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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE APR-APRIN COMPLEX

Authors :   T. Hege, R. E. Feltzer, R. D. Gray, U. Baumann

Date :   03 Jul 01 (Deposition) - 15 Aug 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.74

Chains :   Asym./Biol. Unit : I,P

Keywords :   Pseudomonas Aeruginosa Alkaline Protease Inhibitor, Hydrolase/Hyrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Hege, R. E. Feltzer, R. D. Gray, U. Baumann
Crystal Structure Of A Complex Between Pseudomonas Aeruginosa Alkaline Protease And Its Cognate Inhibitor: Inhibition By A Zinc-Nh2 Coordinative Bond
J. Biol. Chem. V. 276 35087 2001
PubMed-ID: 11445573 | Reference-DOI: 10.1074/JBC.M104020200
(for further references see the PDB file header)

Molecule 1 - ALKALINE METALLOPROTEINASE
	Chains	:	P
	EC Number	:	3.4.24.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287

Molecule 2 - PROTEINASE INHIBITOR
	Chains	:	I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287

		1	2
Asymmetric/Biological Unit	:	I	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 9)

No.	Name	Count	Type	Full Name
1	CA	8	Ligand/Ion	CALCIUM ION
2	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER I:1 , HIS P:176 , HIS P:180 , HIS P:186	BINDING SITE FOR RESIDUE ZN P 481
2	AC2	SOFTWARE	ARG P:253 , GLY P:255 , THR P:257 , ASP P:285 , GLY P:287 , ASP P:290	BINDING SITE FOR RESIDUE CA P 482
3	AC3	SOFTWARE	GLY P:288 , ASP P:290 , THR P:327 , GLU P:329 , HOH P:491 , HOH P:520	BINDING SITE FOR RESIDUE CA P 483
4	AC4	SOFTWARE	GLY P:334 , GLY P:336 , ASP P:338 , GLY P:351 , ALA P:353 , ASP P:356	BINDING SITE FOR RESIDUE CA P 484
5	AC5	SOFTWARE	GLY P:352 , GLY P:354 , ASP P:356 , GLY P:369 , ALA P:371 , ASP P:374	BINDING SITE FOR RESIDUE CA P 485
6	AC6	SOFTWARE	GLY P:370 , GLY P:372 , ASP P:374 , ASP P:400 , HOH P:492 , HOH P:533	BINDING SITE FOR RESIDUE CA P 486
7	AC7	SOFTWARE	ASN P:343 , VAL P:345 , ASN P:347 , GLY P:360 , LEU P:362 , ASP P:365	BINDING SITE FOR RESIDUE CA P 487
8	AC8	SOFTWARE	GLY P:361 , GLY P:363 , ASP P:365 , GLU P:383 , ASP P:390 , HOH P:495	BINDING SITE FOR RESIDUE CA P 488
9	AC9	SOFTWARE	ASP P:446 , SER P:448 , ASP P:450 , HIS P:452 , ASP P:454	BINDING SITE FOR RESIDUE CA P 489

Asymmetric/Biological Unit

No.	Residues
1	I:26	-	I:49

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

Asymmetric/Biological Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_APRA_PSEAE_001 *	D	127	H	APRA_PSEAE	---	---	P	D	118	H
2	UniProt	VAR_APRA_PSEAE_002 *	G	176	A	APRA_PSEAE	---	---	P	G	167	A
3	UniProt	VAR_APRA_PSEAE_003 *	I	350	Y	APRA_PSEAE	---	---	P	I	341	Y
4	UniProt	VAR_APRA_PSEAE_004 *	I	454	V	APRA_PSEAE	---	---	P	I	445	V
5	UniProt	VAR_APRA_PSEAE_005 *	A	460	R	APRA_PSEAE	---	---	P	A	451	R
6	UniProt	VAR_APRA_PSEAE_006 *	V	479	L	APRA_PSEAE	---	---	P	V	470	L
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	APRA_PSEAE	182-191	1	P:173-182
2	HEMOLYSIN_CALCIUM	PS00330	Hemolysin-type calcium-binding region signature.	APRA_PSEAE	365-383	1	P:356-374

(no "Exon" information available for 1JIW)

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 I from PDB  Type:PROTEIN  Length:105
 aligned with INH_PSEAE | Q03026 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:105
                                    35        45        55        65        75        85        95       105       115       125     
            INH_PSEAE    26 SSLILLSASDLAGQWTLQQDEAPAICHLELRDSEVAEASGYDLGGDTACLTRWLPSEPRAWRPTPAGIALLERGGLTLMLLGRQGEGDYRVQKGDGGQLVLRRAT 130
               SCOP domains d1jiwi_ I: Metalloprotease inhibitor                                                                      SCOP domains
               CATH domains 1jiwI00 I:1-105  [code=2.40.128.10, no name defined]                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhheeeeeee.....eeeeeeeeeee....eeeeee.hhhhhhh......eeeee..eeeee.....eeeeeeeee..eeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1jiw I   1 SSLILLSASDLAGQWTLQQDEAPAICHLELRDSEVAEASGYDLGGDTACLTRWLPSEPRAWRPTPAGIALLERGGLTLMLLGRQGEGDYRVQKGDGGQLVLRRAT 105
                                    10        20        30        40        50        60        70        80        90       100

Chain P from PDB  Type:PROTEIN  Length:470
 aligned with APRA_PSEAE | Q03023 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:470
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479
           APRA_PSEAE    10 GRSDAYTQVDNFLHAYARGGDELVNGHPSYTVDQAAEQILREQASWQKAPGDSVLTLSYSFLTKPNDFFNTPWKYVSDIYSLGKFSAFSAQQQAQAKLSLQSWSDVTNIHFVDAGQGDQGDLTFGNFSSSVGGAAFAFLPDVPDALKGQSWYLINSSYSANVNPANGNYGRQTLTHEIGHTLGLSHPGDYNAGEGDPTYADATYAEDTRAYSVMSYWEEQNTGQDFKGAYSSAPLLDDIAAIQKLYGANLTTRTGDTVYGFNSNTERDFYSATSSSSKLVFSVWDAGGNDTLDFSGFSQNQKINLNEKALSDVGGLKGNVSIAAGVTVENAIGGSGSDLLIGNDVANVLKGGAGNDILYGGLGADQLWGGAGADTFVYGDIAESSAAAPDTLRDFVSGQDKIDLSGLDAFVNGGLVLQYVDAFAGKAGQAILSYDAASKAGSLAIDFSGDAHADFAINLIGQATQADIVV 479
               SCOP domains d1jiwp2 P:1-246 Metalloprotease                                                                                                                                                                                                                       d1jiwp1 P:247-470 Metalloprotease                                                                                                                                                                                                SCOP domains
               CATH domains 1jiwP01          1jiwP02 P:18-250 Collagenase (Catalytic Domain)                                                                                                                                                                                          1jiwP01 P:1-17,P:251-470 Alkaline Protease, subunit P, domain 1                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh................hhhhhhhhhh..............eeeeeee....hhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh.eeeeeeee.....eeeeee.......eee...........eeeee..............hhhhhhhhhhhhhhhh..............hhhhh...............hhhhhh...........hhhhhhhhhhhhh..........eee......hhhh..........eee.......eee........eee.....ee........eee.......eee......eee......eee......eee......eee......eee..hhhhhh....eee........eee...hhhhhh.....ee.........eeeeeee....eeeeeee........eeeeee...hhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------H------------------------------------------------A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-------------------------------------------------------------------------------------------------------V-----R------------------L SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOLYSIN_CALCIUM  ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jiw P   1 GRSDAYTQVDNFLHAYARGGDELVNGHPSYTVDQAAEQILREQASWQKAPGDSVLTLSYSFLTKPNDFFNTPWKYVSDIYSLGKFSAFSAQQQAQAKLSLQSWSDVTNIHFVDAGQGDQGDLTFGNFSSSVGGAAFAFLPDVPDALKGQSWYLINSSYSANVNPANGNYGRQTLTHEIGHTLGLSHPGDYNAGEGDPTYADATYAEDTRAYSVMSYWEEQNTGQDFKGAYSSAPLLDDIAAIQKLYGANLTTRTGDTVYGFNSNTERDFYSATSSSSKLVFSVWDAGGNDTLDFSGFSQNQKINLNEKALSDVGGLKGNVSIAAGVTVENAIGGSGSDLLIGNDVANVLKGGAGNDILYGGLGADQLWGGAGADTFVYGDIAESSAAAPDTLRDFVSGQDKIDLSGLDAFVNGGLVLQYVDAFAGKAGQAILSYDAASKAGSLAIDFSGDAHADFAINLIGQATQADIVV 470
                                    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

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 "Pfam Domain" information available for 1JIW)

Asymmetric/Biological Unit(hide GO term definitions)

Chain I (INH_PSEAE | Q03026)

molecular function
	GO:0004866	endopeptidase inhibitor activity	Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
	GO:0004857	enzyme inhibitor activity	Binds to and stops, prevents or reduces the activity of an enzyme.
	GO:0008191	metalloendopeptidase inhibitor activity	Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
cellular component
	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.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain P (APRA_PSEAE | Q03023)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0045959	negative regulation of complement activation, classical pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation by the classical pathway.
	GO:0001869	negative regulation of complement activation, lectin pathway	Any process that stops, prevents, or reduces the rate of complement activation by the lectin pathway.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0010765	positive regulation of sodium ion transport	Any process that increases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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

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	1jiw
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	APRA_PSEAE \| Q03023
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	INH_PSEAE \| Q03026
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	3.4.24.-
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UniProtKB/Swiss-Prot
	APRA_PSEAE \| Q03023	:	1akl 1kap 3vi1
	INH_PSEAE \| Q03026	:	2rn4

1smp	SERRATIA PROTEASE - ERWINIA INHIBITOR - COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 6)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (3, 3)

Pfam Domains (0, 0)

Gene Ontology (22, 22)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File