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(-) Description

Title :  CRYSTAL STRUCTURE OF POSSIBLE 2-HYDROXYCHROMENE-2-CARBOXYLATE ISOMERASE FROM RHODOBACTER SPHAEROIDES
 
Authors :  C. Chang, C. Hatzos, L. Freeman, A. Joachimiak, Midwest Center For S Genomics (Mcsg)
Date :  23 Jan 09  (Deposition) - 03 Feb 09  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Rhodobacter Sphaeroides, 2-Hydroxychromene-2-Carboxylate Isomerase, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, C. Hatzos, L. Freeman, A. Joachimiak
Crystal Structure Of Possible 2-Hydroxychromene-2-Carboxylate Isomerase From Rhodobacter Sphaeroides
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - POSSIBLE 2-HYDROXYCHROMENE-2-CARBOXYLATE ISOMERASE
    Atcc: 17023
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3) MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RHOS4_04980, RSP_1916
    Organism Scientific: RHODOBACTER SPHAEROIDES 2.4.1
    Organism Taxid: 272943
    Strain: 2.4.1 / NCIB 8253 / DSM 158

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 27)

Asymmetric Unit (5, 27)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GSH3Ligand/IonGLUTATHIONE
4MSE20Mod. Amino AcidSELENOMETHIONINE
5PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3GSH2Ligand/IonGLUTATHIONE
4MSE10Mod. Amino AcidSELENOMETHIONINE
5PGE-1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (4, 13)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GSH1Ligand/IonGLUTATHIONE
4MSE10Mod. Amino AcidSELENOMETHIONINE
5PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:12 , TYR A:14 , GLY A:170 , SER A:171 , TRP A:182 , GLY A:183 , TRP A:184 , ASP A:185 , HOH A:257BINDING SITE FOR RESIDUE GSH A 201
2AC2SOFTWAREGLN A:20 , ASP A:114 , HOH A:220 , HOH A:262BINDING SITE FOR RESIDUE CA A 202
3AC3SOFTWAREARG A:186 , SER B:12 , GLY B:13 , TYR B:14 , GLY B:170 , SER B:171 , PRO B:172 , TRP B:182 , GLY B:183 , TRP B:184 , ASP B:185BINDING SITE FOR RESIDUE GSH B 201
4AC4SOFTWARESER C:12 , GLY C:13 , TYR C:14 , GLY C:41 , TRP C:66 , SER C:171 , GLY C:183 , TRP C:184 , ASP C:185 , HOH C:236 , HOH C:237 , HOH C:316 , HOH C:338 , HOH C:413 , HOH C:414 , ARG D:186BINDING SITE FOR RESIDUE GSH C 201
5AC5SOFTWAREGLN C:20 , ASP C:114 , HOH C:207 , HOH C:247 , HOH C:248BINDING SITE FOR RESIDUE CA C 202
6AC6SOFTWAREPRO B:126 , GLU B:127 , GLU D:23 , PRO D:102 , ASP D:103 , THR D:106 , HOH D:209BINDING SITE FOR RESIDUE PGE D 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FZ5)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1His A:83 -Pro A:84
2Ser A:171 -Pro A:172
3His B:83 -Pro B:84
4Ser B:171 -Pro B:172
5His C:83 -Pro C:84
6Ser C:171 -Pro C:172
7His D:83 -Pro D:84
8Ser D:171 -Pro D:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FZ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FZ5)

(-) Exons   (0, 0)

(no "Exon" information available for 3FZ5)

(-) Sequences/Alignments

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:190
 aligned with Q3J568_RHOS4 | Q3J568 from UniProtKB/TrEMBL  Length:199

    Alignment length:200
                             1                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199
         Q3J568_RHOS4     - -MNPIEFWFDFSSGYAFFAAQRIEALAAELGRTVLWRPYMLGAAFSVTGARGLSSTPLKRDYAQRDWARIARQRGLTFRPPADHPHVALAATRAFYWIEAQSPDAATAFAQRVFDLYFSDRLDTASPEAVSRLGPEVGLEPEALLAGIADPALKETVRKIGEDAVARGIFGSPFFLVDDEPFWGWDRMEMMAEWIRTGGW 199
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fz5A00 A:0-199 Glutaredoxin                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhhhhhh..eeeee....----------..hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh......eeee..eeee...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fz5 A   0 AmNPIEFWFDFSSGYAFFAAQRIEALAAELGRTVLWRPYmLG----------LSSTPLKRDYAQRDWARIARQRGLTFRPPADHPHVALAATRAFYWIEAQSPDAATAFAQRVFDLYFSDRLDTASPEAVSRLGPEVGLEPEALLAGIADPALKETVRKIGEDAVARGIFGSPFFLVDDEPFWGWDRmEmmAEWIRTGGW 199
                             |       9        19        29        39 |       -  |     59        69        79        89        99       109       119       129       139       149       159       169       179       189|      199
                             |                                    39-MSE       52                                                                                                                                    187-MSE        
                             1-MSE                                  41                                                                                                                                                 189-MSE      
                                                                                                                                                                                                                        190-MSE     


Chain B from PDB  Type:PROTEIN  Length:186
 aligned with Q3J568_RHOS4 | Q3J568 from UniProtKB/TrEMBL  Length:199

    Alignment length:199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         
         Q3J568_RHOS4     1 MNPIEFWFDFSSGYAFFAAQRIEALAAELGRTVLWRPYMLGAAFSVTGARGLSSTPLKRDYAQRDWARIARQRGLTFRPPADHPHVALAATRAFYWIEAQSPDAATAFAQRVFDLYFSDRLDTASPEAVSRLGPEVGLEPEALLAGIADPALKETVRKIGEDAVARGIFGSPFFLVDDEPFWGWDRMEMMAEWIRTGGW 199
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3fz5B00 B:2-199 Glutaredoxin                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhhhhh...eeeee...-------------.hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee..eeee...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fz5 B   1 mNPIEFWFDFSSGYAFFAAQRIEALAAELGRTVLWRPYmL-------------STPLKRDYAQRDWARIARQRGLTFRPPADHPHVALAATRAFYWIEAQSPDAATAFAQRVFDLYFSDRLDTASPEAVSRLGPEVGLEPEALLAGIADPALKETVRKIGEDAVARGIFGSPFFLVDDEPFWGWDRmEmmAEWIRTGGW 199
                            |       10        20        30        40         -   |    60        70        80        90       100       110       120       130       140       150       160       170       180      |190         
                            1-MSE                                39-MSE         54                                                                                                                                  187-MSE        
                                                                  40                                                                                                                                                  189-MSE      
                                                                                                                                                                                                                       190-MSE     


Chain C from PDB  Type:PROTEIN  Length:192
 aligned with Q3J568_RHOS4 | Q3J568 from UniProtKB/TrEMBL  Length:199

    Alignment length:202
                               1                                                                                                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197  
         Q3J568_RHOS4     - ---MNPIEFWFDFSSGYAFFAAQRIEALAAELGRTVLWRPYMLGAAFSVTGARGLSSTPLKRDYAQRDWARIARQRGLTFRPPADHPHVALAATRAFYWIEAQSPDAATAFAQRVFDLYFSDRLDTASPEAVSRLGPEVGLEPEALLAGIADPALKETVRKIGEDAVARGIFGSPFFLVDDEPFWGWDRMEMMAEWIRTGGW 199
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fz5C00 C:-2-199 Glutaredoxin                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhhhhhhh..eeeee....----------..hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee..eeee...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fz5 C  -2 SNAmNPIEFWFDFSSGYAFFAAQRIEALAAELGRTVLWRPYmLG----------LSSTPLKRDYAQRDWARIARQRGLTFRPPADHPHVALAATRAFYWIEAQSPDAATAFAQRVFDLYFSDRLDTASPEAVSRLGPEVGLEPEALLAGIADPALKETVRKIGEDAVARGIFGSPFFLVDDEPFWGWDRmEmmAEWIRTGGW 199
                               |     7        17        27        37 | |     -    |   57        67        77        87        97       107       117       127       137       147       157       167       177       187 ||    197  
                               1-MSE                                39-MSE       52                                                                                                                                    187-MSE        
                                                                      41                                                                                                                                                 189-MSE      
                                                                                                                                                                                                                          190-MSE     


Chain D from PDB  Type:PROTEIN  Length:186
 aligned with Q3J568_RHOS4 | Q3J568 from UniProtKB/TrEMBL  Length:199

    Alignment length:199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         
         Q3J568_RHOS4     1 MNPIEFWFDFSSGYAFFAAQRIEALAAELGRTVLWRPYMLGAAFSVTGARGLSSTPLKRDYAQRDWARIARQRGLTFRPPADHPHVALAATRAFYWIEAQSPDAATAFAQRVFDLYFSDRLDTASPEAVSRLGPEVGLEPEALLAGIADPALKETVRKIGEDAVARGIFGSPFFLVDDEPFWGWDRMEMMAEWIRTGGW 199
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3fz5D00 D:2-199 Glutaredoxin                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhhhhh...eeeee...-------------...hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee..eeee...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fz5 D   1 mNPIEFWFDFSSGYAFFAAQRIEALAAELGRTVLWRPYmL-------------STPLKRDYAQRDWARIARQRGLTFRPPADHPHVALAATRAFYWIEAQSPDAATAFAQRVFDLYFSDRLDTASPEAVSRLGPEVGLEPEALLAGIADPALKETVRKIGEDAVARGIFGSPFFLVDDEPFWGWDRmEmmAEWIRTGGW 199
                            |       10        20        30        40         -   |    60        70        80        90       100       110       120       130       140       150       160       170       180      |190         
                            1-MSE                                39-MSE         54                                                                                                                                  187-MSE        
                                                                  40                                                                                                                                                  189-MSE      
                                                                                                                                                                                                                       190-MSE
   Legend:   → Mismatch (orange background)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3FZ5)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FZ5)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q3J568_RHOS4 | Q3J568)
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.
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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