1H16 - JenaLib

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Title :   PYRUVATE FORMATE-LYASE (E.COLI) IN COMPLEX WITH PYRUVATE AND COA

Authors :   A. Becker, W. Kabsch

Date :   03 Jul 02 (Deposition) - 01 Nov 02 (Release) - 10 Jun 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.53

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Lyase, Glycyl Radical Enzyme, Transferase, Acyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Becker, W. Kabsch
X-Ray Structure Of Pyruvate Formate-Lyase In Complex With Pyruvate And Coa. How The Enzyme Uses The Cys-418 Thiyl Radical For Pyruvate Cleavage
J. Biol. Chem. V. 277 40036 2002
PubMed-ID: 12163496 | Reference-DOI: 10.1074/JBC.M205821200

Molecule 1 - FORMATE ACETYLTRANSFERASE 1
	Chains	:	A
	EC Number	:	2.3.1.54
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	COMPLEX OF PYRUVATE FORMATE-LYASE WITH ITS SUBSTRATES PYRUVATE AND COA
	Synonym	:	PYRUVATE FORMATE-LYASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 15)

No.	Name	Count	Type	Full Name
1	COA	1	Ligand/Ion	COENZYME A
2	DTL	2	Ligand/Ion	L-TREITOL
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	NA	7	Ligand/Ion	SODIUM ION
5	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PYR	1	Ligand/Ion	PYRUVIC ACID

Biological Unit 1 (4, 14)

No.	Name	Count	Type	Full Name
1	COA	2	Ligand/Ion	COENZYME A
2	DTL	4	Ligand/Ion	L-TREITOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	PG4	6	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PYR	2	Ligand/Ion	PYRUVIC ACID

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:652 , LEU A:654 , GLU A:700 , GLY A:701 , HOH A:3157 , HOH A:3160	BINDING SITE FOR RESIDUE NA A9001
02	AC2	SOFTWARE	GLU A:214 , GLN A:215 , ARG A:218 , HOH A:2595 , HOH A:2920	BINDING SITE FOR RESIDUE NA A9002
03	AC3	SOFTWARE	THR A:80 , ILE A:81 , SER A:268 , HOH A:2138 , HOH A:2140 , HOH A:2327 , HOH A:2330	BINDING SITE FOR RESIDUE NA A9003
04	AC4	SOFTWARE	HOH A:2624 , HOH A:3136 , PG4 A:9013	BINDING SITE FOR RESIDUE NA A9004
05	AC5	SOFTWARE	GLN A:589 , PRO A:599 , HOH A:2558 , HOH A:3027	BINDING SITE FOR RESIDUE NA A9005
06	AC6	SOFTWARE	LYS A:62 , HOH A:2101 , HOH A:2258 , HOH A:3192	BINDING SITE FOR RESIDUE NA A9006
07	AC7	SOFTWARE	PHE A:112 , HOH A:2138 , HOH A:2689 , HOH A:2933 , HOH A:3256 , HOH A:3257	BINDING SITE FOR RESIDUE NA A9007
08	AC8	SOFTWARE	COA A:1000 , HOH A:2498 , HOH A:3250	BINDING SITE FOR RESIDUE MG A9008
09	AC9	SOFTWARE	LYS A:116 , MET A:117 , ASN A:145 , GLN A:146 , PHE A:149 , ASP A:150 , TYR A:152 , ARG A:160 , LYS A:161 , PHE A:200 , HIS A:227 , HOH A:2498 , HOH A:2744 , HOH A:3237 , HOH A:3238 , HOH A:3239 , HOH A:3240 , HOH A:3241 , HOH A:3242 , HOH A:3244 , HOH A:3245 , HOH A:3246 , HOH A:3247 , HOH A:3248 , HOH A:3249 , HOH A:3251 , MG A:9008	BINDING SITE FOR RESIDUE COA A1000
10	BC1	SOFTWARE	ARG A:176 , ALA A:273 , CYS A:418 , PHE A:432 , ARG A:435 , LEU A:604 , ILE A:606 , HOH A:3252	BINDING SITE FOR RESIDUE PYR A1001
11	BC2	SOFTWARE	THR A:138 , GLU A:139 , LYS A:142 , GLU A:225 , ARG A:228 , GLN A:232 , HOH A:2454 , HOH A:2455 , HOH A:3253 , HOH A:3254 , HOH A:3255 , HOH A:3256 , HOH A:3257	BINDING SITE FOR RESIDUE DTL A9009
12	BC3	SOFTWARE	HIS A:68 , PRO A:70 , TYR A:125 , ASP A:324 , ASP A:330 , SER A:741 , HOH A:2297 , HOH A:3259 , HOH A:3260 , HOH A:3261 , HOH A:3262	BINDING SITE FOR RESIDUE DTL A9010
13	BC4	SOFTWARE	GLU A:40	BINDING SITE FOR RESIDUE PG4 A9011
14	BC5	SOFTWARE	ALA A:198 , GLN A:199 , SER A:202 , ARG A:516 , ASP A:517 , HOH A:3266	BINDING SITE FOR RESIDUE PG4 A9012
15	BC6	SOFTWARE	LEU A:648 , THR A:649 , LEU A:688 , GLY A:691 , TYR A:692 , HOH A:3267 , NA A:9004	BINDING SITE FOR RESIDUE PG4 A9013

(no "SS Bond" information available for 1H16)

Asymmetric Unit

No.	Residues
1	Glu A:368	-	Pro A:369

(no "SAP(SNP)/Variant" information available for 1H16)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFL	PS51554	Pyruvate formate-lyase domain profile.	PFLB_ECOLI	3-625	1	A:2-624
2	GLY_RADICAL_2	PS51149	Glycine radical domain profile.	PFLB_ECOLI	632-760	1	A:631-759
3	GLY_RADICAL_1	PS00850	Glycine radical domain signature.	PFLB_ECOLI	730-738	1	A:729-737

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFL	PS51554	Pyruvate formate-lyase domain profile.	PFLB_ECOLI	3-625	2	A:2-624
2	GLY_RADICAL_2	PS51149	Glycine radical domain profile.	PFLB_ECOLI	632-760	2	A:631-759
3	GLY_RADICAL_1	PS00850	Glycine radical domain signature.	PFLB_ECOLI	730-738	2	A:729-737

(no "Exon" information available for 1H16)

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
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Chain A from PDB  Type:PROTEIN  Length:759
 aligned with PFLB_ECOLI | P09373 from UniProtKB/Swiss-Prot  Length:760

    Alignment length:759
                                    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       691       701       711       721       731       741       751         
           PFLB_ECOLI     2 SELNEKLATAWEGFTKGDWQNEVNVRDFIQKNYTPYEGDESFLAGATEATTTLWDKVMEGVKLENRTHAPVDFDTAVASTITSHDAGYINKQLEKIVGLQTEAPLKRALIPFGGIKMIEGSCKAYNRELDPMIKKIFTEYRKTHNQGVFDVYTPDILRCRKSGVLTGLPDAYGRGRIIGDYRRVALYGIDYLMKDKLAQFTSLQADLENGVNLEQTIRLREEIAEQHRALGQMKEMAAKYGYDISGPATNAQEAIQWTYFGYLAAVKSQNGAAMSFGRTSTFLDVYIERDLKAGKITEQEAQEMVDHLVMKLRMVRFLRTPEYDELFSGDPIWATESIGGMGLDGRTLVTKNSFRFLNTLYTMGPSPEPNMTILWSEKLPLNFKKFAAKVSIDTSSLQYENDDLMRPDFNNDDYAIACCVSPMIVGKQMQFFGARANLAKTMLYAINGGVDEKLKMQVGPKSEPIKGDVLNYDEVMERMDHFMDWLAKQYITALNIIHYMHDKYSYEASLMALHDRDVIRTMACGIAGLSVAADSLSAIKYAKVKPIRDEDGLAIDFEIEGEYPQFGNNDPRVDDLAVDLVERFMKKIQKLHTYRDAIPTQSVLTITSNVVYGKKTGNTPDGRRAGAPFGPGANPMHGRDQKGAVASLTSVAKLPFAYAKDGISYTFSIVPNALGKDDEVRKTNLAGLMDGYFHHEASIEGGQHLNVNVMNREMLLDAMENPEKYPQLTIRVSGYAVRFNSLTKEQQQDVITRTFTQSM 760
               SCOP domains d1h16a_ A: Pyruvate formate-lyase, PFL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1h16A00 A:1-759  [code=3.20.70.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.....hhhhh..hhhhhhhhhh.....hhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee...........................eeeehhhhhhhhhhhhhhhh....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhhhhh.......eeeee..........hhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhhhh..eeeehhhhhhhhh...eeee...eeee...eeeeeeeeeehhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeeeeeehhhhhhhhhhhhhhheeeeee.....eeeeeee.........hhhhhhhhhhhhhhhhhhhhh..hhhhheeeeee...hhhhhhhhh...........................hhhhhhhhhhh.hhhhh..ee..eeeehhhhhh.hhhhhhhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhhhhhh...eee....eee.hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PFL  PDB: A:2-624 UniProt: 3-625                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ------GLY_RADICAL_2  PDB: A:631-759 UniProt: 632-760                                                                                    PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLY_RADIC---------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h16 A   1 SELNEKLATAWEGFTKGDWQNEVNVRDFIQKNYTPYEGDESFLAGATEATTTLWDKVMEGVKLENRTHAPVDFDTAVASTITSHDAGYINKQLEKIVGLQTEAPLKRALIPFGGIKMIEGSCKAYNRELDPMIKKIFTEYRKTHNQGVFDVYTPDILRCRKSGVLTGLPDAYGRGRIIGDYRRVALYGIDYLMKDKLAQFTSLQADLENGVNLEQTIRLREEIAEQHRALGQMKEMAAKYGYDISGPATNAQEAIQWTYFGYLAAVKSQNGAAMSFGRTSTFLDVYIERDLKAGKITEQEAQEMVDHLVMKLRMVRFLRTPEYDELFSGDPIWATESIGGMGLDGRTLVTKNSFRFLNTLYTMGPSPEPNMTILWSEKLPLNFKKFAAKVSIDTSSLQYENDDLMRPDFNNDDYAIACCVSPMIVGKQMQFFGARANLAKTMLYAINGGVDEKLKMQVGPKSEPIKGDVLNYDEVMERMDHFMDWLAKQYITALNIIHYMHDKYSYEASLMALHDRDVIRTMACGIAGLSVAADSLSAIKYAKVKPIRDEDGLAIDFEIEGEYPQFGNNDPRVDDLAVDLVERFMKKIQKLHTYRDAIPTQSVLTITSNVVYGKKTGNTPDGRRAGAPFGPGANPMHGRDQKGAVASLTSVAKLPFAYAKDGISYTFSIVPNALGKDDEVRKTNLAGLMDGYFHHEASIEGGQHLNVNVMNREMLLDAMENPEKYPQLTIRVSGYAVRFNSLTKEQQQDVITRTFTQSM 759
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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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: PFL-like glycyl radical enzymes (32)

Superfamily: PFL-like glycyl radical enzymes (32)

Family: PFL-like (11)

Protein domain: Pyruvate formate-lyase, PFL (8)

Escherichia coli [TaxId: 562] (8)

d1h16a_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: Anaerobic Ribonucleotide-triphosphate Reductase Large Chain (15)

Homologous Superfamily: [code=3.20.70.20, no name defined] (15)

Escherichia coli. Organism_taxid: 562 (6)

1h16A00

A:1-759

(no "Pfam Domain" information available for 1H16)

Asymmetric Unit(hide GO term definitions)

Chain A (PFLB_ECOLI | P09373)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0008861	formate C-acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + formate = CoA + pyruvate.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0006006	glucose metabolic process	The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0006567	threonine catabolic process	The chemical reactions and pathways resulting in the breakdown of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.
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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:368 - Pro A:369	[ RasMol ]

Biological Unit
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Access by PDB/NDB ID
	1h16
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	PFLB_ECOLI \| P09373
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	2.3.1.54
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	PFLB_ECOLI \| P09373
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UniProtKB/Swiss-Prot
	PFLB_ECOLI \| P09373	:	1cm5 1h17 1h18 1mzo 1qhm 2pfl 3pfl

1cm5	CRYSTAL STRUCTURE OF C418A,C419A MUTANT OF PFL FROM E.COLI
1h17	PYRUVATE FORMATE-LYASE (E.COLI) IN COMPLEX WITH COA AND THE SUBSTRATE ANALOG OXAMATE
1h18	PYRUVATE FORMATE-LYASE (E.COLI) IN COMPLEX WITH PYRUVATE
1qhm	ESCHERICHIA COLI PYRUVATE FORMATE LYASE LARGE DOMAIN
2pfl	CRYSTAL STRUCTURE OF PFL FROM E.COLI
3pfl	CRYSTAL STRUCTURE OF PFL FROM E.COLI IN COMPLEX WITH SUBSTRATE ANALOGUE OXAMATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

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SCOP Domains (1, 1)

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Gene Ontology (12, 12)

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Related Entries Specified in the PDB File