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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ENOLASE FAMILY MEMBER FROM VIBRIO HARVEYI (EFI-TARGET 501692) WITH HOMOLOGY TO MANNONATE DEHYDRATASE, WITH MG, HEPES, AND ETHYLENE GLYCOL BOUND (ORDERED LOOPS, SPACE GROUP C2221)
 
Authors :  M. W. Vetting, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wa S. Sojitra, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, J. A. Gerlt, S. C. Almo, Function Initiative (Efi)
Date :  06 Aug 12  (Deposition) - 05 Sep 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Enolase, Putative Mannonate Dehydratase, Enzyme Function Initiative, Efi, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Vetting, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wasserman, S. Sojitra, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (Efi)
Crystal Structure Of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) With Homology To Mannonate Dehydratase, With Mg, Hepes, And Ethylene Glycol Bound (Ordered Loops, Space Group C2221)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VME_00770
    Organism Scientific: VIBRIO HARVEYI
    Organism Taxid: 673519
    Strain: 1DA3

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 30)

Asymmetric Unit (5, 30)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2EDO15Ligand/Ion1,2-ETHANEDIOL
3EPE4Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4GOL2Ligand/IonGLYCEROL
5MG5Ligand/IonMAGNESIUM ION
Biological Unit 1 (3, 42)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO30Ligand/Ion1,2-ETHANEDIOL
3EPE8Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4GOL4Ligand/IonGLYCEROL
5MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:247 , ASN B:247 , ASN C:247 , ASN D:247 , HOH D:501 , HOH D:502BINDING SITE FOR RESIDUE MG A 401
02AC2SOFTWAREASP A:205 , GLU A:231 , GLU A:257 , HOH A:501 , HOH A:502 , HOH A:925BINDING SITE FOR RESIDUE MG A 402
03AC3SOFTWAREARG A:18 , HIS A:19 , GLN A:41 , ARG A:382 , HIS A:384 , TRP A:386 , HOH A:651 , HOH A:762 , HOH A:765 , HOH A:815BINDING SITE FOR RESIDUE EPE A 403
04AC4SOFTWAREARG A:118 , ASP A:119 , ASP C:69 , HOH C:862 , THR D:171 , GLY D:394BINDING SITE FOR RESIDUE EDO A 404
05AC5SOFTWAREPRO A:170 , GLN A:172 , GLY A:173 , TYR A:175BINDING SITE FOR RESIDUE EDO A 405
06AC6SOFTWAREGLN A:224 , ASN A:226 , SER A:250 , HOH A:677 , GLN D:221BINDING SITE FOR RESIDUE EDO A 406
07AC7SOFTWAREGLN A:41 , GLN A:42 , TRP A:80 , HIS A:307 , PRO A:309 , ASP A:311 , HOH A:921BINDING SITE FOR RESIDUE EDO A 407
08AC8SOFTWAREPRO A:383 , HIS A:384 , GLU A:385 , HOH A:615BINDING SITE FOR RESIDUE CL A 408
09AC9SOFTWAREASP B:205 , GLU B:231 , GLU B:257 , HOH B:501 , HOH B:502 , HOH B:906BINDING SITE FOR RESIDUE MG B 401
10BC1SOFTWAREARG B:18 , HIS B:19 , GLN B:41 , ARG B:209 , ARG B:382 , HIS B:384 , TRP B:386 , HOH B:725 , HOH B:734 , HOH B:803 , HOH B:809BINDING SITE FOR RESIDUE EPE B 402
11BC2SOFTWAREASN B:226 , SER B:250 , HOH B:632 , GLN C:221BINDING SITE FOR RESIDUE EDO B 403
12BC3SOFTWAREASP B:69 , THR B:171 , ARG B:390 , GLY B:394 , HOH B:692 , ARG D:118 , ASP D:119BINDING SITE FOR RESIDUE EDO B 404
13BC4SOFTWAREGLN B:41 , GLN B:42 , TYR B:79 , TRP B:80 , HIS B:307 , PRO B:309 , ASP B:311 , HOH B:802BINDING SITE FOR RESIDUE EDO B 405
14BC5SOFTWARELYS B:198 , PHE B:200BINDING SITE FOR RESIDUE EDO B 406
15BC6SOFTWAREASP C:205 , GLU C:231 , GLU C:257 , HOH C:501 , HOH C:502 , HOH C:925BINDING SITE FOR RESIDUE MG C 401
16BC7SOFTWAREGLN C:41 , GLN C:42 , HIS C:207 , GLU C:257 , HIS C:307 , PRO C:309 , ASP C:311 , TYR D:79 , TRP D:80BINDING SITE FOR RESIDUE GOL C 402
17BC8SOFTWAREARG C:18 , HIS C:19 , GLN C:41 , ARG C:209 , ARG C:382 , HIS C:384 , TRP C:386 , HOH C:678 , HOH C:734 , HOH C:814BINDING SITE FOR RESIDUE EPE C 403
18BC9SOFTWAREPRO B:227 , PHE B:228 , ASN C:213 , GLN C:214 , GLN C:217 , HOH C:552 , HOH C:579 , HOH C:788BINDING SITE FOR RESIDUE EDO C 404
19CC1SOFTWAREARG B:118 , ASP B:119 , THR C:171 , ARG C:390 , GLY C:394 , ASP D:69 , HOH D:655BINDING SITE FOR RESIDUE EDO C 405
20CC2SOFTWAREGLN A:221 , GLU C:223 , GLN C:224 , ASN C:226 , SER C:250 , HOH C:849 , HOH C:863 , HOH C:875BINDING SITE FOR RESIDUE EDO C 406
21CC3SOFTWAREPRO C:161 , GLN C:172 , GLY C:173BINDING SITE FOR RESIDUE EDO C 407
22CC4SOFTWAREASN C:82 , GLY C:83 , PRO C:84 , VAL C:85 , ILE C:86 , ASN D:82 , GLY D:83 , PRO D:84 , VAL D:85 , ILE D:86BINDING SITE FOR RESIDUE CL C 408
23CC5SOFTWAREPRO C:383 , HIS C:384 , GLU C:385 , HOH C:683BINDING SITE FOR RESIDUE CL C 409
24CC6SOFTWARELEU A:391 , PRO A:392 , ASP A:393 , HOH C:720BINDING SITE FOR RESIDUE CL C 410
25CC7SOFTWAREASP D:205 , GLU D:231 , GLU D:257 , HOH D:503 , HOH D:504 , HOH D:928BINDING SITE FOR RESIDUE MG D 401
26CC8SOFTWARETRP C:80 , GLN D:41 , GLN D:42 , HIS D:207 , GLU D:257 , HIS D:307 , PRO D:309 , ASP D:311BINDING SITE FOR RESIDUE GOL D 402
27CC9SOFTWAREARG D:18 , HIS D:19 , GLN D:41 , ARG D:209 , ARG D:382 , HIS D:384 , TRP D:386 , HOH D:623 , HOH D:657 , HOH D:857BINDING SITE FOR RESIDUE EPE D 403
28DC1SOFTWAREASN B:213 , GLN B:214 , GLN B:217 , HOH B:508 , HOH B:529 , HOH B:756 , PRO D:227BINDING SITE FOR RESIDUE EDO D 404
29DC2SOFTWAREPRO D:170 , THR D:171 , GLN D:172 , GLY D:173 , TYR D:175BINDING SITE FOR RESIDUE EDO D 405
30DC3SOFTWAREPRO A:227 , PHE A:228 , ASN D:213 , GLN D:214 , GLN D:217 , HOH D:620 , HOH D:680BINDING SITE FOR RESIDUE EDO D 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GGH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GGH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GGH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GGH)

(-) Exons   (0, 0)

(no "Exon" information available for 4GGH)

(-) 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:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee......eeeeeeee....eeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......eeeeeeeee.hhhhhhhhhhhhhhh...eeeeee...................ee.hhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhh.....eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhh..ee........hhhhhhhhhhhhhhh.....ee....hhhhhhhh.........ee............hhhhhhh.......hhhh.ee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ggh A   3 KNTISNIECVITKPDRHNLITVIVETESGVTGYGCATFQQRPLAVKTMVDEYLKPLLIGKDANNIEDLWQMMMVNAYWRNGPVINNAISGVDMALWDIKAKIANMPLHQLFGGKSRDAIQVYTHATSDTMEGLYEQVDKYLEQGYQHIRCQLGFYGGVPENIQTAQNPTQGSYYDQDQYIENTVEMFKNLREKYGKQFHILHDVHERLFPNQAIQFAKQIEQYNPFFIEDILPPSQTEWLDNIRNQSSVSLALGELFNNPEEWKALIINRRVDFIRCHVSQIGGITPALKLGHFCESFGVRIAWHCPPDMTPIGAAVNTHLNVHLHNAAIQEHVEYKANTQRVFPNAAEPINGYLYASEIAGIGVEMDREAAQDFPVEYRPHEWTQSRLPDGSIHTP 399
                                    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       392       


Chain B from PDB  Type:PROTEIN  Length:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee......eeeeeeee.....eeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......eeeeeeeee.hhhhhhhhhhhhhhhh..eeeeee...................ee.hhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhh.....eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh....eee....hhhhhhhh.........ee............hhhhhh........hhhh.ee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ggh B   3 KNTISNIECVITKPDRHNLITVIVETESGVTGYGCATFQQRPLAVKTMVDEYLKPLLIGKDANNIEDLWQMMMVNAYWRNGPVINNAISGVDMALWDIKAKIANMPLHQLFGGKSRDAIQVYTHATSDTMEGLYEQVDKYLEQGYQHIRCQLGFYGGVPENIQTAQNPTQGSYYDQDQYIENTVEMFKNLREKYGKQFHILHDVHERLFPNQAIQFAKQIEQYNPFFIEDILPPSQTEWLDNIRNQSSVSLALGELFNNPEEWKALIINRRVDFIRCHVSQIGGITPALKLGHFCESFGVRIAWHCPPDMTPIGAAVNTHLNVHLHNAAIQEHVEYKANTQRVFPNAAEPINGYLYASEIAGIGVEMDREAAQDFPVEYRPHEWTQSRLPDGSIHTP 399
                                    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       392       


Chain C from PDB  Type:PROTEIN  Length:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee......eeeeeeee....eeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh......eeeeeeeee.hhhhhhhhhhhhhhh...eeeeee...................ee.hhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhh.....eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhh..ee........hhhhhhhhhhhhhhh.....ee....hhhhhhhh.........ee............hhhhhhh.......hhhh.ee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ggh C   3 KNTISNIECVITKPDRHNLITVIVETESGVTGYGCATFQQRPLAVKTMVDEYLKPLLIGKDANNIEDLWQMMMVNAYWRNGPVINNAISGVDMALWDIKAKIANMPLHQLFGGKSRDAIQVYTHATSDTMEGLYEQVDKYLEQGYQHIRCQLGFYGGVPENIQTAQNPTQGSYYDQDQYIENTVEMFKNLREKYGKQFHILHDVHERLFPNQAIQFAKQIEQYNPFFIEDILPPSQTEWLDNIRNQSSVSLALGELFNNPEEWKALIINRRVDFIRCHVSQIGGITPALKLGHFCESFGVRIAWHCPPDMTPIGAAVNTHLNVHLHNAAIQEHVEYKANTQRVFPNAAEPINGYLYASEIAGIGVEMDREAAQDFPVEYRPHEWTQSRLPDGSIHTP 399
                                    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       392       


Chain D from PDB  Type:PROTEIN  Length:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee......eeeeeeee....eeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......eeeeeeeee.hhhhhhhhhhhhhhh...eeeeee...................ee.hhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhh.....eee.....hhhhhhhhhhh....ee..hhhhh.hhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh.....ee....hhhhhhhh.........ee............hhhhhhh.......hhhh.ee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ggh D   3 KNTISNIECVITKPDRHNLITVIVETESGVTGYGCATFQQRPLAVKTMVDEYLKPLLIGKDANNIEDLWQMMMVNAYWRNGPVINNAISGVDMALWDIKAKIANMPLHQLFGGKSRDAIQVYTHATSDTMEGLYEQVDKYLEQGYQHIRCQLGFYGGVPENIQTAQNPTQGSYYDQDQYIENTVEMFKNLREKYGKQFHILHDVHERLFPNQAIQFAKQIEQYNPFFIEDILPPSQTEWLDNIRNQSSVSLALGELFNNPEEWKALIINRRVDFIRCHVSQIGGITPALKLGHFCESFGVRIAWHCPPDMTPIGAAVNTHLNVHLHNAAIQEHVEYKANTQRVFPNAAEPINGYLYASEIAGIGVEMDREAAQDFPVEYRPHEWTQSRLPDGSIHTP 399
                                    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       392
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(no "CATH Domain" information available for 4GGH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GGH)

(-) Gene Ontology  (5, 5)

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        IMAND_VIBH1 | D0X4R4: 4gir 4gis

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