1PQH - JenaLib

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Title :   SERINE 25 TO THREONINE MUTATION OF ASPARTATE DECARBOXYLASE

Authors :   F. Schmitzberger, M. L. Kilkenny, C. M. C. Lobley, M. E. Webb, M. Vinkovi D. Matak-Vinkovic, M. Witty, D. Y. Chirgadze, A. G. Smith, C. Abell, T. L. Blundell

Date :   18 Jun 03 (Deposition) - 18 Nov 03 (Release) - 29 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.29

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Pyruvoyl Dependent Decarboxylase, Protein Self-Processing, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Schmitzberger, M. L. Kilkenny, C. M. C. Lobley, M. E. Webb, M. Vinkovic, D. Matak-Vinkovic, M. Witty, D. Y. Chirgadze, A. G. Smith C. Abell, T. L. Blundell
Structural Constraints On Protein Self-Processing In L-Aspartate-Alpha-Decarboxylase
Embo J. V. 22 6193 2003
PubMed-ID: 14633979 | Reference-DOI: 10.1093/EMBOJ/CDG575
(for further references see the PDB file header)

Molecule 1 - ASPARTATE 1-DECARBOXYLASE
	Chains	:	A, B
	EC Number	:	4.1.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSETA
	Expression System Strain	:	C41 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PAND
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	ASPARTATE ALPHA-DECARBOXYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CSX	2	Mod. Amino Acid	S-OXY CYSTEINE
2	MLA	3	Ligand/Ion	MALONIC ACID
3	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	CSX	4	Mod. Amino Acid	S-OXY CYSTEINE
2	MLA	6	Ligand/Ion	MALONIC ACID
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:14 , HOH A:539 , PRO B:103 , ASN B:104 , HOH B:514	BINDING SITE FOR RESIDUE NA A 393
2	AC2	SOFTWARE	ARG A:12 , VAL A:49 , THR A:50 , HOH A:579 , HIS B:21 , ARG B:102	BINDING SITE FOR RESIDUE MLA A 390
3	AC3	SOFTWARE	LYS A:9 , ARG A:54 , ILE A:86 , GLY B:24 , THR B:57 , TYR B:58 , ALA B:74 , ALA B:75 , HOH B:432	BINDING SITE FOR RESIDUE MLA B 391
4	AC4	SOFTWARE	GLY A:24 , THR A:57 , TYR A:58 , ASN A:72 , GLY A:73 , ALA A:74 , ALA A:75 , HOH A:405 , LYS B:9 , TRP B:47 , ARG B:54 , ILE B:86	BINDING SITE FOR RESIDUE MLA A 392

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

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

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

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

(no "Exon" information available for 1PQH)

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
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Chain A from PDB  Type:PROTEIN  Length:119
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                               1                                                                                                                   
                               |     7        17        27        37        47        57        67        77        87        97       107         
           PAND_ECOLI     - ---MIRTMLQGKLHRVKVTHADLHYEGSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKR 116
               SCOP domains d1pqha_ A: Pyruvoyl dependent aspartate decarboxylase, ADC                                                              SCOP domains
               CATH domains 1pqhA00 A:-2-116  [code=2.40.40.20, no name defined]                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeee...........eeeehhhhhhhh.....eeeeee.....eeeeeeeee......ee.hhhhhhh.....eeeeeeeeeeehhhhh....eeeeee...ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1pqh A  -2 RGSMIRTMLQGKLHRVKVTHADLHYEGTCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHcASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKR 116
                                     7        17        27        37        47        57        67        77|       87        97       107         
                                                                                                           78-CSX

Chain B from PDB  Type:PROTEIN  Length:115
 aligned with PAND_ECOLI | P0A790 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:115
                                    10        20        30        40        50        60        70        80        90       100       110     
           PAND_ECOLI     1 MIRTMLQGKLHRVKVTHADLHYEGSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMK 115
               SCOP domains d1pqhb_ B: Pyruvoyl dependent aspartate decarboxylase, ADC                                                          SCOP domains
               CATH domains 1pqhB00 B:1-115  [code=2.40.40.20, no name defined]                                                                 CATH domains
           Pfam domains (1) Asp_decarbox-1pqhB01 B:1-115                                                                                        Pfam domains (1)
           Pfam domains (2) Asp_decarbox-1pqhB02 B:1-115                                                                                        Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeeee...........eeeehhhhhhhh.....eeeeee.....eeeeeeeee......ee.hhhhhhh.....eeeeeeeeeeehhhhh....eeeeee...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1pqh B   1 MIRTMLQGKLHRVKVTHADLHYEGTCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHcASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMK 115
                                    10        20        30        40        50        60        70       |80        90       100       110     
                                                                                                        78-CSX

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Double psi beta-barrel (111)

Superfamily: ADC-like (88)

Family: Pyruvoyl dependent aspartate decarboxylase, ADC (12)

Protein domain: Pyruvoyl dependent aspartate decarboxylase, ADC (11)

Escherichia coli [TaxId: 562] (9)

1a	d1pqha_	A:
1b	d1pqhb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Barwin-like endoglucanases (75)

Homologous Superfamily: [code=2.40.40.20, no name defined] (63)

Escherichia coli. Organism_taxid: 562. (9)

1a	1pqhA00	A:-2-116
1b	1pqhB00	B:1-115

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: AcetylDC-like (37)

Family: Asp_decarbox (13)

Escherichia coli (strain K12) (8)

1a	Asp_decarbox-1pqhB01	B:1-115
1b	Asp_decarbox-1pqhB02	B:1-115

Asymmetric Unit(hide GO term definitions)

Chain A,B (PAND_ECOLI | P0A790)

molecular function
	GO:0004068	aspartate 1-decarboxylase activity	Catalysis of the reaction: L-aspartate = beta-alanine + CO2.
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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:0006523	alanine biosynthetic process	The chemical reactions and pathways resulting in the formation of alanine, 2-aminopropanoic acid.
	GO:0015940	pantothenate biosynthetic process	The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
	GO:0016540	protein autoprocessing	Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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 Unit
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Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (4, 4)

SS Bonds (0, 0)

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