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Title :   X-RAY CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN-RELATED FACTOR A FROM BACILLUS STEAROTHERMOPHILUS

Authors :   J. Osipiuk, H. Li, S. Moy, F. Collart, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)

Date :   19 Nov 04 (Deposition) - 07 Dec 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Structural Genomics, Protein Structure Initiative, Psi, Midwest Center For Structural Genomics, Mcsg, Penicillin- Binding Protein, Recombination (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Osipiuk, H. Li, S. Moy, F. Collart, A. Joachimiak
X-Ray Crystal Structure Of Penicillin-Binding Protein-Related Factor A From Bacillus Stearothermophilus
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PENICILLIN-BINDING PROTEIN-RELATED FACTOR A
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RBSTP1992
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422
	Synonym	:	PRFA, RECU

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 21)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
2	NI	2	Ligand/Ion	NICKEL (II) ION
3	SO4	11	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:38 , HIS A:53 , LYS A:54 , HOH A:346	BINDING SITE FOR RESIDUE SO4 A 301
02	AC2	SOFTWARE	HIS A:177 , SER A:178 , HOH A:336 , LYS C:106	BINDING SITE FOR RESIDUE SO4 A 302
03	AC3	SOFTWARE	ASN B:38 , ARG B:45 , HIS B:53 , LYS B:54 , HOH B:324	BINDING SITE FOR RESIDUE SO4 B 303
04	AC4	SOFTWARE	THR B:103 , LYS B:104 , ASN B:105 , LYS B:112	BINDING SITE FOR RESIDUE SO4 B 304
05	AC5	SOFTWARE	ASP B:148 , HIS B:151 , HIS B:175 , HIS B:177 , HOH B:313 , HOH B:339	BINDING SITE FOR RESIDUE SO4 B 305
06	AC6	SOFTWARE	TYR B:43 , ARG B:47 , ILE B:49 , GLN C:170 , ARG C:174	BINDING SITE FOR RESIDUE SO4 B 306
07	AC7	SOFTWARE	ASN C:38 , ARG C:45 , HIS C:53 , LYS C:54 , HOH C:354 , HOH C:357	BINDING SITE FOR RESIDUE SO4 C 307
08	AC8	SOFTWARE	THR C:103 , LYS C:104 , PRO C:110 , LYS C:112 , ASN C:113	BINDING SITE FOR RESIDUE SO4 C 308
09	AC9	SOFTWARE	ARG D:45 , HIS D:53 , LYS D:54 , HOH D:333	BINDING SITE FOR RESIDUE SO4 D 309
10	BC1	SOFTWARE	THR D:103 , LYS D:104 , ASN D:105 , LYS D:112	BINDING SITE FOR RESIDUE SO4 D 310
11	BC2	SOFTWARE	GLN A:170 , ARG A:174 , TYR D:43 , ARG D:47	BINDING SITE FOR RESIDUE SO4 D 311
12	BC3	SOFTWARE	HIS A:151 , GLU A:171 , HIS A:175 , HOH A:340	BINDING SITE FOR RESIDUE NI A 321
13	BC4	SOFTWARE	HIS C:151 , GLU C:171 , HIS C:175 , HOH C:328	BINDING SITE FOR RESIDUE NI C 322

(no "SS Bond" information available for 1Y1O)

Asymmetric/Biological Unit

No.	Residues
1	Gln A:184	-	Pro A:185
2	Gln B:184	-	Pro B:185
3	Gln C:184	-	Pro C:185
4	Gln D:184	-	Pro D:185

(no "SAP(SNP)/Variant" information available for 1Y1O)

(no "PROSITE Motif" information available for 1Y1O)

(no "Exon" information available for 1Y1O)

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:168
 aligned with RECU_GEOKA | Q5KXY4 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:168
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        
           RECU_GEOKA    31 MTLEDDLNATNEYYRERGIAVIHKKPTPVQIVRVDYPKRSAAVITEAYFRQASTTDYNGVYRGKYIDFEAKETKNKTAFPLKNFHAHQIRHMEQVVAHGGICFAILRFSLLNETYLLDASHLIAWWNKQEAGGRKSIPKQEIERHGHSIPLGYQPRIDYISVVDNVYF 198
               SCOP domains d1y1oa_ A: Recombination protein U (RecU)/PBP related factor A (PrfA)                                                                                                    SCOP domains
               CATH domains -1y1oA00 A:32-198  [code=3.40.1350.10, no name defined]                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...eeee....eeeeeee.......eeeeeee.......eeeee..eeeeeeeeee....eee.hhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeehhhhhhhhhhh......eeehhhhhhhhee.........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y1o A  31 mTLEDDLNATNEYYRERGIAVIHKKPTPVQIVRVDYPKRSAAVITEAYFRQASTTDYNGVYRGKYIDFEAKETKNKTAFPLKNFHAHQIRHmEQVVAHGGICFAILRFSLLNETYLLDASHLIAWWNKQEAGGRKSIPKQEIERHGHSIPLGYQPRLDYISVVDNVYF 198
                            |       40        50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190        
                            |                                                                                        122-MSE                                                                        
                           31-MSE

Chain B from PDB  Type:PROTEIN  Length:168
 aligned with RECU_GEOKA | Q5KXY4 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:168
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        
           RECU_GEOKA    31 MTLEDDLNATNEYYRERGIAVIHKKPTPVQIVRVDYPKRSAAVITEAYFRQASTTDYNGVYRGKYIDFEAKETKNKTAFPLKNFHAHQIRHMEQVVAHGGICFAILRFSLLNETYLLDASHLIAWWNKQEAGGRKSIPKQEIERHGHSIPLGYQPRIDYISVVDNVYF 198
               SCOP domains d1y1ob_ B: Recombination protein U (RecU)/PBP related factor A (PrfA)                                                                                                    SCOP domains
               CATH domains -1y1oB00 B:32-198  [code=3.40.1350.10, no name defined]                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...eeee....eeeeeee.......eeeeeee.......eeeee..eeeeeeeeee....eee.hhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeehhhhhhhhhhhhh....eeehhhhhhhhee.........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y1o B  31 mTLEDDLNATNEYYRERGIAVIHKKPTPVQIVRVDYPKRSAAVITEAYFRQASTTDYNGVYRGKYIDFEAKETKNKTAFPLKNFHAHQIRHmEQVVAHGGICFAILRFSLLNETYLLDASHLIAWWNKQEAGGRKSIPKQEIERHGHSIPLGYQPRLDYISVVDNVYF 198
                            |       40        50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190        
                           31-MSE                                                                                    122-MSE

Chain C from PDB  Type:PROTEIN  Length:168
 aligned with RECU_GEOKA | Q5KXY4 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:168
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        
           RECU_GEOKA    31 MTLEDDLNATNEYYRERGIAVIHKKPTPVQIVRVDYPKRSAAVITEAYFRQASTTDYNGVYRGKYIDFEAKETKNKTAFPLKNFHAHQIRHMEQVVAHGGICFAILRFSLLNETYLLDASHLIAWWNKQEAGGRKSIPKQEIERHGHSIPLGYQPRIDYISVVDNVYF 198
               SCOP domains d1y1oc_ C: Recombination protein U (RecU)/PBP related factor A (PrfA)                                                                                                    SCOP domains
               CATH domains -1y1oC00 C:32-198  [code=3.40.1350.10, no name defined]                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...eeee....eeeeeee.......eeeeeee.......eeeee..eeeeeeeeee....eee.hhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeehhhhhhhhhh.......eeehhhhhhhhee.........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y1o C  31 mTLEDDLNATNEYYRERGIAVIHKKPTPVQIVRVDYPKRSAAVITEAYFRQASTTDYNGVYRGKYIDFEAKETKNKTAFPLKNFHAHQIRHmEQVVAHGGICFAILRFSLLNETYLLDASHLIAWWNKQEAGGRKSIPKQEIERHGHSIPLGYQPRLDYISVVDNVYF 198
                            |       40        50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190        
                           31-MSE                                                                                    122-MSE

Chain D from PDB  Type:PROTEIN  Length:168
 aligned with RECU_GEOKA | Q5KXY4 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:168
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        
           RECU_GEOKA    31 MTLEDDLNATNEYYRERGIAVIHKKPTPVQIVRVDYPKRSAAVITEAYFRQASTTDYNGVYRGKYIDFEAKETKNKTAFPLKNFHAHQIRHMEQVVAHGGICFAILRFSLLNETYLLDASHLIAWWNKQEAGGRKSIPKQEIERHGHSIPLGYQPRIDYISVVDNVYF 198
               SCOP domains d1y1od_ D: Recombination protein U (RecU)/PBP related factor A (PrfA)                                                                                                    SCOP domains
               CATH domains -1y1oD00 D:32-198  [code=3.40.1350.10, no name defined]                                                                                                                  CATH domains
           Pfam domains (1) RecU-1y1oD01 D:31-196                                                                                                                                                 -- Pfam domains (1)
           Pfam domains (2) RecU-1y1oD02 D:31-196                                                                                                                                                 -- Pfam domains (2)
           Pfam domains (3) RecU-1y1oD03 D:31-196                                                                                                                                                 -- Pfam domains (3)
           Pfam domains (4) RecU-1y1oD04 D:31-196                                                                                                                                                 -- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhh...eeee....eeeeeee.......eeeeeee.......eeeee..eeeeeeeeee....eee.hhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeehhhhhhhhhhhhh....eeehhhhhhhhee.........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y1o D  31 mTLEDDLNATNEYYRERGIAVIHKKPTPVQIVRVDYPKRSAAVITEAYFRQASTTDYNGVYRGKYIDFEAKETKNKTAFPLKNFHAHQIRHmEQVVAHGGICFAILRFSLLNETYLLDASHLIAWWNKQEAGGRKSIPKQEIERHGHSIPLGYQPRLDYISVVDNVYF 198
                            |       40        50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190        
                           31-MSE                                                                                    122-MSE

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Restriction endonuclease-like (209)

Superfamily: Restriction endonuclease-like (170)

Family: RecU-like (4)

Protein domain: Recombination protein U (RecU)/PBP related factor A (PrfA) (2)

Bacillus stearothermophilus [TaxId: 1422] (1)

1a	d1y1oa_	A:
1b	d1y1ob_	B:
1c	d1y1oc_	C:
1d	d1y1od_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Trna Endonuclease; Chain: A, domain 1 (24)

Homologous Superfamily: [code=3.40.1350.10, no name defined] (24)

Geobacillus stearothermophilus. Organism_taxid: 1422. (1)

1a	1y1oA00	A:32-198
1b	1y1oB00	B:32-198
1c	1y1oC00	C:32-198
1d	1y1oD00	D:32-198

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDDEXK (13)

Family: RecU (3)

Geobacillus kaustophilus (1)

1a	RecU-1y1oD01	D:31-196
1b	RecU-1y1oD02	D:31-196
1c	RecU-1y1oD03	D:31-196
1d	RecU-1y1oD04	D:31-196

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (RECU_GEOKA | Q5KXY4)

molecular function
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
biological process
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0007059	chromosome segregation	The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
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
		Gln A:184 - Pro A:185	[ RasMol ]
		Gln B:184 - Pro B:185	[ RasMol ]
		Gln C:184 - Pro C:185	[ RasMol ]
		Gln D:184 - Pro D:185	[ RasMol ]

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1rzn	CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN-RELATED FACTOR A FROM BACILLUS SUBTILIS RELATED ID: APC35922 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 21)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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