3VH9 - JenaLib

Title :   CRYSTAL STRUCTURE OF AEROMONAS PROTEOLYTICA AMINOPEPTIDASE COMPLEXED WITH 8-QUINOLINOL

Authors :   S. Saijo, K. Hanaya, M. Suetsugu, K. Kobayashi, I. Yamato, S. Aoki

Date :   24 Aug 11 (Deposition) - 02 May 12 (Release) - 02 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.29

Chains :   Asym./Biol. Unit : A

Keywords :   8-Quinolinol, Dinuclear Zinc Hydrolases, Aminopeptidase, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Hanaya, M. Suetsugu, S. Saijo, I. Yamato, S. Aoki
Potent Inhibition Of Dinuclear Zinc(Ii) Peptidase, An Aminopeptidase From Aeromonas Proteolytica, By 8-Quinolinol Derivatives: Inhibitor Design Based On Zn(2+) Fluorophores, Kinetic, And X-Ray Crystallographic Study.
J. Biol. Inorg. Chem. V. 17 517 2012
PubMed-ID: 22311113 | Reference-DOI: 10.1007/S00775-012-0873-4

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 24)

Sites (24, 24)

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:117 , GLU A:152 , HIS A:256 , ZN A:302 , HQY A:303	BINDING SITE FOR RESIDUE ZN A 301
02	AC2	SOFTWARE	HIS A:97 , ASP A:117 , GLU A:152 , ASP A:179 , ZN A:301 , HQY A:303	BINDING SITE FOR RESIDUE ZN A 302
03	AC3	SOFTWARE	HIS A:97 , ASP A:117 , GLU A:152 , ASP A:179 , GLY A:224 , TYR A:225 , CYS A:227 , TYR A:251 , ILE A:255 , HIS A:256 , ZN A:301 , ZN A:302 , HOH A:451 , HOH A:508	BINDING SITE FOR RESIDUE HQY A 303
04	AC4	SOFTWARE	THR A:194 , THR A:197 , HOH A:468 , HOH A:600 , HOH A:625	BINDING SITE FOR RESIDUE NA A 304
05	AC5	SOFTWARE	SER A:51 , ASN A:74 , NA A:312 , HOH A:496 , HOH A:498 , HOH A:501 , HOH A:623	BINDING SITE FOR RESIDUE NA A 305
06	AC6	SOFTWARE	TYR A:218 , HOH A:441 , HOH A:455 , HOH A:471 , HOH A:510 , HOH A:620	BINDING SITE FOR RESIDUE NA A 306
07	AC7	SOFTWARE	ASN A:249 , HOH A:357 , HOH A:442 , HOH A:515 , HOH A:525 , HOH A:561	BINDING SITE FOR RESIDUE NA A 307
08	AC8	SOFTWARE	THR A:268 , SER A:270 , HOH A:355 , HOH A:567 , HOH A:609 , HOH A:627	BINDING SITE FOR RESIDUE NA A 308
09	AC9	SOFTWARE	THR A:11 , HOH A:352 , HOH A:353 , HOH A:473 , HOH A:619	BINDING SITE FOR RESIDUE NA A 309
10	BC1	SOFTWARE	GLU A:152 , HOH A:451 , HOH A:479 , HOH A:534 , HOH A:535	BINDING SITE FOR RESIDUE NA A 310
11	BC2	SOFTWARE	HOH A:329 , HOH A:333 , HOH A:359 , HOH A:378 , HOH A:416 , HOH A:579	BINDING SITE FOR RESIDUE NA A 311
12	BC3	SOFTWARE	ASN A:74 , NA A:305 , HOH A:501 , HOH A:549 , HOH A:565 , HOH A:616 , HOH A:691	BINDING SITE FOR RESIDUE NA A 312
13	BC4	SOFTWARE	LEU A:213 , PRO A:214 , SER A:215	BINDING SITE FOR RESIDUE CL A 313
14	BC5	SOFTWARE	ALA A:19 , LYS A:273 , HOH A:590	BINDING SITE FOR RESIDUE CL A 314
15	BC6	SOFTWARE	THR A:257 , THR A:258 , GLN A:259	BINDING SITE FOR RESIDUE CL A 315
16	BC7	SOFTWARE	THR A:38 , TYR A:73 , ASN A:74 , HOH A:397 , HOH A:549	BINDING SITE FOR RESIDUE CL A 316
17	BC8	SOFTWARE	GLY A:72 , HOH A:466	BINDING SITE FOR RESIDUE CL A 317
18	BC9	SOFTWARE	GLN A:6 , ALA A:8 , THR A:9 , HOH A:516	BINDING SITE FOR RESIDUE CL A 318
19	CC1	SOFTWARE	GLY A:24 , SER A:27 , SER A:28 , ASN A:200 , HOH A:493	BINDING SITE FOR RESIDUE CL A 319
20	CC2	SOFTWARE	LYS A:184 , HOH A:366 , HOH A:387	BINDING SITE FOR RESIDUE CL A 320
21	CC3	SOFTWARE	GLY A:219 , PHE A:220 , HOH A:345	BINDING SITE FOR RESIDUE CL A 321
22	CC4	SOFTWARE	THR A:194 , SER A:199 , THR A:202 , GLN A:203 , LEU A:262 , HOH A:625	BINDING SITE FOR RESIDUE SCN A 322
23	CC5	SOFTWARE	TRP A:13 , GLN A:16 , ASN A:135 , HOH A:352 , HOH A:539	BINDING SITE FOR RESIDUE SCN A 323
24	CC6	SOFTWARE	SER A:28 , SER A:31 , PHE A:32 , HOH A:411	BINDING SITE FOR RESIDUE GOL A 324

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:291
 aligned with AMPX_VIBPR | Q01693 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:291
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396 
           AMPX_VIBPR   107 MPPITQQATVTAWLPQVDASQITGTISSLESFTNRFYTTTSGAQASDWIASEWQALSASLPNASVKQVSHSGYNQKSVVMTITGSEAPDEWIVIGGHLDSTIGSHTNEQSVAPGADDDASGIAAVTEVIRVLSENNFQPKRSIAFMAYAAEEVGLRGSQDLANQYKSEGKNVVSALQLDMTNYKGSAQDVVFITDYTDSNFTQYLTQLMDEYLPSLTYGFDTCGYACSDHASWHNAGYPAAMPFESKFNDYNPRIHTTQDTLANSDPTGSHAKKFTQLGLAYAIEMGSATG 397
               SCOP domains d3vh9a_ A: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeeeee....eeeeeeeeeee....................hhhhhhhhhhhhhhhhhh.....eeeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee............eeee....hhhhhhhhhhhhhhhh....eeee.......hhhhhhhh...ee.ee..hhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vh9 A   1 MPPITQQATVTAWLPQVDASQITGTISSLESFTNRFYTTTSGAQASDWIASEWQALSASLPNASVKQVSHSGYNQKSVVMTITGSEAPDEWIVIGGHLDSTIGSHTNEQSVAPGADDDASGIAAVTEVIRVLSENNFQPKRSIAFMAYAAEEVGLRGSQDLANQYKSEGKNVVSALQLDMTNYKGSAQDVVFITDYTDSNFTQYLTQLMDEYLPSLTYGFDTCGYACSDHASWHNAGYPAAMPFESKFNDYNPRIHTTQDTLANSDPTGSHAKKFTQLGLAYAIEMGSATG 291
                                    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

Legend:		→ Mismatch	(orange background)
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	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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (AMPX_VIBPR | Q01693)

molecular function
	GO:0004177	aminopeptidase activity	Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
	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: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: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.

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	Cis Peptide Bonds
		Asp A:117 - Asp A:118	[ RasMol ]

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	3vh9
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	3.4.11.10
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Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1amp	THE SAME PROTEIN AT 1.80 ANGSTROM RESOLUTION
1cp6	THE SAME PROTEIN COMPLEXED WITH 1-BUTANEBORONIC ACID
1ft7	THE SAME PROTEIN COMPLEXED WITH L-LEUCINE PHOSPHONIC ACID
1igb	THE SAME PROTEIN COMPLEXED WITH PARA-IODO-D-PHENYLALANINE HYDROXAMIC ACID
1lok	THE SAME PROTEIN COMPLEXED WITH TRIS
1rtq	THE SAME PROTEIN AT 0.95 ANGSTROM RESOLUTION
1txr	THE SAME PROTEIN COMPLEXED WITH BESTATIN
1xry	THE SAME PROTEIN COMPLEXED WITH BESTATIN
2anp	E151H MUTANT
2dea	THE SAME PROTEIN AT PH 4.7
2iq6	THE SAME PROTEIN COMPLEXED WITH LEUCYL-LEUCYL-LEUCINE
2nyq	THE SAME PROTEIN COMPLEXED WITH D-LEU-L-TRP-L-CYS-L-PHE
2prq	THE CO(II)-SUBSTITUTED FORM COMPLEXED WITH TRIS
3b35	M180A MUTANT
3b3c	M180A MUTANT COMPLEXED WITH LEUCINE PHOSPHONIC ACID
3b3s	M180A MUTANT COMPLEXED WITH LEUCINE
3b3t	D118N MUTANT
3b3v	S228A MUTANT COMPLEXED WITH AMINO ACID
3b3w	S228A MUTANT COMPLEXED WITH LEUCINE
3b7i	S228A MUTANT COMPLEXED WITH LEUCINE PHOSPHONIC ACID
3fh4	THE RECOMBINANT PROTEIN EXPRESSED IN ESCHERICHIA COLI

Description