2HP5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE OXA-10 W154G MUTANT AT PH 7.0

Authors :   F. Kerff, C. Falzone, R. Herman, E. Sauvage, P. Charlier

Date :   17 Jul 06 (Deposition) - 03 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Class D Beta-Lactamase, Lysine Carboxylation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Baurin, L. Vercheval, F. Bouillenne, C. Falzone, A. Brans, L. Jacquamet, J. L. Ferrer, E. Sauvage, D. Dehareng, J. M. Frere, P. Charlier, M. Galleni, F. Kerff
Critical Role Of Tryptophan 154 For The Activity And Stability Of Class D Beta-Lactamases.
Biochemistry V. 48 11252 2009
PubMed-ID: 19860471 | Reference-DOI: 10.1021/BI901548C

Molecule 1 - BETA-LACTAMASE PSE-2
	Chains	:	A, B, C, D
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22BKANR
	Expression System Strain	:	BL21(DE3) HOTSTAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PSE2, OXA10
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Synonym	:	BETA LACTAMASE OXA-10

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 14)

No.	Name	Count	Type	Full Name
1	CO	4	Ligand/Ion	COBALT (II) ION
2	SO4	10	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:67 , SER A:115 , LYS A:205 , THR A:206 , GLY A:207 , PHE A:208 , ARG A:250	BINDING SITE FOR RESIDUE SO4 A 267
02	AC2	SOFTWARE	SER B:67 , SER B:115 , THR B:206 , GLY B:207 , PHE B:208 , ARG B:250	BINDING SITE FOR RESIDUE SO4 B 267
03	AC3	SOFTWARE	SER C:67 , SER C:115 , LYS C:205 , THR C:206 , GLY C:207 , PHE C:208 , ARG C:250	BINDING SITE FOR RESIDUE SO4 C 267
04	AC4	SOFTWARE	SER D:115 , THR D:206 , GLY D:207 , PHE D:208 , ARG D:250	BINDING SITE FOR RESIDUE SO4 D 267
05	AC5	SOFTWARE	ARG A:104 , THR B:80 , ARG B:131 , TYR B:135	BINDING SITE FOR RESIDUE SO4 B 268
06	AC6	SOFTWARE	THR A:80 , ARG A:131 , LYS A:134 , TYR A:135	BINDING SITE FOR RESIDUE SO4 A 268
07	AC7	SOFTWARE	PRO C:248 , ARG C:250 , LYS C:251	BINDING SITE FOR RESIDUE SO4 C 268
08	AC8	SOFTWARE	THR D:80 , ARG D:131 , TYR D:135	BINDING SITE FOR RESIDUE SO4 D 268
09	AC9	SOFTWARE	PRO D:248 , ARG D:250 , LYS D:251	BINDING SITE FOR RESIDUE SO4 D 269
10	BC1	SOFTWARE	PRO B:248 , ARG B:250 , LYS B:251	BINDING SITE FOR RESIDUE SO4 B 269
11	BC2	SOFTWARE	LEU A:201 , HIS A:203 , GLU A:227 , GLU B:190 , HOH B:278	BINDING SITE FOR RESIDUE CO A 269
12	BC3	SOFTWARE	GLU A:190 , HOH A:283 , LEU B:201 , HIS B:203 , GLU B:227	BINDING SITE FOR RESIDUE CO B 270
13	BC4	SOFTWARE	GLU C:190 , HOH C:270 , HIS D:203 , GLU D:227	BINDING SITE FOR RESIDUE CO D 270
14	BC5	SOFTWARE	HIS C:203 , GLU C:227 , HOH C:275 , GLU D:190	BINDING SITE FOR RESIDUE CO C 269

Asymmetric Unit

No.	Residues
1	A:44	-	A:51
2	B:44	-	B:51
3	C:44	-	C:51
4	D:44	-	D:51

(no "Cis Peptide Bond" information available for 2HP5)

(no "SAP(SNP)/Variant" information available for 2HP5)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_D	PS00337	Beta-lactamase class-D active site.	BLO10_PSEAI	65-75	4	A:65-75 B:65-75 C:65-75 D:65-75

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_D	PS00337	Beta-lactamase class-D active site.	BLO10_PSEAI	65-75	2	A:65-75 B:65-75 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_D	PS00337	Beta-lactamase class-D active site.	BLO10_PSEAI	65-75	2	- - C:65-75 D:65-75

(no "Exon" information available for 2HP5)

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
	(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:246
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:246
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258      
          BLO10_PSEAI    19 AGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
               SCOP domains d2hp5a_ A: Class D beta-lactamase                                                                                                                                                                                                                      SCOP domains
               CATH domains 2hp5A00 A:19-264 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhh...eeeeeee....eeee.hhhhhhh...hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------BETA_LACTAM--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2hp5 A  19 MGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFGLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:246
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258      
          BLO10_PSEAI    19 AGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
               SCOP domains d2hp5b_ B: Class D beta-lactamase                                                                                                                                                                                                                      SCOP domains
               CATH domains 2hp5B00 B:19-264 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee...hhhhhhhh...eeeeeee.....eee.hhhhhh.ee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....--------.......eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------BETA_LACTAM--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2hp5 B  19 MGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQN--------GLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
                                    28        38        48        58        68        78        88        98       108       118       128       138      |  -     | 158       168       178       188       198       208       218       228       238       248       258      
                                                                                                                                                        145      154

Chain C from PDB  Type:PROTEIN  Length:231
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:245
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259     
          BLO10_PSEAI    20 GSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
               SCOP domains d2hp5c_ C: Class D beta-lactamase                                                                                                                                                                                                                     SCOP domains
               CATH domains 2hp5C00 C:20-264 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhh....eeeeeee....eeee.hhhhhhhee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....--------------..eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------BETA_LACTAM--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hp5 C  20 GSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQ--------------LRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
                                    29        39        49        59        69        79        89        99       109       119       129       139    |    -       159       169       179       189       199       209       219       229       239       249       259     
                                                                                                                                                      144            159

Chain D from PDB  Type:PROTEIN  Length:233
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:244
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
          BLO10_PSEAI    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
               SCOP domains d2hp5d_ D: Class D beta-lactamase                                                                                                                                                                                                                    SCOP domains
               CATH domains 2hp5D00 D:21-264 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhh....eeeeeee.....eee.hhhhhhh...hhhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...-----------.......hhhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------BETA_LACTAM--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hp5 D  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGN-----------LEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
                                    30        40        50        60        70        80        90       100       110       120       130       140  |      -    |  160       170       180       190       200       210       220       230       240       250       260    
                                                                                                                                                    143         155

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: beta-lactamase/transpeptidase-like (515)

Superfamily: beta-lactamase/transpeptidase-like (515)

Family: beta-Lactamase/D-ala carboxypeptidase (411)

Protein domain: Class D beta-lactamase (32)

Pseudomonas aeruginosa, OXA-10 [TaxId: 287] (25)

1a	d2hp5a_	A:
1b	d2hp5b_	B:
1c	d2hp5c_	C:
1d	d2hp5d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Beta-lactamase (339)

Homologous Superfamily: DD-peptidase/beta-lactamase superfamily (335)

Pseudomonas aeruginosa. Organism_taxid: 287. (10)

1a	2hp5A00	A:19-264
1b	2hp5B00	B:19-264
1c	2hp5D00	D:21-264
1d	2hp5C00	C:20-264

(no "Pfam Domain" information available for 2HP5)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (BLO10_PSEAI | P14489)

molecular function
	GO:0008800	beta-lactamase activity	Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
	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:0008658	penicillin binding	Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
biological process
	GO:0017001	antibiotic catabolic process	The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2hp5)

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1k4f	1K4F IS THE CRYSTAL STRUCTURE OF THE WILD TYPE PROTEIN OXA- 10
2hp6	2HP6 IS THE CRYSTAL STRUCTURE OF THE OXA-10 W154A MUTANT AT PH 7.5
2hp9	2HP9 IS THE CRYSTAL STRUCTURE OF THE OXA-10 W154A MUTANT AT PH 6.0
2hpb	2HPB IS THE CRYSTAL STRUCTURE OF THE OXA-10 W154A MUTANT AT PH 9.0

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 14)

Sites (14, 14)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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Gene Ontology (5, 5)

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