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(-) Description

Title :  CRYSTAL STRUCTURE OF DEGV FAMILY PROTEIN CG2579 FROM CORYNEBACTERIUM GLUTAMICUM
 
Authors :  Y. Kim, C. Tesar, J. Abdullah, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)
Date :  11 Sep 08  (Deposition) - 23 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Alpha-Beta-Alpha Sandwich, Methylated Lysines, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kim, C. Tesar, J. Abdullah, A. Joachimiak
Crystal Structure Of Degv Family Protein Cg2579 From Corynebacterium Glutamicum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DEGV FAMILY PROTEIN
    Atcc13032
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System StrainBL21DE3
    Expression System Vector TypePLASMID
    GeneCGL2349, CG2579
    Organism CommonBREVIBACTERIUM FLAVUM
    Organism ScientificCORYNEBACTERIUM GLUTAMICUM
    Organism Taxid196627
    StrainATCC 13032
    SynonymUPF0230 PROTEIN CGL2349/CG2579

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 55)

Asymmetric Unit (4, 55)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2MLY24Mod. Amino AcidN-DIMETHYL-LYSINE
3MSE27Mod. Amino AcidSELENOMETHIONINE
4PLM3Ligand/IonPALMITIC ACID
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1FMT-1Ligand/IonFORMIC ACID
2MLY8Mod. Amino AcidN-DIMETHYL-LYSINE
3MSE9Mod. Amino AcidSELENOMETHIONINE
4PLM1Ligand/IonPALMITIC ACID
Biological Unit 2 (3, 18)
No.NameCountTypeFull Name
1FMT-1Ligand/IonFORMIC ACID
2MLY8Mod. Amino AcidN-DIMETHYL-LYSINE
3MSE9Mod. Amino AcidSELENOMETHIONINE
4PLM1Ligand/IonPALMITIC ACID
Biological Unit 3 (4, 19)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2MLY8Mod. Amino AcidN-DIMETHYL-LYSINE
3MSE9Mod. Amino AcidSELENOMETHIONINE
4PLM1Ligand/IonPALMITIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:39 , SER A:40 , GLY A:41 , SER A:73 , THR A:136 , ILE A:138 , ARG A:151 , LEU A:244 , HIS A:247 , SER A:248 , SER A:254 , HOH A:424 , HOH A:425BINDING SITE FOR RESIDUE PLM A 275
2AC2SOFTWARETHR B:39 , SER B:40 , GLY B:41 , LEU B:72 , SER B:73 , LEU B:99 , GLY B:100 , ILE B:138 , ILE B:146 , ARG B:151 , HIS B:247 , SER B:254 , HOH B:300 , HOH B:331BINDING SITE FOR RESIDUE PLM B 275
3AC3SOFTWARETHR C:39 , SER C:40 , GLY C:41 , LEU C:72 , SER C:73 , ILE C:138 , ARG C:151 , HOH C:391 , HOH C:393BINDING SITE FOR RESIDUE PLM C 275
4AC4SOFTWARETRP C:147 , ILE C:152 , THR C:154BINDING SITE FOR RESIDUE FMT C 276

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEGVPS51482 DegV domain profile.Y2349_CORGL3-259
 
 
  3A:3-259
B:3-259
C:3-259
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEGVPS51482 DegV domain profile.Y2349_CORGL3-259
 
 
  1A:3-259
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEGVPS51482 DegV domain profile.Y2349_CORGL3-259
 
 
  1-
B:3-259
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEGVPS51482 DegV domain profile.Y2349_CORGL3-259
 
 
  1-
-
C:3-259

(-) Exons   (0, 0)

(no "Exon" information available for 3EGL)

(-) 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:264
 aligned with Y2349_CORGL | Q8NN60 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:264
                             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    
          Y2349_CORGL     - -MPVRVIVDSSACLPTHVAEDLDITVINLHVMNNGEERSTSGLSSLELAASYARQLERGGDDGVLALHISKELSSTWSAAVTAAAVFDDDSVRVVDTSSLGMAVGAAAMAAARMAKDGASLQECYDIAVDTLKRSETWIYLHRIDEIWKSGRISTATAMVSTALATRPIMRFNGGRMEIAAKTRTQSKAFAKLVELAQIRADGEPVFIAIGQNEAREAAKQLEELLRNALPEGSSFMSVDIDPTLAVHSGPGAVSVSAVFANQA 263
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee.hhh.hhhhhhhh.eeee..eeee....eeee..hhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhheeeeee...hhhhhhh.........hhhhhh...eeeee..eeeeee...hhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhh..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---DEGV  PDB: A:3-259 UniProt: 3-259                                                                                                                                                                                                                                ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3egl A   0 AmPVRVIVDSSACLPTHVAEDLDITVINLHVmNNGEERSTSGLSSLELAASYARQLERGGDDGVLALHISkELSSTWSAAVTAAAVFDDDSVRVVDTSSLGmAVGAAAmAAARmAkDGASLQECYDIAVDTLkRSETWIYLHRIDEIWkSGRISTATAmVSTALATRPImRFNGGRmEIAAkTRTQSkAFAkLVELAQIRADGEPVFIAIGQNEAREAAkQLEELLRNALPEGSSFmSVDIDPTLAVHSGPGAVSVSAVFANQA 263
                             |       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    
                             |                            31-MSE                                 70-MLY                        101-MSE  |    | |              132-MLY         148-MLY   158-MSE    169-MSE  |    |     |   |                         219-MLY          236-MSE                       
                             1-MSE                                                                                                    108-MSE| |                                                          176-MSE|     |   |                                                                        
                                                                                                                                           113-MSE                                                             181-MLY |   |                                                                        
                                                                                                                                             115-MLY                                                                 187-MLY                                                                        
                                                                                                                                                                                                                         191-MLY                                                                    

Chain B from PDB  Type:PROTEIN  Length:266
 aligned with Y2349_CORGL | Q8NN60 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:267
                               1                                                                                                                                                                                                                                                                       
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       
          Y2349_CORGL     - ---MPVRVIVDSSACLPTHVAEDLDITVINLHVMNNGEERSTSGLSSLELAASYARQLERGGDDGVLALHISKELSSTWSAAVTAAAVFDDDSVRVVDTSSLGMAVGAAAMAAARMAKDGASLQECYDIAVDTLKRSETWIYLHRIDEIWKSGRISTATAMVSTALATRPIMRFNGGRMEIAAKTRTQSKAFAKLVELAQIRADGEPVFIAIGQNEAREAAKQLEELLRNALPEGSSFMSVDIDPTLAVHSGPGAVSVSAVFANQAP 264
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.hhh.hhhhhhhh..eee..eeeee..eeeee..hhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhheeeeee...hhhhhhh...hhhhhhhhhh-....eeeee..eeeeee...hhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhh..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----DEGV  PDB: B:3-259 UniProt: 3-259                                                                                                                                                                                                                                ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3egl B  -2 SNAmPVRVIVDSSACLPTHVAEDLDITVINLHVmNNGEERSTSGLSSLELAASYARQLERGGDDGVLALHISkELSSTWSAAVTAAAVFDDDSVRVVDTSSLGmAVGAAAmAAARmAkDGASLQECYDIAVDTLkRSETWIYLHRIDEIWkSGRISTATAmVSTA-ATRPImRFNGGRmEIAAkTRTQSkAFAkLVELAQIRADGEPVFIAIGQNEAREAAkQLEELLRNALPEGSSFmSVDIDPTLAVHSGPGAVSVSAVFANQAP 264
                               |     7        17        27   |    37        47        57        67  |     77        87        97   |   107|    | 117       127    |  137       147|      157|   | |167 |     177   |   187   |   197       207       217 |     227       237       247       257       
                               1-MSE                        31-MSE                                 70-MLY                        101-MSE  |    | |              132-MLY         148-MLY   158-MSE |    |      |    |     |   |                         219-MLY          236-MSE                        
                                                                                                                                        108-MSE| |                                              164    |      |    |     |   |                                                                         
                                                                                                                                             113-MSE                                                 169-MSE  |    |     |   |                                                                         
                                                                                                                                               115-MLY                                                      176-MSE|     |   |                                                                         
                                                                                                                                                                                                                 181-MLY |   |                                                                         
                                                                                                                                                                                                                       187-MLY                                                                         
                                                                                                                                                                                                                           191-MLY                                                                     

Chain C from PDB  Type:PROTEIN  Length:263
 aligned with Y2349_CORGL | Q8NN60 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:265
                             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     
          Y2349_CORGL     - -MPVRVIVDSSACLPTHVAEDLDITVINLHVMNNGEERSTSGLSSLELAASYARQLERGGDDGVLALHISKELSSTWSAAVTAAAVFDDDSVRVVDTSSLGMAVGAAAMAAARMAKDGASLQECYDIAVDTLKRSETWIYLHRIDEIWKSGRISTATAMVSTALATRPIMRFNGGRMEIAAKTRTQSKAFAKLVELAQIRADGEPVFIAIGQNEAREAAKQLEELLRNALPEGSSFMSVDIDPTLAVHSGPGAVSVSAVFANQAP 264
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.hhh.hhhhhhhh..eee..eee..--..eee..hhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhh......eeeee....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhheeeeee...hhhhhhh...hhhhhhhh.......eeeee..eeeeee...hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhh....eeeeee.hhhhhhh.....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---DEGV  PDB: C:3-259 UniProt: 3-259                                                                                                                                                                                                                                ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3egl C   0 AmPVRVIVDSSACLPTHVAEDLDITVINLHVmNN--ERSTSGLSSLELAASYARQLERGGDDGVLALHISkELSSTWSAAVTAAAVFDDDSVRVVDTSSLGmAVGAAAmAAARmAkDGASLQECYDIAVDTLkRSETWIYLHRIDEIWkSGRISTATAmVSTALATRPImRFNGGRmEIAAkTRTQSkAFAkLVELAQIRADGEPVFIAIGQNEAREAAkQLEELLRNALPEGSSFmSVDIDPTLAVHSGPGAVSVSAVFANQAP 264
                             |       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     
                             1-MSE                        31-MSE6                                70-MLY                        101-MSE  |    | |              132-MLY         148-MLY   158-MSE    169-MSE  |    |     |   |                         219-MLY          236-MSE                        
                                                            33                                                                        108-MSE| |                                                          176-MSE|     |   |                                                                         
                                                                                                                                           113-MSE                                                             181-MLY |   |                                                                         
                                                                                                                                             115-MLY                                                                 187-MLY                                                                         
                                                                                                                                                                                                                         191-MLY                                                                     

   Legend:   → Mismatch (orange background)
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    → 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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Y2349_CORGL | Q8NN60)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.

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