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(-) Description

Title :  CRYSTAL STRUCTURE OF A GLUCARATE DEHYDRATASE RELATED PROTEIN, FROM ACTINOBACILLUS SUCCINOGENES, TARGET EFI-502312, WITH SODIUM AND SULFATE BOUND, ORDERED LOOP
 
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 :  23 Jul 12  (Deposition) - 15 Aug 12  (Release) - 15 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Enolase, Putative Glucarate Dehydratase, Enzyme Function Initiative, Efi, Structural Genomics, Lyase (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 A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, With Sodium And Sulfate Bound, Ordered Loop
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUCARATE DEHYDRATASE
    Chains: A, B, C, D
    EC Number: 4.2.1.40
    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: ASUC_1847
    Organism Scientific: ACTINOBACILLUS SUCCINOGENES
    Organism Taxid: 339671
    Strain: 130Z

 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, 19)

Asymmetric Unit (5, 19)
No.NameCountTypeFull Name
1DTT3Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2DTU1Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3GOL7Ligand/IonGLYCEROL
4NA4Ligand/IonSODIUM ION
5SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2DTU1Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3GOL6Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION
5SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2DTU-1Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3GOL1Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION
5SO42Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:23 , HIS A:28 , THR A:99 , TYR A:146 , PHE A:148 , LYS A:203 , ASN A:337 , HIS A:364 , ARG A:418 , HOH A:625 , HOH A:681 , HOH A:1103BINDING SITE FOR RESIDUE SO4 A 501
02AC2SOFTWAREASP A:231 , ASN A:233 , GLU A:256 , ASP A:257 , ASN A:285BINDING SITE FOR RESIDUE NA A 502
03AC3SOFTWAREARG A:275 , GLY A:279 , LEU A:280 , PRO A:281 , ASP A:304 , HOH A:799 , HOH A:950 , HOH A:1102BINDING SITE FOR RESIDUE GOL A 503
04AC4SOFTWARETHR A:86 , PHE A:87 , ASP A:89 , HIS A:90 , GLY D:430 , HOH D:706 , HOH D:957BINDING SITE FOR RESIDUE GOL A 504
05AC5SOFTWARECYS A:168 , LYS A:194 , HOH A:629BINDING SITE FOR RESIDUE DTU A 505
06AC6SOFTWAREASN B:23 , HIS B:28 , THR B:99 , TYR B:146 , LYS B:203 , ASN B:337 , HIS B:364 , ARG B:418 , HOH B:636 , HOH B:654 , HOH B:718BINDING SITE FOR RESIDUE SO4 B 501
07AC7SOFTWAREASP B:231 , ASN B:233 , GLU B:256 , ASP B:257 , ASN B:285BINDING SITE FOR RESIDUE NA B 502
08AC8SOFTWAREASP A:134 , GLN A:323 , MET B:80 , THR B:314 , GLN B:316 , ARG B:320 , HOH B:713 , HOH B:782 , HOH B:846BINDING SITE FOR RESIDUE GOL B 503
09AC9SOFTWAREMET A:80 , THR A:314 , ARG A:320 , GLY B:133 , ASP B:134 , GLN B:323 , HOH B:705 , HOH B:733 , HOH B:930BINDING SITE FOR RESIDUE GOL B 504
10BC1SOFTWAREARG B:275 , GLY B:279 , LEU B:280 , PRO B:281 , ASP B:304 , HOH B:700 , HOH B:992 , ARG C:276BINDING SITE FOR RESIDUE GOL B 505
11BC2SOFTWARETHR B:86 , PHE B:87 , ASP B:89 , HIS B:90 , HOH B:899 , ILE C:428 , PRO C:429 , GLY C:430 , TRP C:431 , HOH C:659 , HOH C:760BINDING SITE FOR RESIDUE GOL B 506
12BC3SOFTWARECYS B:168 , HOH B:1024 , LYS C:154BINDING SITE FOR RESIDUE DTT B 507
13BC4SOFTWAREASN C:23 , HIS C:28 , THR C:99 , TYR C:146 , LYS C:203 , ASN C:337 , HIS C:364 , ARG C:418 , HOH C:634 , HOH C:684 , HOH C:1012BINDING SITE FOR RESIDUE SO4 C 501
14BC5SOFTWAREASP C:231 , GLU C:256 , ASN C:285 , HOH C:728 , HOH C:746 , HOH C:1044BINDING SITE FOR RESIDUE NA C 502
15BC6SOFTWAREARG B:276 , GLY B:279 , HOH B:700 , ARG C:275 , GLY C:279 , LEU C:280 , PRO C:281 , ASP C:304 , HOH C:897 , HOH C:1055BINDING SITE FOR RESIDUE GOL C 503
16BC7SOFTWARECYS C:168 , GLU C:193 , HOH C:751BINDING SITE FOR RESIDUE DTT C 504
17BC8SOFTWAREASN D:23 , HIS D:28 , THR D:99 , PHE D:148 , LYS D:203 , ASN D:337 , HIS D:364 , ARG D:418 , HOH D:626 , HOH D:635 , HOH D:945BINDING SITE FOR RESIDUE SO4 D 501
18BC9SOFTWAREASP D:231 , ASN D:233 , GLU D:256 , ASN D:285 , HOH D:715 , HOH D:753 , HOH D:1072BINDING SITE FOR RESIDUE NA D 502
19CC1SOFTWARECYS D:168 , GLU D:193 , LYS D:194 , HOH D:689 , HOH D:960BINDING SITE FOR RESIDUE DTT D 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G8T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G8T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G8T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G8T)

(-) Exons   (0, 0)

(no "Exon" information available for 4G8T)

(-) 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:441
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4g8ta1 A:2-133 automated matches                                                                                                   d4g8ta2 A:134-442 automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee....ee..ee...eeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh..hhhhh.......eee..eee....hhhhh...........hhhhhhh.....hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh......ee.........hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh...........hhhhhh...........ee..eee...........hhhhhhhhhhhhhhh......hhhhhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8t A   2 STPIITEMQVIPVAGHDSMLLNLSGAHSPYFTRNIVILKDNSGNTGVGEVPGGEKIRQTLEDAKPLVIGKTLGEYKNVMNTVRQTFNDHDAGGRGLQTFDLRTTIHVVTAIEAAMLDLLGQFLGVTVASLLGDGQQRDAVEMLGYLFFIGDRKKTTLAYQNQENDPCDWYRVRHEEAMTPESVVRLAEAAYEKYGFNDFKLKGGVLDGFEEAEAVTALAKRFPDARITLDPNGAWSLDEAVKIGKQLKGVLAYAEDPCGAEQGYSGREIMAEFRRATGLPTATNMIATDWRQMGHTISLQSVDIPLADPHFWTMQGSIRVAQMCHEWGLTWGSHSNNHFDISLAMFTHVAAAAPGDITAIDTHWIWQEGNQRLTKEPFQIKGGLVEVPKKPGLGVELDMDQVMKANELYKSMGLGARDDAMAMQFLIPGWKFDNKKPCLVR 442
                                    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       391       401       411       421       431       441 


Chain B from PDB  Type:PROTEIN  Length:441
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4g8tb1 B:2-133 automated matches                                                                                                   d4g8tb2 B:134-442 automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee....ee..ee...eeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh..hhhhh.......eee..eee....hhhhh...........hhhhhhh.....hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh......ee.........hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh...........hhhhhh...........ee..eee...........hhhhhhhhhhhhhhh......hhhhhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8t B   2 STPIITEMQVIPVAGHDSMLLNLSGAHSPYFTRNIVILKDNSGNTGVGEVPGGEKIRQTLEDAKPLVIGKTLGEYKNVMNTVRQTFNDHDAGGRGLQTFDLRTTIHVVTAIEAAMLDLLGQFLGVTVASLLGDGQQRDAVEMLGYLFFIGDRKKTTLAYQNQENDPCDWYRVRHEEAMTPESVVRLAEAAYEKYGFNDFKLKGGVLDGFEEAEAVTALAKRFPDARITLDPNGAWSLDEAVKIGKQLKGVLAYAEDPCGAEQGYSGREIMAEFRRATGLPTATNMIATDWRQMGHTISLQSVDIPLADPHFWTMQGSIRVAQMCHEWGLTWGSHSNNHFDISLAMFTHVAAAAPGDITAIDTHWIWQEGNQRLTKEPFQIKGGLVEVPKKPGLGVELDMDQVMKANELYKSMGLGARDDAMAMQFLIPGWKFDNKKPCLVR 442
                                    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       391       401       411       421       431       441 


Chain C from PDB  Type:PROTEIN  Length:441
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4g8tc1 C:2-133 automated matches                                                                                                   d4g8tc2 C:134-442 automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee....ee..ee...eeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh..hhhhh.......eee..eee....hhhhh...........hhhhhhh.....hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh......ee.........hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh...........hhhhhh...........ee..eee...........hhhhhhhhhhhhhhh......hhhhhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8t C   2 STPIITEMQVIPVAGHDSMLLNLSGAHSPYFTRNIVILKDNSGNTGVGEVPGGEKIRQTLEDAKPLVIGKTLGEYKNVMNTVRQTFNDHDAGGRGLQTFDLRTTIHVVTAIEAAMLDLLGQFLGVTVASLLGDGQQRDAVEMLGYLFFIGDRKKTTLAYQNQENDPCDWYRVRHEEAMTPESVVRLAEAAYEKYGFNDFKLKGGVLDGFEEAEAVTALAKRFPDARITLDPNGAWSLDEAVKIGKQLKGVLAYAEDPCGAEQGYSGREIMAEFRRATGLPTATNMIATDWRQMGHTISLQSVDIPLADPHFWTMQGSIRVAQMCHEWGLTWGSHSNNHFDISLAMFTHVAAAAPGDITAIDTHWIWQEGNQRLTKEPFQIKGGLVEVPKKPGLGVELDMDQVMKANELYKSMGLGARDDAMAMQFLIPGWKFDNKKPCLVR 442
                                    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       391       401       411       421       431       441 


Chain D from PDB  Type:PROTEIN  Length:441
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4g8td1 D:2-133 automated matches                                                                                                   d4g8td2 D:134-442 automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee....ee..ee...eeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh..hhhhh.......eee..eee....hhhhh...........hhhhhhh.....hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh.....eee.........hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh..........hhhhhh...........ee..eee...........hhhhhhhhhhhhhhh......hhhhhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8t D   2 STPIITEMQVIPVAGHDSMLLNLSGAHSPYFTRNIVILKDNSGNTGVGEVPGGEKIRQTLEDAKPLVIGKTLGEYKNVMNTVRQTFNDHDAGGRGLQTFDLRTTIHVVTAIEAAMLDLLGQFLGVTVASLLGDGQQRDAVEMLGYLFFIGDRKKTTLAYQNQENDPCDWYRVRHEEAMTPESVVRLAEAAYEKYGFNDFKLKGGVLDGFEEAEAVTALAKRFPDARITLDPNGAWSLDEAVKIGKQLKGVLAYAEDPCGAEQGYSGREIMAEFRRATGLPTATNMIATDWRQMGHTISLQSVDIPLADPHFWTMQGSIRVAQMCHEWGLTWGSHSNNHFDISLAMFTHVAAAAPGDITAIDTHWIWQEGNQRLTKEPFQIKGGLVEVPKKPGLGVELDMDQVMKANELYKSMGLGARDDAMAMQFLIPGWKFDNKKPCLVR 442
                                    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       391       401       411       421       431       441
   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  (2, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G8T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G8T)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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