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Title :  CRYSTAL STRUCTURE OF SUGAR PHOSPHATE ISOMERASE FROM A CUPIN SUPERFAMILY SPO2919 FROM SILICIBACTER POMEROYI (YP_168127.1) FROM SILICIBACTER POMEROYI DSS-3 AT 2.30 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  08 Jul 09  (Deposition) - 21 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Yp_168127. 1, Sugar Phosphate Isomerase From A Cupin Superfamily Spo2919 From Silicibacter Pomeroyi, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Sugar Metabolism, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Sugar Phosphate Isomerase From A Cupin Superfamily Spo2919 From Silicibacter Pomeroyi (Yp_168127. 1 From Silicibacter Pomeroyi Dss-3 At 2. 30 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUGAR PHOSPHATE ISOMERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SPO2919, YP_168127.1
    Organism Scientific: RUEGERIA POMEROYI DSS-3
    Organism Taxid: 246200

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric/Biological Unit (5, 20)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CAC2Ligand/IonCACODYLATE ION
3CL1Ligand/IonCHLORIDE ION
4MSE15Mod. Amino AcidSELENOMETHIONINE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:132 , GLN A:156 , ASP B:132 , GLN B:156BINDING SITE FOR RESIDUE CL A 163
2AC2SOFTWARETYR A:17 , HIS A:59 , HIS A:61 , TYR A:128 , HOH A:181 , HOH A:184BINDING SITE FOR RESIDUE CAC A 164
3AC3SOFTWARESER A:55 , SER A:56 , GLU A:66 , HIS A:102 , GLN A:103 , HOH A:242BINDING SITE FOR RESIDUE ACT A 165
4AC4SOFTWARETYR B:17 , HIS B:59 , HIS B:61 , TYR B:128 , HOH B:188 , HOH B:239BINDING SITE FOR RESIDUE CAC B 163
5AC5SOFTWAREASP B:26 , GLY B:27 , ARG B:28 , HOH B:183 , HOH B:206BINDING SITE FOR RESIDUE PEG B 164

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I7D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I7D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I7D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I7D)

(-) Exons   (0, 0)

(no "Exon" information available for 3I7D)

(-) Sequences/Alignments

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:157
 aligned with Q5LPC9_RUEPO | Q5LPC9 from UniProtKB/TrEMBL  Length:162

    Alignment length:157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       
         Q5LPC9_RUEPO     2 PKLDLDSIERRIGSVYPGRLNAAMDGRSSLRLGDAGGLSQFGVNLVRLEPGAKSSLRHYHMEQDEFVMVTEGALVLVDDQGEHPMVPGDCAAFPAGDPNGHQFVNRTDAPATFLVVGTRTPTETAYYSDMDMMVKQDASGFAFTRKDGSPLTADQIG 158
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee....hhhhhhhhh.eeeeehhhhh....eeeeeeee.........eee....eeeeeee..eeeee..eeeee....eeee........eee......eeeeeeee....eeeee....eeeee....eeee.......hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i7d A   2 PKLDLDSIERRIGSVYPGRLNAAmDGRSSLRLGDAGGLSQFGVNLVRLEPGAKSSLRHYHmEQDEFVmVTEGALVLVDDQGEHPmVPGDCAAFPAGDPNGHQFVNRTDAPATFLVVGTRTPTETAYYSDmDmmVKQDASGFAFTRKDGSPLTADQIG 158
                                    11        21   |    31        41        51        61|      |71        81    |   91       101       111       121       131 ||    141       151       
                                                  25-MSE                               62-MSE 69-MSE           86-MSE                                      131-MSE                       
                                                                                                                                                             133-MSE                     
                                                                                                                                                              134-MSE                    


Chain B from PDB  Type:PROTEIN  Length:158
 aligned with Q5LPC9_RUEPO | Q5LPC9 from UniProtKB/TrEMBL  Length:162

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
         Q5LPC9_RUEPO     1 MPKLDLDSIERRIGSVYPGRLNAAMDGRSSLRLGDAGGLSQFGVNLVRLEPGAKSSLRHYHMEQDEFVMVTEGALVLVDDQGEHPMVPGDCAAFPAGDPNGHQFVNRTDAPATFLVVGTRTPTETAYYSDMDMMVKQDASGFAFTRKDGSPLTADQIG 158
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee....hhhhhhhhh.eeeeehhhhh....eeeeeeee.........eee....eeeeeee..eeeee..eeeee....eeee........eee......eeeeeeee....eeeee.....eeeee..eeeee.......hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i7d B   1 mPKLDLDSIERRIGSVYPGRLNAAmDGRSSLRLGDAGGLSQFGVNLVRLEPGAKSSLRHYHmEQDEFVmVTEGALVLVDDQGEHPmVPGDCAAFPAGDPNGHQFVNRTDAPATFLVVGTRTPTETAYYSDmDmmVKQDASGFAFTRKDGSPLTADQIG 158
                            |       10        20    |   30        40        50        60 |      70        80     |  90       100       110       120       130| ||   140       150        
                            1-MSE                  25-MSE                               62-MSE 69-MSE           86-MSE                                      131-MSE                       
                                                                                                                                                              133-MSE                     
                                                                                                                                                               134-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 3I7D)

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(no "CATH Domain" information available for 3I7D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I7D)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5LPC9_RUEPO | Q5LPC9)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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