1IBU - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE AT 25 C

Authors :   S. Worley, E. Schelp, A. F. Monzingo, S. Ernst, J. D. Robertus

Date :   29 Mar 01 (Deposition) - 13 Mar 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F  (2x)
Biol. Unit 2: A,B,C,D,E,F  (1x)

Keywords :   Helix Disorder, Less Active Form, Site-Directed Mutant, Pyruvoyl, Carboxy-Lyase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Worley, E. Schelp, A. F. Monzingo, S. Ernst, J. D. Robertus
Structure And Cooperativity Of A T-State Mutant Of Histidin Decarboxylase From Lactobacillus 30A.
Proteins V. 46 321 2002
PubMed-ID: 11835507 | Reference-DOI: 10.1002/PROT.10042

Molecule 1 - HISTIDINE DECARBOXYLASE BETA CHAIN
	Chains	:	A, C, E
	EC Number	:	4.1.1.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	BETA CHAIN (RESIDUES 1-81)
	Gene	:	HDCA
	Mutation	:	YES
	Organism Scientific	:	LACTOBACILLUS SP.
	Organism Taxid	:	1593
	Strain	:	30A
	Synonym	:	PI CHAIN

Molecule 2 - HISTIDINE DECARBOXYLASE ALPHA CHAIN
	Chains	:	B, D, F
	EC Number	:	4.1.1.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	ALPHA CHAIN (RESIDUES 82-310)
	Gene	:	HDCA
	Organism Scientific	:	LACTOBACILLUS SP.
	Organism Taxid	:	1593
	Strain	:	30A

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (2x)	:	A	B	C	D	E	F
Biological Unit 2 (1x)	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	PYR	3	Mod. Amino Acid	PYRUVIC ACID

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	PYR	6	Mod. Amino Acid	PYRUVIC ACID

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	PYR	3	Mod. Amino Acid	PYRUVIC ACID

(no "Site" information available for 1IBU)

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

(no "Cis Peptide Bond" information available for 1IBU)

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

(no "PROSITE Motif" information available for 1IBU)

(no "Exon" information available for 1IBU)

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:65
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:81
                                    11        21        31        41        51        61        71        81 
           DCHS_LACS3     2 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDDDVLDGIVSYDRAETKNAYIGQINMTTAS  82
               SCOP domains d1ibu.1 A:,B: Histidine decarboxylase                                             SCOP domains
               CATH domains 1ibuA00 A:1-81 Pyruvoyl-Dependent Histidine Dec                arboxylas, subunit CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh......eee.............eee..eeeeeeeeeee----------------..........eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1ibu A   1 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGV----------------RAETKNAYIGQINMTTAS  81
                                    10        20        30        40      |  -         -   |    70        80 
                                                                         47               64

Chain B from PDB  Type:PROTEIN  Length:229
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:229
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302         
           DCHS_LACS3    83 SFTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 311
               SCOP domains d1ibu.1 A:,B: Histidine decarboxylase                                                                                                                                                                                                 SCOP domains
               CATH domains -1ibuB00 B:83-310 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) eee....eee.......hhhhhh....eeee..--------hhhhhhhhhhhhh-..eee.....eeeeeeeeeeeeeee............eeeeeeeeeee........eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..eeeeeeeeeeeeeee..hhh......hhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------eeeeeeeee----------eee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ibu B  82 xFTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 310
                            |       91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
                           82-PYR

Chain C from PDB  Type:PROTEIN  Length:67
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:81
                                    11        21        31        41        51        61        71        81 
           DCHS_LACS3     2 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDDDVLDGIVSYDRAETKNAYIGQINMTTAS  82
               SCOP domains d1ibu.2 C:,D: Histidine decarboxylase                                             SCOP domains
               CATH domains 1ibuC00 C:1-81 Pyruvoyl-Dependent Histidine Decar              boxylas, subunit A CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh......eee.............eee..eeeeeeeeeeeee--------------..........eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1ibu C   1 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRD--------------RAETKNAYIGQINMTTAS  81
                                    10        20        30        40        |-         -   |    70        80 
                                                                           49             64

Chain D from PDB  Type:PROTEIN  Length:229
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:229
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302         
           DCHS_LACS3    83 SFTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 311
               SCOP domains d1ibu.2 C:,D: Histidine decarboxylase                                                                                                                                                                                                 SCOP domains
               CATH domains -1ibuD00 D:83-310 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) eee....eee.......hhhhhh....eeee..--------hhhhhhhhhhhhh-..eee.....eeeeeeeeeeeeeee............eeeeeeeeeee........eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..eeeeeeeeeeeeeee..hhh......hhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------eeeeeeeee----------eee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ibu D  82 xFTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 310
                            |       91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
                           82-PYR

Chain E from PDB  Type:PROTEIN  Length:70
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:81
                                    11        21        31        41        51        61        71        81 
           DCHS_LACS3     2 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDDDVLDGIVSYDRAETKNAYIGQINMTTAS  82
               SCOP domains d1ibu.3 E:,F: Histidine decarboxylase                                             SCOP domains
               CATH domains 1ibuE00 E:1-81 Pyruvoyl-Dependent Histidine Decarbo           xylas, subunit A    CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh......eee.............eee..eeeeeeeeeeeeee.-----------...........eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1ibu E   1 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKS-----------DRAETKNAYIGQINMTTAS  81
                                    10        20        30        40        50|        -  |     70        80 
                                                                             51          63

Chain F from PDB  Type:PROTEIN  Length:229
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:229
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302         
           DCHS_LACS3    83 SFTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 311
               SCOP domains d1ibu.3 E:,F: Histidine decarboxylase                                                                                                                                                                                                 SCOP domains
               CATH domains -1ibuF00 F:83-310 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) eee....eee.......hhhhhh....eeee..--------hhhhhhhhhhhhh-..eee.....eeeeeeeeeeeeeee............eeeeeeeeeee........eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeeee..eeeeeeeeeeeeeee..hhh......hhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------eeeeeeeee----------eee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ibu F  82 xFTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 310
                            |       91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
                           82-PYR

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Pyruvoyl-dependent histidine and arginine decarboxylases (10)

Superfamily: Pyruvoyl-dependent histidine and arginine decarboxylases (10)

Family: Histidine decarboxylase (6)

Protein domain: Histidine decarboxylase (6)

Lactobacillus sp., strain 30a [TaxId: 1591] (6)

1a	d1ibu.1	A:,B:
1b	d1ibu.2	C:,D:
1c	d1ibu.3	E:,F:

(no "Pfam Domain" information available for 1IBU)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (DCHS_LACS3 | P00862)

molecular function
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	GO:0004398	histidine decarboxylase activity	Catalysis of the reaction: L-histidine = histamine + CO2.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
	GO:0006547	histidine metabolic process	The chemical reactions and pathways involving histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.

Asymmetric Unit
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	DCHS_LACS3 \| P00862	:	1hq6 1ibt 1ibv 1ibw 1pya

1hq6	STRUCTURE OF PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE AT PH 8
1ibt	STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE AT -170 C
1ibv	STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE BOUND WITH HISTIDINE METHYL ESTER AT -170 C
1ibw	STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE BOUND WITH HISTIDINE METHYL ESTER AT 25 C
1pya	STRUCTURE OF PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE AT PH 4.8

Description

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