1Y79 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE E.COLI DIPEPTIDYL CARBOXYPEPTIDASE DCP IN COMPLEX WITH A PEPTIDIC INHIBITOR

Authors :   M. Comellas-Bigler, R. Lang, W. Bode, K. Maskos

Date :   08 Dec 04 (Deposition) - 24 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : 1

Keywords :   Hinge Bending; Peptidyl Dipeptidase; Carboxypeptidase; Dcp; Neurolysin; Ace, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Comellas-Bigler, R. Lang, W. Bode, K. Maskos
Crystal Structure Of The E. Coli Dipeptidyl Carboxypeptidase Dcp: Further Indication Of A Ligand-Dependant Hinge Movement Mechanism
J. Mol. Biol. V. 349 99 2005
PubMed-ID: 15876371 | Reference-DOI: 10.1016/J.JMB.2005.03.016
(for further references see the PDB file header)

Molecule 1 - PEPTIDYL-DIPEPTIDASE DCP
	Chains	:	1
	EC Number	:	3.4.15.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRBI-DSBC PDCP
	Expression System Strain	:	JM83
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DCP
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DIPEPTIDYL CARBOXYPEPTIDASE

		1
Asymmetric/Biological Unit	:	1

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 5)

No.	Name	Count	Type	Full Name
1	ASP	1	Mod. Amino Acid	ASPARTIC ACID
2	GLY	1	Mod. Amino Acid	GLYCINE
3	LYS	1	Mod. Amino Acid	LYSINE
4	TRP	1	Mod. Amino Acid	TRYPTOPHAN
5	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS 1:469 , HIS 1:473 , GLU 1:498 , SER 1:501 , TRP 1:702	BINDING SITE FOR RESIDUE ZN 1 700
2	AC2	SOFTWARE	TRP 1:425 , MET 1:426 , TRP 1:702	BINDING SITE FOR RESIDUE LYS 1 701
3	AC3	SOFTWARE	ALA 1:424 , HIS 1:469 , GLU 1:470 , HIS 1:473 , GLU 1:498 , HIS 1:601 , TYR 1:607 , TYR 1:614 , ZN 1:700 , LYS 1:701 , GLY 1:703	BINDING SITE FOR RESIDUE TRP 1 702
4	AC4	SOFTWARE	HIS 1:469 , GLU 1:470 , HIS 1:601 , TYR 1:614 , TRP 1:702 , ASP 1:704 , HOH 1:1040 , HOH 1:1087	BINDING SITE FOR RESIDUE GLY 1 703
5	AC5	SOFTWARE	ARG 1:593 , TYR 1:594 , TYR 1:611 , TYR 1:614 , GLY 1:703 , HOH 1:1067 , HOH 1:1081 , HOH 1:1082 , HOH 1:1308	BINDING SITE FOR RESIDUE ASP 1 704

(no "SS Bond" information available for 1Y79)

(no "Cis Peptide Bond" information available for 1Y79)

(no "SAP(SNP)/Variant" information available for 1Y79)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	DCP_ECOLI	467-476	1	1:466-475

(no "Exon" information available for 1Y79)

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 1 from PDB  Type:PROTEIN  Length:684
 aligned with DCP_ECOLI | P24171 from UniProtKB/Swiss-Prot  Length:681

    Alignment length:684
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 681    
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681    
            DCP_ECOLI     2 TTMNPFLVQSTLPYLAPHFDQIANHHYRPAFDEGMQQKRAEIAAIALNPQMPDFNNTILALEQSGELLTRVTSVFFAMTAAHTNDELQRLDEQFSAELAELANDIYLNGELFARVDAVWQRRESLGLDSESIRLVEVIHQRFVLAGAKLAQADKAKLKVLNTEAATLTSQFNQRLLAANKSGGLVVNDIAQLAGMSEQEIALAAEAAREKGLDNKWLIPLLNTTQQPALAEMRDRATREKLFIAGWTRAEKNDANDTRAIIQRLVEIRAQQATLLGFPHYAAWKIADQMAKTPEAALNFMREIVPAARQRASDELASIQAVIDKQQGGFSAQPWDWAFYAEQVRREKFDLDEAQLKPYFELNTVLNEGVFWTANQLFGIKFVERFDIPVYHPDVRVWEIFDHNGVGLALFYGDFFARDSKSGGAWMGNFVEQSTLNKTHPVIYNVCNYQKPAAGEPALLLWDDVITLFHEFGHTLHGLFARQRYATLSGTNTPRDFVEFPSQINEHWATHPQVFARYARHYQSGAAMPDELQQKMRNASLFNKGYEMSELLSAALLDMRWHCLEENEAMQDVDDFELRALVAENMDLPAIPPRYRSSYFAHIFGGGYAAGYYAYLWTQMLADDGYQWFVEQGGLTRENGLRFREAILSRGNSEDLERLYRQWRGKAPKIMPMLQHRGLNI----   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Peptidase_M3-1y79101 1:228-678                                                                                                                                                                                                                                                                                                                                                                                                                                     ------ Pfam domains
         Sec.struct. author ...hhhhh...hhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.hhhhhh..hhhhhhhhhhhhhhh.....eee.......hhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..........eeeeee.....eeeeeeeeee.........eeeeee..........eeeeeeee...........hhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhh..hhhhhhhhh.........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...........hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.......hhhhhhhhhhh....hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y79 1   1 TTMNPFLVQSTLPYLAPHFDQIANHHYRPAFDEGMQQKRAEIAAIALNPQMPDFNNTILALEQSGELLTRVTSVFFAMTAAHTNDELQRLDEQFSAELAELANDIYLNGELFARVDAVWQRRESLGLDSESIRLVEVIHQRFVLAGAKLAQADKAKLKVLNTEAATLTSQFNQRLLAANKSGGLVVNDIAQLAGMSEQEIALAAEAAREKGLDNKWLIPLLNTTQQPALAEMRDRATREKLFIAGWTRAEKNDANDTRAIIQRLVEIRAQQATLLGFPHYAAWKIADQMAKTPEAALNFMREIVPAARQRASDELASIQAVIDKQQGGFSAQPWDWAFYAEQVRREKFDLDEAQLKPYFELNTVLNEGVFWTANQLFGIKFVERFDIPVYHPDVRVWEIFDHNGVGLALFYGDFFARDSKSGGAWMGNFVEQSTLNKTHPVIYNVCNYQKPAAGEPALLLWDDVITLFHEFGHTLHGLFARQRYATLSGTNTPRDFVEFPSQINEHWATHPQVFARYARHYQSGAAMPDELQQKMRNASLFNKGYEMSELLSAALLDMRWHCLEENEAMQDVDDFELRALVAENMDLPAIPPRYRSSYFAHIFGGGYAAGYYAYLWTQMLADDGYQWFVEQGGLTRENGLRFREAILSRGNSEDLERLYRQWRGKAPKIMPMLQHRGLNIKWGD 704
                                    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       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680|   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 680|   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  701

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 '\|'

(no "SCOP Domain" information available for 1Y79)

(no "CATH Domain" information available for 1Y79)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MA (251)

Family: Peptidase_M3 (2)

Escherichia coli (strain K12) (1)

Peptidase_M3-1y79101

1:228-678

Asymmetric/Biological Unit(hide GO term definitions)

Chain 1 (DCP_ECOLI | P24171)

molecular function
	GO:0004180	carboxypeptidase activity	Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
	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:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain 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: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.
biological process
	GO:0006518	peptide metabolic process	The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
	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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1y79)

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	1y79
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Description

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Chains, Units

Ligands, Modified Residues, Ions (5, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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