1KAH - JenaLib

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Title :   L-HISTIDINOL DEHYDROGENASE (HISD) STRUCTURE COMPLEXED WITH L-HISTIDINE (PRODUCT), ZN AND NAD (COFACTOR)

Authors :   J. A. R. G. Barbosa, J. Sivaraman, Y. Li, R. Larocque, A. Matte, J. D. Schr M. Cygler

Date :   02 Nov 01 (Deposition) - 12 Jun 02 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   L-Histidinol Dehydrogenase, Homodimer, Rossmann Fold, 4 Domains, Hisd, L-Histidine Biosynthesis, Nad Cofactor, 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

Molecule 1 - 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
	Gene	:	HISD
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	HDH

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 17)

No.	Name	Count	Type	Full Name
1	HIS	2	Mod. Amino Acid	HISTIDINE
2	MSE	13	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:262 , GLU A:356 , ASP A:360 , HIS A:502 , HIS B:419	BINDING SITE FOR RESIDUE ZN A 501
2	AC2	SOFTWARE	HIS A:419 , HIS A:503 , HIS B:262 , GLU B:356 , ASP B:360	BINDING SITE FOR RESIDUE ZN B 502
3	AC3	SOFTWARE	LEU A:138 , SER A:237 , HIS A:262 , GLU A:326 , HIS A:327 , GLU A:356 , ASP A:360 , TYR A:361 , HIS A:367 , ZN A:501 , GLU B:414 , LEU B:416 , HIS B:419	BINDING SITE FOR RESIDUE HIS A 502
4	AC4	SOFTWARE	GLU A:414 , LEU A:416 , HIS A:419 , SER B:140 , HIS B:262 , ASP B:360 , TYR B:361 , HIS B:367 , ZN B:502	BINDING SITE FOR RESIDUE HIS A 503

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

Asymmetric/Biological Unit

No.	Residues
1	Pro A:163	-	Pro A:164
2	Pro B:163	-	Pro B:164

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISOL_DEHYDROGENASE	PS00611	Histidinol dehydrogenase signature.	HISX_ECOLI	230-262	2	A:230-262 B:230-262

(no "Exon" information available for 1KAH)

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:433
 aligned with HISX_ECOLI | P06988 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:433
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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|  
           HISX_ECOLI     4 NTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQDVFNVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVLVIADSGATPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQALNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRVNALKEQA--   -
               SCOP domains d1kaha_ A: L-histidinol dehydrogenase HisD                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --1kahA01            ---1kahA02 A:28-102,A:121-230,A:382-388                                       ------------------1kahA02 A:28-102,A:121-230,A:382-388 Nitrogenase molybdenum iron protein domain                               -----1kahA01 A:6-24,A:236-364,A:370-378 Nitrogenase molybdenum iron protein domain                                                    -----1kahA01  ---1kahA02------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeeeee..eeeee........hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhhh........eee...hhhhhhhhhhhhh.....ee.......eeeeee....hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhh....hhhhhhhhh..eeee..hhhhhhhhhhhhh..eeeee..hhhhhhhhh....eeee....hhhhhhhh..........hhhhh....hhhh.eeeeeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HISOL_DEHYDROGENASE              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kah A   4 NTIIDWNSCTAEQQRQLLmRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKVSAEEIAAASERLSDELKQAmAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGLYIPGGSAPLFSTVLmLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQDVFNVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDmPAGPSEVLVIADSGATPDFVASDLLSQAEHGPDSQVILLTPAADmARRVAEAVERQLAELPRAETARQALNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRmTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRVNALKEQAHH 503
                                    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                                     434| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         502

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

    Alignment length:434
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430    
           HISX_ECOLI     1 MSFNTIIDWNSCTAEQQRQLLMRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKVSAEEIAAASERLSDELKQAMAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGLYIPGGSAPLFSTVLMLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQDVFNVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDMPAGPSEVLVIADSGATPDFVASDLLSQAEHGPDSQVILLTPAADMARRVAEAVERQLAELPRAETARQALNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRMTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRVNALKEQA 434
               SCOP domains d1kahb_ B: L-histidinol dehydrogenase HisD                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -----1kahB01            ---1kahB02 B:28-102,B:121-230,B:382-388                                       ------------------1kahB02 B:28-102,B:121-230,B:382-388 Nitrogenase molybdenum iron protein domain                               -----1kahB01 B:6-24,B:236-364,B:370-378 Nitrogenase molybdenum iron protein domain                                                    -----1kahB01  ---1kahB02---------------------------------------------- CATH domains
           Pfam domains (1) ----------------Histidinol_dh-1kahB01 B:17-428                                                                                                                                                                                                                                                                                                                                                                                              ------ Pfam domains (1)
           Pfam domains (2) ----------------Histidinol_dh-1kahB02 B:17-428                                                                                                                                                                                                                                                                                                                                                                                              ------ Pfam domains (2)
         Sec.struct. author ......ee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeeeee..eeeee........hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhhh........eee...hhhhhhhhhhhhhh....ee.......eeeeee....hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhh....hhhhhhhhh..eeee..hhhhhhhhhhhhh..eeeee..hhhhhhh......eeee....hhhhhhhh..........hhhhh....hhhh.eeeeeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HISOL_DEHYDROGENASE              ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kah B   1 mSFNTIIDWNSCTAEQQRQLLmRPAISASESITRTVNDILDNVKARGDEALREYSAKFDKTTVTALKVSAEEIAAASERLSDELKQAmAVAVKNIETFHTAQKLPPVDVETQPGVRCQQVTRPVASVGLYIPGGSAPLFSTVLmLATPASIAGCKKVVLCSPPPIADEILYAAQLCGVQDVFNVGGAQAIAALAFGTESVPKVDKIFGPGNAFVTEAKRQVSQRLDGAAIDmPAGPSEVLVIADSGATPDFVASDLLSQAEHGPDSQVILLTPAADmARRVAEAVERQLAELPRAETARQALNASRLIVTKDLAQCVEISNQYGPEHLIIQTRNARELVDSITSAGSVFLGDWSPESAGDYASGTNHVLPTYGYTATCSSLGLADFQKRmTVQELSKEGFSALASTIETLAAAERLTAHKNAVTLRVNALKEQA 434
                            |       10        20 |      30        40        50        60        70        80       |90       100       110       120       130       140   |   150       160       170       180       190       200       210       220       230 |     240       250       260       270      |280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430    
                            |                   22-MSE                                                            88-MSE                                                 144-MSE                                                                                 232-MSE                                      277-MSE                                                                                                          390-MSE                                        
                            1-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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: ALDH-like (168)

Superfamily: ALDH-like (168)

Family: L-histidinol dehydrogenase HisD (4)

Protein domain: L-histidinol dehydrogenase HisD (4)

Escherichia coli [TaxId: 562] (4)

1a	d1kaha_	A:
1b	d1kahb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

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)

1a	1kahA01	A:6-24,A:236-364,A:370-378
1b	1kahA02	A:28-102,A:121-230,A:382-388
1c	1kahB02	B:28-102,B:121-230,B:382-388
1d	1kahB01	B:6-24,B:236-364,B:370-378

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ALDH-like (49)

Family: Histidinol_dh (4)

Escherichia coli (strain K12) (4)

1a	Histidinol_dh-1kahB01	B:17-428
1b	Histidinol_dh-1kahB02	B:17-428

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Pro A:163 - Pro A:164	[ RasMol ]
		Pro B:163 - Pro B:164	[ RasMol ]

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	1kah
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	HISX_ECOLI \| P06988
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	1.1.1.23
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		Domain Information	:	XDom
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UniProtKB/Swiss-Prot
	HISX_ECOLI \| P06988	:	1k75 1kae 1kar

1k75	L-HISTIDINOL DEHYDROGENASE (HISD) STRUCTURE IMPLICATES DOMAIN SWAPPING AND GENE DUPLICATION
1kae	L-HISTIDINOL DEHYDROGENASE (HISD) STRUCTURE COMPLEXED WITH L-HISTIDINOL (SUBSTRATE), ZINC AND NAD (COFACTOR)
1kar	L-HISTIDINOL DEHYDROENASE (HISD) STRUCTURE COMPLEXED WITH HISTAMINE (INHIBITOR), ZINC AND NAD (COFACTOR)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 17)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 4)

Pfam Domains (1, 2)

Gene Ontology (11, 11)

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