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(-) Description

Title :  CRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS COMPLEXED WITH MAGNESIUM
 
Authors :  A. A. Fedorov, E. V. Fedorov, A. Sakai, C. Millikin, J. A. Gerlt, S. C. Alm
Date :  29 Sep 12  (Deposition) - 30 Oct 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (8x)
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, C. Millikin, J. A. Gerlt, S. C. Almo
Crystal Structure Of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed With Magnesium
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ISOMERASE/LACTONIZING ENZYME
    Chains: A
    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

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (8x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2MG3Ligand/IonMAGNESIUM ION
3MSE11Mod. Amino AcidSELENOMETHIONINE
4NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 22)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3MSE22Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 88)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3MSE88Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:163 , ARG A:330 , LEU A:349 , MSE A:353BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWARELYS A:347 , PHE A:373 , THR A:374BINDING SITE FOR RESIDUE CL A 402
3AC3SOFTWAREPRO A:59 , HIS A:60 , HOH A:882BINDING SITE FOR RESIDUE CL A 403
4AC4SOFTWAREHOH A:516 , HOH A:591BINDING SITE FOR RESIDUE CL A 404
5AC5SOFTWAREASP A:206 , GLU A:232 , GLU A:258 , HOH A:963 , HOH A:964 , HOH A:966BINDING SITE FOR RESIDUE MG A 405
6AC6SOFTWARESER A:247 , LEU A:250 , HOH A:514 , HOH A:721 , HOH A:786 , HOH A:972BINDING SITE FOR RESIDUE MG A 406
7AC7SOFTWAREHIS A:343 , LEU A:346 , HOH A:752 , HOH A:973 , HOH A:994BINDING SITE FOR RESIDUE MG A 407
8AC8SOFTWARESER A:247 , ASP A:248 , GLY A:274 , HOH A:551 , HOH A:722 , HOH A:724 , HOH A:773BINDING SITE FOR RESIDUE NA A 408
9AC9SOFTWAREASP A:206 , ALA A:207 , HIS A:209 , GLU A:232 , GLU A:233BINDING SITE FOR RESIDUE NA A 409

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HCD)

(-) 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 d4hcda1 A:-1-126 automated matches                                                                                              d4hcda2 A:127-382 automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee....eeeeeehhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......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
                 4hcd 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    
                              |                                  37-MSE                                                                                              138-MSE                             174-MSE    185-MSE            204-MSE                        235-MSE                                                      296-MSE 304-MSE   314-MSE                                353-MSE                         
                              1-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

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 4HCD)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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UniProtKB/TrEMBL
        Q7CSI0_AGRFC | Q7CSI0: 1rvk 4hch 4hcl 4mmw

(-) Related Entries Specified in the PDB File

1rvk 4hch 4hcl 4hcm