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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE ISOMERASE FROM SINORHIZOBIUM MELILOTI
 
Authors :  U. A. Ramagopal, R. Toro, M. Dickey, C. Logan, C. Groshong, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Struct Genomics (Nysgxrc)
Date :  30 Apr 07  (Deposition) - 22 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Structural Genomics, Isomerase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. A. Ramagopal, R. Toro, M. Dickey, C. Logan, C. Groshong, J. M. Sauder S. K. Burley, S. C. Almo
Crystal Structure Of Putative Isomerase From Sinorhizobium Meliloti.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE ISOMERASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: BC-PSGX4(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RA0374, SMA0708
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 266834
    Strain: 1021

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 36)

Asymmetric Unit (1, 36)
No.NameCountTypeFull Name
1MSE36Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 72)
No.NameCountTypeFull Name
1MSE72Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2PPG)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PPG)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:371 -Pro A:372
2Gly C:23 -Lys C:24
3Gly D:23 -Lys D:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PPG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PPG)

(-) Exons   (0, 0)

(no "Exon" information available for 2PPG)

(-) 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:387
 aligned with Q92ZS5_RHIME | Q92ZS5 from UniProtKB/TrEMBL  Length:389

    Alignment length:387
                                    12        22        32        42        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       342       352       362       372       382       
         Q92ZS5_RHIME     3 DRVKKIESFTLTLPRETPYLGKPRPGEEPNGRGYLVRKANRTVYPTFDRSVLVRIETENGAVGWGETYGLVAPRATMEIIDDLLADFTIGRDPFDAAAIHDDLYDLMRVRGYTGGFYVDALAAIDIALWDLAGKLAGLPVCKLLGGQRRDRIAAYISGLPEDTRAKRAELAAAWQAKGFSSFKFASPVADDGVAKEMEILRERLGPAVRIACDMHWAHTASEAVALIKAMEPHGLWFAEAPVRTEDIDGLARVAASVSTAIAVGEEWRTVHDMVPRVARRALAIVQPEMGHKGITQFMRIGAYAHVHHIKVIPHATIGAGIFLAASLQASAALANVDCHEFQHSIFEPNRRLLVGDMDCLNGEYVVPTGPGLGVEPSKEAQGLLKKH 389
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ppgA01 A:3-148,A:370-389 Enolase-like, N-terminal domain                                                                                         2ppgA02 A:149-369 Enolase superfamily                                                                                                                                                                                        2ppgA01              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee....................eee.hhhh.eee..eeeeeeeeee....eeeeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.......eeeeeee.....hhhhhhhhhhhhhhh...eeeee.hhh..hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh..eeee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhh..ee........hhhhhhhhhhhhhh.....eeehhhhhh.hhh.eee..eee..eee........eeehhhhhhhhee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ppg A   3 DRVKKIESFTLTLPRETPYLGKPRPGEEPNGRGYLVRKANRTVYPTFDRSVLVRIETENGAVGWGETYGLVAPRATmEIIDDLLADFTIGRDPFDAAAIHDDLYDLmRVRGYTGGFYVDALAAIDIALWDLAGKLAGLPVCKLLGGQRRDRIAAYISGLPEDTRAKRAELAAAWQAKGFSSFKFASPVADDGVAKEmEILRERLGPAVRIACDmHWAHTASEAVALIKAmEPHGLWFAEAPVRTEDIDGLARVAASVSTAIAVGEEWRTVHDmVPRVARRALAIVQPEmGHKGITQFmRIGAYAHVHHIKVIPHATIGAGIFLAASLQASAALANVDCHEFQHSIFEPNRRLLVGDmDCLNGEYVVPTGPGLGVEPSKEAQGLLKKH 389
                                    12        22        32        42        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       342       352      |362       372       382       
                                                                                                       79-MSE                       109-MSE                                                                                   199-MSE          216-MSE         232-MSE                                    275-MSE         291-MSE  300-MSE                                                    359-MSE                          


Chain B from PDB  Type:PROTEIN  Length:370
 aligned with Q92ZS5_RHIME | Q92ZS5 from UniProtKB/TrEMBL  Length:389

    Alignment length:388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381        
         Q92ZS5_RHIME     2 SDRVKKIESFTLTLPRETPYLGKPRPGEEPNGRGYLVRKANRTVYPTFDRSVLVRIETENGAVGWGETYGLVAPRATMEIIDDLLADFTIGRDPFDAAAIHDDLYDLMRVRGYTGGFYVDALAAIDIALWDLAGKLAGLPVCKLLGGQRRDRIAAYISGLPEDTRAKRAELAAAWQAKGFSSFKFASPVADDGVAKEMEILRERLGPAVRIACDMHWAHTASEAVALIKAMEPHGLWFAEAPVRTEDIDGLARVAASVSTAIAVGEEWRTVHDMVPRVARRALAIVQPEMGHKGITQFMRIGAYAHVHHIKVIPHATIGAGIFLAASLQASAALANVDCHEFQHSIFEPNRRLLVGDMDCLNGEYVVPTGPGLGVEPSKEAQGLLKKH 389
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ppgB01 B:2-148,             B:370-389 Enolase-like, N-terminal domain                                                                             2ppgB02 B:149-369 Enolase superfamily                                                                                                                                                                                        2ppgB01              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee.-------------.....eee......eee.eeeeeeeeeee....eeeeeee...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeee.....hhhhhhhhhhhhhh....eeeee..-----hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh...eeeee......hhhhhhhhhh....eeee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhh..ee........hhhhhhhhhhhhhh.....eeehhhhhhhhhh.eee..eee..eee........eeehhhhhhhhee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ppg B   2 SDRVKKIESFTLTLPR-------------PNGRGYLVRKANRTVYPTFDRSVLVRIETENGAVGWGETYGLVAPRATmEIIDDLLADFTIGRDPFDAAAIHDDLYDLmRVRGYTGGFYVDALAAIDIALWDLAGKLAGLPVCKLLGGQRRDRIAAYISGLPEDTRAKRAELAAAWQAKGFSSFKFASP-----VAKEmEILRERLGPAVRIACDmHWAHTASEAVALIKAmEPHGLWFAEAPVRTEDIDGLARVAASVSTAIAVGEEWRTVHDmVPRVARRALAIVQPEmGHKGITQFmRIGAYAHVHHIKVIPHATIGAGIFLAASLQASAALANVDCHEFQHSIFEPNRRLLVGDmDCLNGEYVVPTGPGLGVEPSKEAQGLLKKH 389
                                    11     |   -        31        41        51        61        71       |81        91       101       111       121       131       141       151       161       171       181       | -   |   201       211    |  221       231|      241       251       261       271   |   281       291       301       311       321       331       341       351       361       371       381        
                                          17            31                                              79-MSE                       109-MSE                                                                         189   195   |              216-MSE         232-MSE                                    275-MSE         291-MSE  300-MSE                                                    359-MSE                          
                                                                                                                                                                                                                               199-MSE                                                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:382
 aligned with Q92ZS5_RHIME | Q92ZS5 from UniProtKB/TrEMBL  Length:389

    Alignment length:389
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380         
         Q92ZS5_RHIME     1 MSDRVKKIESFTLTLPRETPYLGKPRPGEEPNGRGYLVRKANRTVYPTFDRSVLVRIETENGAVGWGETYGLVAPRATMEIIDDLLADFTIGRDPFDAAAIHDDLYDLMRVRGYTGGFYVDALAAIDIALWDLAGKLAGLPVCKLLGGQRRDRIAAYISGLPEDTRAKRAELAAAWQAKGFSSFKFASPVADDGVAKEMEILRERLGPAVRIACDMHWAHTASEAVALIKAMEPHGLWFAEAPVRTEDIDGLARVAASVSTAIAVGEEWRTVHDMVPRVARRALAIVQPEMGHKGITQFMRIGAYAHVHHIKVIPHATIGAGIFLAASLQASAALANVDCHEFQHSIFEPNRRLLVGDMDCLNGEYVVPTGPGLGVEPSKEAQGLLKKH 389
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ppgC01 C:1-148,C:370-389 Enolase-like, N-terminal domain                                                                                           2ppgC02 C:149-369 Enolase superfamily                                                                                                                                                                                        2ppgC01              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee....................eeee....eeee..eeeeeeeeee....eeeeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeee......hhhhhhhhhhhhhh....eeeee.hhh.hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhh..eeee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhh..ee........hhhhhhhhhhhhhh.....eee.-------...ee...eee..eee.........eehhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ppg C   1 LSDRVKKIESFTLTLPRETPYLGKPRPGEEPNGRGYLVRKANRTVYPTFDRSVLVRIETENGAVGWGETYGLVAPRATmEIIDDLLADFTIGRDPFDAAAIHDDLYDLmRVRGYTGGFYVDALAAIDIALWDLAGKLAGLPVCKLLGGQRRDRIAAYISGLPEDTRAKRAELAAAWQAKGFSSFKFASPVADDGVAKEmEILRERLGPAVRIACDmHWAHTASEAVALIKAmEPHGLWFAEAPVRTEDIDGLARVAASVSTAIAVGEEWRTVHDmVPRVARRALAIVQPEmGHKGITQFmRIGAYAHVHHIKVIPHATIGAGIFLAASLQASAALANVDCHEFQ-------RRLLVGDmDCLNGEYVVPTGPGLGVEPSKEAQGLLKKH 389
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     | 220       230 |     240       250       260       270    |  280       290|      300       310       320       330       340   |     - |     360       370       380         
                                                                                                         79-MSE                       109-MSE                                                                                   199-MSE          216-MSE         232-MSE                                    275-MSE         291-MSE  300-MSE                                     344     352      |                              
                                                                                                                                                                                                                                                                                                                                                                                                359-MSE                          


Chain D from PDB  Type:PROTEIN  Length:383
 aligned with Q92ZS5_RHIME | Q92ZS5 from UniProtKB/TrEMBL  Length:389

    Alignment length:388
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381        
         Q92ZS5_RHIME     2 SDRVKKIESFTLTLPRETPYLGKPRPGEEPNGRGYLVRKANRTVYPTFDRSVLVRIETENGAVGWGETYGLVAPRATMEIIDDLLADFTIGRDPFDAAAIHDDLYDLMRVRGYTGGFYVDALAAIDIALWDLAGKLAGLPVCKLLGGQRRDRIAAYISGLPEDTRAKRAELAAAWQAKGFSSFKFASPVADDGVAKEMEILRERLGPAVRIACDMHWAHTASEAVALIKAMEPHGLWFAEAPVRTEDIDGLARVAASVSTAIAVGEEWRTVHDMVPRVARRALAIVQPEMGHKGITQFMRIGAYAHVHHIKVIPHATIGAGIFLAASLQASAALANVDCHEFQHSIFEPNRRLLVGDMDCLNGEYVVPTGPGLGVEPSKEAQGLLKKH 389
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ppgD01 D:2-148,     D:370-389 Enolase-like, N-terminal domain                                                                                     2ppgD02 D:149-369 Enolase superfamily                                                                                                                                                                                        2ppgD01              CATH domains
           Pfam domains (1) --------------------------------------MR_MLE_N-2ppgD01 D:40-147                                                                                   ----------------------------------------------------------------------------------------------------------------------MR_MLE_C-2ppgD05 D:266-377                                                                                      ------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------MR_MLE_N-2ppgD02 D:40-147                                                                                   ----------------------------------------------------------------------------------------------------------------------MR_MLE_C-2ppgD06 D:266-377                                                                                      ------------ Pfam domains (2)
           Pfam domains (3) --------------------------------------MR_MLE_N-2ppgD03 D:40-147                                                                                   ----------------------------------------------------------------------------------------------------------------------MR_MLE_C-2ppgD07 D:266-377                                                                                      ------------ Pfam domains (3)
           Pfam domains (4) --------------------------------------MR_MLE_N-2ppgD04 D:40-147                                                                                   ----------------------------------------------------------------------------------------------------------------------MR_MLE_C-2ppgD08 D:266-377                                                                                      ------------ Pfam domains (4)
         Sec.struct. author ...eeeeeeeeee...-----.............eee......eee...eeeeeeeee....eeeeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeee........hhhhhhhhhhh....eeeee......hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh..eeee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhh..ee........hhhhhhhhhhhhhh.....eee....hhhhh..eee..ee...eee........eeehhhhhhhhee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ppg D   2 SDRVKKIESFTLTLPR-----GKPRPGEEPNGRGYLVRKANRTVYPTFDRSVLVRIETENGAVGWGETYGLVAPRATmEIIDDLLADFTIGRDPFDAAAIHDDLYDLmRVRGYTGGFYVDALAAIDIALWDLAGKLAGLPVCKLLGGQRRDRIAAYISGLPEDTRAKRAELAAAWQAKGFSSFKFASPVADDGVAKEmEILRERLGPAVRIACDmHWAHTASEAVALIKAmEPHGLWFAEAPVRTEDIDGLARVAASVSTAIAVGEEWRTVHDmVPRVARRALAIVQPEmGHKGITQFmRIGAYAHVHHIKVIPHATIGAGIFLAASLQASAALANVDCHEFQHSIFEPNRRLLVGDmDCLNGEYVVPTGPGLGVEPSKEAQGLLKKH 389
                                    11     |   - |      31        41        51        61        71       |81        91       101       111       121       131       141       151       161       171       181       191       201       211    |  221       231|      241       251       261       271   |   281       291       301       311       321       331       341       351       361       371       381        
                                          17    23                                                      79-MSE                       109-MSE                                                                                   199-MSE          216-MSE         232-MSE                                    275-MSE         291-MSE  300-MSE                                                    359-MSE
   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 2PPG)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: Enolase_N (69)
(-)
Clan: Enolase_TIM (82)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q92ZS5_RHIME | Q92ZS5)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009063    cellular amino acid catabolic process    The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
    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.

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        Q92ZS5_RHIME | Q92ZS5: 4h1z

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