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(-) Description

Title :  THE L-HISTIDINOL DEHYDROGENASE (HISD) STRUCTURE IMPLICATES DOMAIN SWAPPING AND GENE DUPLICATION.
 
Authors :  J. A. R. G. Barbosa, J. Sivaraman, Y. Li, R. Larocque, A. Matte, J. Schrag M. Cygler, Montreal-Kingston Bacterial Structural Genomics In (Bsgi)
Date :  18 Oct 01  (Deposition) - 27 Feb 02  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  L-Histidinol Dehydrogenase, Homodimer, Rossmann Fold, 4 Domains, Hisd, L-Histidine Biosynthesis, Nad Cofactor, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. R. G. Barbosa, J. Sivaraman, Y. Li, R. Larocque, A. Matte, J. D. Schrag, M. Cygler
Mechanism Of Action And Nad+-Binding Mode Revealed By The Crystal Structure Of L-Histidinol Dehydrogenase.
Proc. Natl. Acad. Sci. Usa V. 99 1859 2002
PubMed-ID: 11842181  |  Reference-DOI: 10.1073/PNAS.022476199

(-) Compounds

Molecule 1 - L-HISTIDINOL DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DL41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SE-MET DERIVED DIMER
    Gene: HISD
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:236 , SER A:237 , HIS A:262 , GLY A:263 , PRO A:264 , ASP A:265 , SER A:266 , HOH A:2075 , HOH A:2156 , HOH A:2425BINDING SITE FOR RESIDUE SO4 A 2001
2AC2SOFTWAREPRO B:236 , SER B:237 , HIS B:262 , GLY B:263 , PRO B:264 , ASP B:265 , SER B:266 , HOH B:2119 , HOH B:2287 , HOH B:2397BINDING SITE FOR RESIDUE SO4 B 2002
3AC3SOFTWAREPRO B:249 , ARG B:280 , HOH B:2010BINDING SITE FOR RESIDUE SO4 B 2003
4AC4SOFTWAREPRO A:249 , ARG A:280 , HOH A:2051 , ARG B:287BINDING SITE FOR RESIDUE SO4 A 2004
5AC5SOFTWAREGLU A:72 , ILE A:165 , ASN A:183 , HOH A:2118 , HOH A:2268BINDING SITE FOR RESIDUE GOL A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K75)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:163 -Pro A:164
2Pro B:163 -Pro B:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K75)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISOL_DEHYDROGENASEPS00611 Histidinol dehydrogenase signature.HISX_ECOLI230-262
 		  2A:230-262
B:230-262

(-) Exons   (0, 0)

(no "Exon" information available for 1K75)

(-) 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:431
 aligned with HISX_ECOLI | P06988 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:431
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433 
           HISX_ECOLI     4 NTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQDVFNVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVLVIADSGATPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQALNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRVNALKEQA 434
               SCOP domains d1k75a_ A: L-histidinol dehydrogenase HisD                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --1k75A03            ---1k75A01 A:28-102,A:121-230,A:382-388                                       ------------------1k75A01 A:28-102,A:121-230,A:382-388 Nitrogenase molybdenum iron protein domain                               -----1k75A03 A:6-24,A:236-364,A:370-378 Nitrogenase molybdenum iron protein domain                                                    -----1k75A03  ---1k75A01---------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeeeeeeee..eeeee.......hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhhh........eee...hhhhhhhhhhhhhh....ee.......eeeeee....hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh...hhhhhhhhh..eeee..hhhhhhhhhhhhh..eeeee..hhhhhhhhh....eeee....hhhhhhhh..........hhhhh....hhhh.eeeeeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HISOL_DEHYDROGENASE              ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k75 A   4 NTIIDWNSCTAEQQRQLLmRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKVSAEEIAAASERLSDELKQAmAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGLYIPGGSAPLFSTVLmLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQDVFNVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDmPAGPSEVLVIADSGATPDFVASDLLSQAEHGPDSQVILLTPAADmARRVAEAVERQLAELPRAETARQALNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRmTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRVNALKEQA 434
                                    13        23        33        43        53        63        73        83    |   93       103       113       123       133       143|      153       163       173       183       193       203       213       223       233       243       253       263       273   |   283       293       303       313       323       333       343       353       363       373       383      |393       403       413       423       433 
                                             22-MSE                                                            88-MSE                                                 144-MSE                                                                                 232-MSE                                      277-MSE                                                                                                          390-MSE                                        


Chain B from PDB  Type:PROTEIN  Length:431
 aligned with HISX_ECOLI | P06988 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:431
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433 
           HISX_ECOLI     4 NTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQDVFNVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVLVIADSGATPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQALNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRVNALKEQA 434
               SCOP domains d1k75b_ B: L-histidinol dehydrogenase HisD                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --1k75B01            ---1k75B02 B:28-102,B:121-230,B:382-388                                       ------------------1k75B02 B:28-102,B:121-230,B:382-388 Nitrogenase molybdenum iron protein domain                               -----1k75B01 B:6-24,B:236-364,B:370-378 Nitrogenase molybdenum iron protein domain                                                    -----1k75B01  ---1k75B02---------------------------------------------- CATH domains
           Pfam domains (1) -------------Histidinol_dh-1k75B01 B:17-428                                                                                                                                                                                                                                                                                                                                                                                              ------ Pfam domains (1)
           Pfam domains (2) -------------Histidinol_dh-1k75B02 B:17-428                                                                                                                                                                                                                                                                                                                                                                                              ------ Pfam domains (2)
         Sec.struct. author ..eee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeeeeeeee..eeeee........hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhhh........eee...hhhhhhhhhhhhhh....ee.......eeeeee....hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh...hhhhhhhhh..eeee..hhhhhhhhhhhhh..eeeee..hhhhhhhhh....eeee....hhhhhhhh..........hhhhh....hhhh.eeeeeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HISOL_DEHYDROGENASE              ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k75 B   4 NTIIDWNSCTAEQQRQLLmRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKVSAEEIAAASERLSDELKQAmAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGLYIPGGSAPLFSTVLmLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQDVFNVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDmPAGPSEVLVIADSGATPDFVASDLLSQAEHGPDSQVILLTPAADmARRVAEAVERQLAELPRAETARQALNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRmTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRVNALKEQA 434
                                    13        23        33        43        53        63        73        83    |   93       103       113       123       133       143|      153       163       173       183       193       203       213       223       233       243       253       263       273   |   283       293       303       313       323       333       343       353       363       373       383      |393       403       413       423       433 
                                             22-MSE                                                            88-MSE                                                 144-MSE                                                                                 232-MSE                                      277-MSE                                                                                                          390-MSE
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Topology: Rossmann fold (7312)
(-)
Homologous Superfamily: Nitrogenase molybdenum iron protein domain (45)
(-)
Escherichia coli. Organism_taxid: 562. (7)
1a1k75A03A:6-24,A:236-364,A:370-378
1b1k75A01A:28-102,A:121-230,A:382-388
1c1k75B02B:28-102,B:121-230,B:382-388
1d1k75B01B:6-24,B:236-364,B:370-378

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: ALDH-like (49)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HISX_ECOLI | P06988)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0004399    histidinol dehydrogenase activity    Catalysis of the reaction: L-histidinol + NAD+ = L-histidine + NADH + H+.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0000105    histidine biosynthetic process    The chemical reactions and pathways resulting in the formation of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  1k75
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  HISX_ECOLI | P06988
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  1.1.1.23
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HISX_ECOLI | P06988: 1kae 1kah 1kar

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1K75)