-3-EPIMERASE (NP_954699) FROM HOMO SAPIENS AT 2.20 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   14 Jan 11 (Deposition) - 09 Mar 11 (Release) - 20 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B

Keywords :   Tim Barrel Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A D-Ribulose-5-Phosphate-3-Epimerase (Np_954699) From Homo Sapiens At 2. 20 A Resolution
To Be Published
PubMed: search

Molecule 1 - D-RIBULOSE-5-PHOSPHATE-3-EPIMERASE
	Chains	:	A, B
	EC Number	:	5.1.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RPE, HUSSY-17
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RIBULOSE-5-PHOSPHATE-3-EPIMERASE, RIBULOSE-PHOSPHATE 3- EPIMERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 38)

No.	Name	Count	Type	Full Name
1	FE	2	Ligand/Ion	FE (III) ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	30	Mod. Amino Acid	SELENOMETHIONINE
4	NI	2	Ligand/Ion	NICKEL (II) ION
5	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:35 , ASP A:37 , HIS A:70 , ASP A:175 , GOL A:232 , HOH A:463	BINDING SITE FOR RESIDUE ZN A 229
2	AC2	SOFTWARE	HIS A:35 , ASP A:37 , HIS A:70 , ASP A:175 , GOL A:232 , HOH A:463	BINDING SITE FOR RESIDUE NI A 230
3	AC3	SOFTWARE	HIS A:35 , ASP A:37 , HIS A:70 , ASP A:175 , GOL A:232 , HOH A:463	BINDING SITE FOR RESIDUE FE A 231
4	AC4	SOFTWARE	ASP A:37 , MSE A:39 , HIS A:70 , MSE A:72 , PRO A:145 , GLY A:146 , ASP A:175 , ZN A:229 , NI A:230 , FE A:231 , HOH A:463	BINDING SITE FOR RESIDUE GOL A 232
5	AC5	SOFTWARE	HIS B:35 , ASP B:37 , HIS B:70 , ASP B:175 , GOL B:232 , HOH B:456	BINDING SITE FOR RESIDUE ZN B 229
6	AC6	SOFTWARE	HIS B:35 , ASP B:37 , HIS B:70 , ASP B:175 , GOL B:232 , HOH B:456	BINDING SITE FOR RESIDUE NI B 230
7	AC7	SOFTWARE	HIS B:35 , ASP B:37 , HIS B:70 , ASP B:175 , GOL B:232 , HOH B:456	BINDING SITE FOR RESIDUE FE B 231
8	AC8	SOFTWARE	ASP B:37 , MSE B:39 , HIS B:70 , MSE B:72 , PRO B:145 , GLY B:146 , ASP B:175 , ZN B:229 , NI B:230 , FE B:231 , HOH B:404 , HOH B:456	BINDING SITE FOR RESIDUE GOL B 232

Asymmetric/Biological Unit

No.	Residues
1	A:5	-	A:217
2	B:5	-	B:217

(no "Cis Peptide Bond" information available for 3QC3)

(no "SAP(SNP)/Variant" information available for 3QC3)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBUL_P_3_EPIMER_1	PS01085	Ribulose-phosphate 3-epimerase family signature 1.	RPE_HUMAN	34-48	2	A:34-48 B:34-48
2	RIBUL_P_3_EPIMER_2	PS01086	Ribulose-phosphate 3-epimerase family signature 2.	RPE_HUMAN	138-160	2	A:138-160 B:138-160

(no "Exon" information available for 3QC3)

Asymmetric/Biological 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:225
 aligned with RPE_HUMAN | Q96AT9 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:225
                             1                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
            RPE_HUMAN     - -MASGCKIGPSILNSDLANLGAECLRMLDSGADYLHLDVMDGHFVPNITFGHPVVESLRKQLGQDPFFDMHMMVSKPEQWVKPMAVAGANQYTFHLEATENPGALIKDIRENGMKVGLAIKPGTSVEYLAPWANQIDMALVMTVEPGFGGQKFMEDMMPKVHWLRTQFPSLDIEVDGGVGPDTVHKCAEAGANMIVSGSAIMRSEDPRSVINLLRNVCSEAAQKR 224
               SCOP domains d3qc3a_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....hhhhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhh..eeeee.hhh.hhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhh...eeeee......hhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------RIBUL_P_3_EPIME-----------------------------------------------------------------------------------------RIBUL_P_3_EPIMER_2     ---------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qc3 A   0 GmASGCKIGPSILNSDLANLGAECLRmLDSGADYLHLDVmDGHFVPNITFGHPVVESLRKQLGQDPFFDmHmmVSKPEQWVKPmAVAGANQYTFHLEATENPGALIKDIRENGmKVGLAIKPGTSVEYLAPWANQIDmALVmTVEPGFGGQKFmEDmmPKVHWLRTQFPSLDIEVDGGVGPDTVHKCAEAGANmIVSGSAImRSEDPRSVINLLRNVCSEAAQKR 224
                             |       9        19      | 29        39        49        59        69 ||     79   |    89        99       109   |   119       129       139 |     149   |  |159       169       179       189   |   199 |     209       219     
                             |                       26-MSE       39-MSE                        69-MSE        83-MSE                       113-MSE                 137-MSE         153-MSE                                 193-MSE 201-MSE                   
                             1-MSE                                                                71-MSE                                                               141-MSE        156-MSE                                                                
                                                                                                   72-MSE                                                                              157-MSE

Chain B from PDB  Type:PROTEIN  Length:225
 aligned with RPE_HUMAN | Q96AT9 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:225
                             1                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     
            RPE_HUMAN     - -MASGCKIGPSILNSDLANLGAECLRMLDSGADYLHLDVMDGHFVPNITFGHPVVESLRKQLGQDPFFDMHMMVSKPEQWVKPMAVAGANQYTFHLEATENPGALIKDIRENGMKVGLAIKPGTSVEYLAPWANQIDMALVMTVEPGFGGQKFMEDMMPKVHWLRTQFPSLDIEVDGGVGPDTVHKCAEAGANMIVSGSAIMRSEDPRSVINLLRNVCSEAAQKR 224
               SCOP domains d3qc3b_ B: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------Ribul_P_3_epim-3qc3B01 B:6-204                                                                                                                                                                         -------------------- Pfam domains (1)
           Pfam domains (2) ------Ribul_P_3_epim-3qc3B02 B:6-204                                                                                                                                                                         -------------------- Pfam domains (2)
         Sec.struct. author ......ee.......hhhhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhh..eeeee.hhh.hhhhhhhhhhhh..eeeeee....hhhhhh.hhhhh.eeeee...........hhhhhhhhhhhhhhh...eeeee......hhhhhhhhh..eee.hhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------RIBUL_P_3_EPIME-----------------------------------------------------------------------------------------RIBUL_P_3_EPIMER_2     ---------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qc3 B   0 GmASGCKIGPSILNSDLANLGAECLRmLDSGADYLHLDVmDGHFVPNITFGHPVVESLRKQLGQDPFFDmHmmVSKPEQWVKPmAVAGANQYTFHLEATENPGALIKDIRENGmKVGLAIKPGTSVEYLAPWANQIDmALVmTVEPGFGGQKFmEDmmPKVHWLRTQFPSLDIEVDGGVGPDTVHKCAEAGANmIVSGSAImRSEDPRSVINLLRNVCSEAAQKR 224
                             |       9        19      | 29        39        49        59        69 ||     79   |    89        99       109   |   119       129       139 |     149   |  |159       169       179       189   |   199 |     209       219     
                             1-MSE                   26-MSE       39-MSE                        69-MSE        83-MSE                       113-MSE                 137-MSE         153-MSE                                 193-MSE 201-MSE                   
                                                                                                  71-MSE                                                               141-MSE        156-MSE                                                                
                                                                                                   72-MSE                                                                              157-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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Ribulose-phoshate binding barrel (356)

Family: automated matches (38)

Protein domain: automated matches (38)

Human (Homo sapiens) [TaxId: 9606] (4)

1a	d3qc3a_	A:
1b	d3qc3b_	B:

(no "CATH Domain" information available for 3QC3)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: Ribul_P_3_epim (7)

Homo sapiens (Human) (4)

1a	Ribul_P_3_epim-3qc3B01	B:6-204
1b	Ribul_P_3_epim-3qc3B02	B:6-204

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RPE_HUMAN | Q96AT9)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0016857	racemase and epimerase activity, acting on carbohydrates and derivatives	Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule.
	GO:0004750	ribulose-phosphate 3-epimerase activity	Catalysis of the reaction: D-ribulose 5-phosphate = D-xylulose 5-phosphate.
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:0044262	cellular 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, as carried out by individual cells.
	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.
	GO:0019323	pentose catabolic process	The chemical reactions and pathways resulting in the breakdown of a pentose, any monosaccharide with a chain of five carbon atoms in the molecule.
	GO:0006098	pentose-phosphate shunt	The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
	GO:0009052	pentose-phosphate shunt, non-oxidative branch	The branch of the pentose-phosphate shunt which does not involve oxidation reactions. It comprises a series of sugar phosphate interconversions, starting with ribulose 5-P and producing fructose 6-P and glyceraldehyde 3-P.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 38)

Sites (8, 8)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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