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(-) Description

Title :  CRYSTAL STRUCTURE OF SUGAR PHOSPHATE ISOMERASE/EPIMERASE (YP_001303399.1) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  14 Dec 09  (Deposition) - 16 Feb 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Sugar Phosphate Isomerase/Epimerase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Sugar Phosphate Isomerase/Epimerase (Yp_001303399. 1) From Parabacteroides Distasonis Atcc 8503 At 1. 70 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUGAR PHOSPHATE ISOMERASE/EPIMERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Vector Type: PLASMID
    Gene: BDI_2046
    Organism Scientific: PARABACTEROIDES DISTASONIS
    Organism Taxid: 435591
    Strain: ATCC 8503 / DSM 20701 / NCTC 11152

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 25)

Asymmetric Unit (3, 25)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2MG1Ligand/IonMAGNESIUM ION
3MSE19Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3MSE19Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 48)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3MSE38Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:14 , HOH A:15 , HIS A:196 , ASP A:247 , HIS A:273 , GLU A:306BINDING SITE FOR RESIDUE MG A 1
2AC2SOFTWAREASP A:71 , MSE A:72BINDING SITE FOR RESIDUE EDO A 2
3AC3SOFTWAREEDO A:6 , LYS A:241 , LYS A:321BINDING SITE FOR RESIDUE EDO A 3
4AC4SOFTWARETYR A:82 , GLY A:83 , LYS A:84 , TYR A:140 , THR A:144BINDING SITE FOR RESIDUE EDO A 4
5AC5SOFTWAREGLU A:45 , GLY A:47 , LYS A:76 , ASP A:302 , TYR A:303BINDING SITE FOR RESIDUE EDO A 5
6AC6SOFTWAREEDO A:3 , ASN A:178 , ASP A:182 , LYS A:241 , HOH A:460BINDING SITE FOR RESIDUE EDO A 6

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L23)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L23)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L23)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L23)

(-) Exons   (0, 0)

(no "Exon" information available for 3L23)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:282
 aligned with A6LDL3_PARD8 | A6LDL3 from UniProtKB/TrEMBL  Length:334

    Alignment length:292
                                    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       322       332  
         A6LDL3_PARD8    43 GKEIGLQIYSLSQELYKGDVAANLRKVKDMGYSKLELAGYGKGAIGGVPMMDFKKMAEDAGLKIISSHVNPVDTSISDPFKAMIFKYSKEVTPKIMEYWKATAADHAKLGCKYLIQPMMPTITTHDEAKLVCDIFNQASDVIKAEGIATGFGYHNHNMEFNRVATKEQQEKVKGNPFAAFMKVGDQIYDLMLKDTDPSKVYFEMDVYWTVMGQNDPVEYMQKHPDRIKVLHIKDRAVFGQSGMMNFEMIFKQMYANGIKDYFVELEQMPDGRTQFAGVKDCADYLIKAPFVK 334
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------AP_endonuc_2-3l23A01 A:66-296                                                                                                                                                                                                          -------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhhhhhhhh.hhhhhhhhhhhh...eeee..ee..ee..eehhhhhhhhhhh..eeeeee......................hhhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhhhhhh.....eeee..hhhh.ee......----------.....eehhhhhhhhh....eeeeeehhhhhhh..hhhhhhhhh...eeeeee............hhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l23 A  43 GKEIGLQIYSLSQELYKGDVAANLRKVKDmGYSKLELAGYGKGAIGGVPmmDFKKmAEDAGLKIISSHVNPVDTSISDPFKAmIFKYSKEVTPKImEYWKATAADHAKLGCKYLIQPmmPTITTHDEAKLVCDIFNQASDVIKAEGIATGFGYHNHNmEFNRVATKEQQ----------FmKVGDQIYDLmLKDTDPSKVYFEmDVYWTVmGQNDPVEYmQKHPDRIKVLHIKDRAVFGQSGmmNFEmIFKQmYANGIKDYFVELEQmPDGRTQFAGVKDCADYLIKAPFVK 334
                                    52        62        72        82        92|    | 102       112       122  |    132     | 142       152       162       172       182       192       202        |-       222|      232|      242   |   252|      262       272       282  ||   292  |    302       312       322       332  
                                                        72-MSE              92-MSE |                        125-MSE      138-MSE               160-MSE                                 200-MSE    211        222|       233-MSE      246-MSE  |      262-MSE                285-MSE|    |            310-MSE                    
                                                                             93-MSE|                                                            161-MSE                                                       223-MSE                       253-MSE                          286-MSE    |                                       
                                                                                  98-MSE                                                                                                                                                                                         290-MSE|                                       
                                                                                                                                                                                                                                                                                      295-MSE
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3L23)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L23)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (A6LDL3_PARD8 | A6LDL3)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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