1LFW - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PEPV

Authors :   D. Jozic, G. Bourenkow, H. Bartunik, H. Scholze, V. Dive, B. Henrich, R. W. Bode, K. Maskos

Date :   12 Apr 02 (Deposition) - 23 Oct 02 (Release) - 19 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Dipeptidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Jozic, G. Bourenkow, H. Bartunik, H. Scholze, V. Dive, B. Henrich, R. Huber, W. Bode, K. Maskos
Crystal Structure Of The Dinuclear Zinc Aminopeptidase Pepv From Lactobacillus Delbrueckii Unravels Its Preference For Dipeptides
Structure V. 10 1097 2002
PubMed-ID: 12176387 | Reference-DOI: 10.1016/S0969-2126(02)00805-5

Molecule 1 - PEPV
	Chains	:	A
	EC Number	:	3.4.13.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKV104
	Expression System Strain	:	JM83
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	LACTOBACILLUS DELBRUECKII
	Organism Taxid	:	29397
	Strain	:	LACTIS
	Synonym	:	XAA-HIS DIPEPTIDASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	AEP	1	Ligand/Ion	3-[(1-AMINO-2-CARBOXY-ETHYL)-HYDROXY-PHOSPHINOYL]-2-METHYL-PROPIONIC ACID
2	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:119 , GLU A:154 , HIS A:439 , AEP A:683	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	HIS A:87 , ASP A:119 , ASP A:177 , AEP A:683	BINDING SITE FOR RESIDUE ZN A 1002
3	AC3	SOFTWARE	HIS A:87 , ASP A:119 , GLU A:153 , GLU A:154 , ASP A:177 , ASN A:217 , HIS A:269 , ARG A:350 , GLY A:414 , GLY A:415 , MET A:438 , HIS A:439 , ZN A:1001 , ZN A:1002 , HOH A:1164 , HOH A:1512	BINDING SITE FOR RESIDUE AEP A 683

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

Asymmetric/Biological Unit

No.	Residues
1	Asp A:119	-	Asp A:120
2	Tyr A:180	-	Pro A:181

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARGE_DAPE_CPG2_1	PS00758	ArgE / dapE / ACY1 / CPG2 / yscS family signature 1.	PEPV_LACDL	82-91	1	A:82-91
2	ARGE_DAPE_CPG2_2	PS00759	ArgE / dapE / ACY1 / CPG2 / yscS family signature 2.	PEPV_LACDL	117-156	1	A:117-156

(no "Exon" information available for 1LFW)

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:468
 aligned with PEPV_LACDL | P45494 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:468
                                    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       440       450       460        
           PEPV_LACDL     1 MDLNFKELAEAKKDAILKDLEELIAIDSSEDLENATEEYPVGKGPVDAMTKFLSFAKRDGFDTENFANYAGRVNFGAGDKRLGIIGHMDVVPAGEGWTRDPFKMEIDEEGRIYGRGSADDKGPSLTAYYGMLLLKEAGFKPKKKIDFVLGTNEETNWVGIDYYLKHEPTPDIVFSPDAEYPIINGEQGIFTLEFSFKNDDTKGDYVLDKFKAGIATNVTPQVTRATISGPDLEAVKLAYESFLADKELDGSFEINDESADIVLIGQGAHASAPQVGKNSATFLALFLDQYAFAGRDKNFLHFLAEVEHEDFYGKKLGIFHHDDLMGDLASSPSMFDYEHAGKASLLNNVRYPQGTDPDTMIKQVLDKFSGILDVTYNGFEEPHYVPGSDPMVQTLLKVYEKQTGKPGHEVVIGGGTYGRLFERGVAFGAQPENGPMVMHAANEFMMLDDLILSIAIYAEAIYELTKDE 468
               SCOP domains d1lfwa1 A:1-186,A:383-468 Aminopeptidase PepV                                                                                                                                             d1lfwa2 A:187-382 Aminopeptidase PepV                                                                                                                                                               d1lfwa1 A:1-186,A:383-468 Aminopeptidase PepV                                          SCOP domains
               CATH domains 1lfwA01 A:1-186,A:381-468 Zn peptidases                                                                                                                                                   1lfwA02           1lfwA03 A:205-292  [code=3.30.70.360, no name defined]                                  1lfwA02 A:187-204,A:293-380  [code=3.30.70.360, no name defined]                        1lfwA01 A:1-186,A:381-468 Zn peptidases                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhh.....hhhhh......hhhhhhhhhhhhhhhhhh..eeeee...eeeeee.....eeeeeee.................ee....eee......hhhhhhhhhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhh....eeee..ee..eeeee.eeeeeeeee.........eeeeeee.........eeeeeee..hhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee.......hhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhh..............ee...ee.eeeeeeeeee....eeeeeeeee....hhhhhhhhhhhhhh..eeee.......ee....hhhhhhhhhhhhhhhh....eeee...hhhhhh...ee..ee.............eeehhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------ARGE_DAPE_-------------------------ARGE_DAPE_CPG2_2  PDB: A:117-156        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lfw A   1 MDLNFKELAEAKKDAILKDLEELIAIDSSEDLENATEEYPVGKGPVDAMTKFLSFAKRDGFDTENFANYAGRVNFGAGDKRLGIIGHMDVVPAGEGWTRDPFKMEIDEEGRIYGRGSADDKGPSLTAYYGMLLLKEAGFKPKKKIDFVLGTNEETNWVGIDYYLKHEPTPDIVFSPDAEYPIINGEQGIFTLEFSFKNDDTKGDYVLDKFKAGIATNVTPQVTRATISGPDLEAVKLAYESFLADKELDGSFEINDESADIVLIGQGAHASAPQVGKNSATFLALFLDQYAFAGRDKNFLHFLAEVEHEDFYGKKLGIFHHDDLMGDLASSPSMFDYEHAGKASLLNNVRYPQGTDPDTMIKQVLDKFSGILDVTYNGFEEPHYVPGSDPMVQTLLKVYEKQTGKPGHEVVIGGGTYGRLFERGVAFGAQPENGPMVMHAANEFMMLDDLILSIAIYAEAIYELTKDE 468
                                    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       440       450       460

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.360, no name defined] (23)

Eubacteria (Bacteria) (1)

1a	1lfwA02	A:187-204,A:293-380
1b	1lfwA03	A:205-292

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Aminopeptidase (284)

Homologous Superfamily: Zn peptidases (137)

Eubacteria (Bacteria) (1)

1lfwA01

A:1-186,A:381-468

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PEPV_LACDL | P45494)

molecular function
	GO:0016805	dipeptidase activity	Catalysis of the hydrolysis of a dipeptide.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:119 - Asp A:120	[ RasMol ]
		Tyr A:180 - Pro A:181	[ RasMol ]

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	1lfw
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	3.4.13.3
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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