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(-) Description

Title :  CRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS COMPLEXED WITH MAGNESIUM AND L-LYXAROHYDROXAMATE
 
Authors :  A. A. Fedorov, E. V. Fedorov, A. Sakai, J. A. Gerlt, S. C. Almo
Date :  30 Sep 12  (Deposition) - 24 Oct 12  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  A,B  (4x)
Keywords :  Enolase Fold, D-Glucarate Dehydratase, D-Glucarate, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, A. Sakai, J. A. Gerlt, S. C. Almo
Crystal Structure Of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed With Magnesium And L-Lyxarohydroxamate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ISOMERASE/LACTONIZING ENZYME
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ATU3453
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 176299
    Strain: C58 / ATCC 33970

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A (1x)B (1x)
Biological Unit 2 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1LLH2Ligand/Ion(2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYDROXYAMINO)-5-OXOPENTANOIC ACID
2MG4Ligand/IonMAGNESIUM ION
3PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1LLH1Ligand/Ion(2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYDROXYAMINO)-5-OXOPENTANOIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1LLH8Ligand/Ion(2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYDROXYAMINO)-5-OXOPENTANOIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3PG44Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:206 , GLU A:232 , GLU A:258 , LLH A:403 , HOH A:767BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWARESER A:247 , LEU A:250 , HOH A:507 , HOH A:513 , HOH A:517 , HOH A:783BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWAREHIS A:24 , LYS A:169 , HIS A:171 , ASP A:206 , HIS A:209 , GLU A:232 , GLU A:258 , ARG A:280 , HIS A:309 , GLU A:329 , MG A:401 , HOH A:633 , HOH A:635 , HOH A:767 , ARG B:90BINDING SITE FOR RESIDUE LLH A 403
4AC4SOFTWARESER A:259 , ALA A:260 , ALA A:261 , GLN B:238 , ALA B:261BINDING SITE FOR RESIDUE PG4 A 404
5AC5SOFTWAREASP B:206 , GLU B:232 , GLU B:258 , LLH B:403 , HOH B:770BINDING SITE FOR RESIDUE MG B 401
6AC6SOFTWARESER B:247 , LEU B:250 , HOH B:512 , HOH B:515 , HOH B:517 , HOH B:788BINDING SITE FOR RESIDUE MG B 402
7AC7SOFTWAREARG A:90 , HIS B:24 , CYS B:139 , LYS B:169 , HIS B:171 , MET B:174 , ASP B:206 , HIS B:209 , GLU B:232 , GLU B:258 , ARG B:280 , HIS B:309 , GLU B:329 , MG B:401 , HOH B:599 , HOH B:627 , HOH B:770BINDING SITE FOR RESIDUE LLH B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Pro A:175 -Pro A:176
2Ala A:180 -Pro A:181
3Gly A:256 -Pro A:257
4Gly A:331 -Leu A:332
5Pro B:175 -Pro B:176
6Ala B:180 -Pro B:181
7Gly B:256 -Pro B:257
8Gly B:331 -Leu B:332

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HCL)

(-) 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:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4hcla1 A:-1-126 automated matches                                                                                              d4hcla2 A:127-382 automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee....eeeeeehhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eeeeeeee...........hhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh....eee......hhhhhhhhhhhh...eee.....hhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhh.....eeeeee....hhhhh...............eee...........hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hcl A  -1 SHMIITDVEVRVFRTTTRRHSDSAGHAHPGPAHQVEQAMLTVRTEDGQEGHSFTAPEIVRPHVIEKFVKKVLIGEDHRDRERLWQDLAHWQRGSAAQLTDRTLAVVDCALWDLAGRSLGQPVYKLIGGYRDKVLAYGSIMCGDELEGGLATPEDYGRFAETLVKRGYKGIKLHTWMPPVSWAPDVKMDLKACAAVREAVGPDIRLMIDAFHWYSRTDALALGRGLEKLGFDWIEEPMDEQSLSSYKWLSDNLDIPVVGPESAAGKHWHRAEWIKAGACDILRTGVNDVGGITPALKTMHLAEAFGMECEVHGNTAMNLHVVAATKNCRWYERGLLHPFLEYDDGHDYLKSLSDPMDRDGFVHVPDRPGLGEDIDFTFIDNNRVR 382
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378    


Chain B from PDB  Type:PROTEIN  Length:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4hclb1 B:-1-126 automated matches                                                                                              d4hclb2 B:127-382 automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee....eeeeeehhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eeeeeeee...........hhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh....eee......hhhhhhhhhhhh...eee.....hhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhh.....eeeeee....hhhhh...............eee...........hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hcl B  -1 SHMIITDVEVRVFRTTTRRHSDSAGHAHPGPAHQVEQAMLTVRTEDGQEGHSFTAPEIVRPHVIEKFVKKVLIGEDHRDRERLWQDLAHWQRGSAAQLTDRTLAVVDCALWDLAGRSLGQPVYKLIGGYRDKVLAYGSIMCGDELEGGLATPEDYGRFAETLVKRGYKGIKLHTWMPPVSWAPDVKMDLKACAAVREAVGPDIRLMIDAFHWYSRTDALALGRGLEKLGFDWIEEPMDEQSLSSYKWLSDNLDIPVVGPESAAGKHWHRAEWIKAGACDILRTGVNDVGGITPALKTMHLAEAFGMECEVHGNTAMNLHVVAATKNCRWYERGLLHPFLEYDDGHDYLKSLSDPMDRDGFVHVPDRPGLGEDIDFTFIDNNRVR 382
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 4)

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 4HCL)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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        Q7CSI0_AGRFC | Q7CSI0: 1rvk 4hcd 4hch 4mmw

(-) Related Entries Specified in the PDB File

1rvk 4hcd 4hch 4hcm