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(-) Description

Title :  STRUCTURE OF ICDH-1 FROM M.TUBERCULOSIS COMPLEXED WITH NADPH & MN2+
 
Authors :  S. Hazra, J. Blanchard
Date :  01 Oct 12  (Deposition) - 27 Feb 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Icdh-1, Rossmann Fold, Dehydrogenase, Nadp Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. E. Quartararo, S. Hazra, T. Hadi, J. S. Blanchard
Structural, Kinetic And Chemical Mechanism Of Isocitrate Dehydrogenase-1 From Mycobacterium Tuberculosis.
Biochemistry V. 52 1765 2013
PubMed-ID: 23409873  |  Reference-DOI: 10.1021/BI400037W

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP]
    Chains: A, B
    EC Number: 1.1.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ICD, RV3339C, MT3442, MTV016.39C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: IDH, IDP, NADP(+)-SPECIFIC ICDH, OXALOSUCCINATE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MN2Ligand/IonMANGANESE (II) ION
3NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:278 , ASP A:282 , HOH A:708 , ASP B:255 , HOH B:604BINDING SITE FOR RESIDUE MN A 501
2AC2SOFTWARELYS A:75 , ALA A:77 , THR A:78 , ILE A:79 , THR A:80 , ARG A:85 , GLU A:309 , HIS A:312 , GLY A:313 , THR A:314 , VAL A:315 , THR A:316 , ARG A:317 , HIS A:318 , THR A:330 , ASN A:331 , HOH A:608 , HOH A:610 , HOH A:612 , HOH A:724 , HOH A:754BINDING SITE FOR RESIDUE NDP A 502
3AC3SOFTWAREGLY A:139 , ARG A:143BINDING SITE FOR RESIDUE CL A 503
4AC4SOFTWAREASP A:255 , HOH A:607 , ASP B:278 , ASP B:282 , HOH B:720BINDING SITE FOR RESIDUE MN B 501
5AC5SOFTWARELYS B:75 , ALA B:77 , THR B:78 , THR B:80 , ARG B:85 , ASN B:99 , GLU B:309 , HIS B:312 , GLY B:313 , THR B:314 , VAL B:315 , THR B:316 , HIS B:318 , THR B:330 , ASN B:331 , HOH B:606 , HOH B:686 , HOH B:702 , HOH B:707BINDING SITE FOR RESIDUE NDP B 502
6AC6SOFTWAREPHE B:138 , GLY B:139 , ARG B:143 , HOH B:658BINDING SITE FOR RESIDUE CL B 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser A:296 -Val A:297
2Asp A:302 -Gly A:303
3Asp A:350 -Gly A:351
4Ser B:296 -Val B:297
5Asp B:302 -Gly B:303
6Asp B:350 -Gly B:351

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HCX)

(-) Sequences/Alignments

Asymmetric/Biological 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:402
                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4hcxa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee....eeeee.hhhhhhhhhhhhhhhh...ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeee...hhhhhheeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhh.hhh.eeeeee......eeeee....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hcx A   5 PKIKVSGPVVELDGDEMTRVIWKLIKDMLILPYLDIRLDYYDLGIEHRDATDDQVTIDAAYAIKKHGVGVKCATITPDEARVEEFNLKKMWLSPNGTIRNILGGTIFREPIVISNVPRLVPGWTKPIVIGRHAFGDQYRATNFKVDQPGTVTLTFTPADGSAPIVHEMVSIPEDGGVVLGMYNFKESIRDFARASFSYGLNAKWPVYLSTKNTILKAYDGMFKDEFERVYEEEFKAQFEAAGLTYEHRLIDDMVAACLKWEGGYVWACKNYDGDVQSDTVAQGYGSLGLMTSVLMTADGKTVEAEAAHGTVTRHYRQYQAGKPTSTNPIASIFAWTRGLQHRGKLDGTPEVIDFAHKLESVVIATVESGKMTKDLAILIGPEQDWLNSEEFLDAIADNLEKE 406
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404  


Chain B from PDB  Type:PROTEIN  Length:402
                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4hcxb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee....eeeee.hhhhhhhhhhhhhhhh...ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeee...hhhhhheeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhh.ee..ee......eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hcx B   5 PKIKVSGPVVELDGDEMTRVIWKLIKDMLILPYLDIRLDYYDLGIEHRDATDDQVTIDAAYAIKKHGVGVKCATITPDEARVEEFNLKKMWLSPNGTIRNILGGTIFREPIVISNVPRLVPGWTKPIVIGRHAFGDQYRATNFKVDQPGTVTLTFTPADGSAPIVHEMVSIPEDGGVVLGMYNFKESIRDFARASFSYGLNAKWPVYLSTKNTILKAYDGMFKDEFERVYEEEFKAQFEAAGLTYEHRLIDDMVAACLKWEGGYVWACKNYDGDVQSDTVAQGYGSLGLMTSVLMTADGKTVEAEAAHGTVTRHYRQYQAGKPTSTNPIASIFAWTRGLQHRGKLDGTPEVIDFAHKLESVVIATVESGKMTKDLAILIGPEQDWLNSEEFLDAIADNLEKE 406
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:302 - Gly A:303   [ RasMol ]  
    Asp A:350 - Gly A:351   [ RasMol ]  
    Asp B:302 - Gly B:303   [ RasMol ]  
    Asp B:350 - Gly B:351   [ RasMol ]  
    Ser A:296 - Val A:297   [ RasMol ]  
    Ser B:296 - Val B:297   [ RasMol ]  
 

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