2VFQ - JenaLib

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Title :   LOW TEMPERATURE STRUCTURE OF P22 TAILSPIKE PROTEIN FRAGMENT (109-666), MUTANT V450A

Authors :   M. Becker, J. J. Mueller, U. Heinemann, R. Seckler

Date :   05 Nov 07 (Deposition) - 16 Dec 08 (Release) - 16 Dec 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   P22 Tailspike Protein, Salmonella Bacteriophage P22, Protein Folding, Protein Stability, Right-Handed Parallel Beta-Helix, Hydrolase, Late Protein, Endoglycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Becker, J. J. Mueller, T. Weikl, U. Heinemann, R. Seckler
Side-Chain Stacking And Beta-Helix Stability In P22 Tailspike Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - P22 TAILSPIKE PROTEIN,
	Chains	:	A
	EC Number	:	3.2.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P450ADN
	Expression System Strain	:	JM83
	Expression System Taxid	:	562
	Expression System Vector	:	PASK31
	Fragment	:	RESIDUES 110-667 LACKING THE N-TERMINAL HEAD- BINDING DOMAIN
	Mutation	:	YES
	Organism Common	:	BACTERIOPHAGE P22
	Organism Scientific	:	ENTEROBACTERIA PHAGE P22
	Organism Taxid	:	10754
	Synonym	:	P22 TAILSPIKE PROTEIN, MUTANT V450A, LATE PROTEIN GP9,TAILSPIKE-PROTEIN, TSP, ENDORHAMNOSIDASE, ENDO-1,3-ALPHA-L-RHAMNOSIDASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	12	Ligand/Ion	GLYCEROL
3	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:170 , ALA A:171 , LYS A:172 , LYS A:186 , HOH A:2802 , HOH A:2803	BINDING SITE FOR RESIDUE GOL A1667
2	AC2	SOFTWARE	GLU A:359 , LYS A:363 , HOH A:2495 , HOH A:2522 , HOH A:2804	BINDING SITE FOR RESIDUE GOL A1668
3	AC3	SOFTWARE	TYR A:555 , SER A:557 , ALA A:559 , LYS A:561 , HOH A:2805 , HOH A:2806 , HOH A:2807	BINDING SITE FOR RESIDUE GOL A1669
4	AC4	SOFTWARE	THR A:307 , TRP A:365 , VAL A:369 , HOH A:2420 , HOH A:2808	BINDING SITE FOR RESIDUE GOL A1670
5	AC5	SOFTWARE	THR A:235 , VAL A:236 , LYS A:302 , HOH A:2494 , HOH A:2809 , HOH A:2810 , HOH A:2811 , HOH A:2812	BINDING SITE FOR RESIDUE SO4 A1671
6	AC6	SOFTWARE	GLY A:244 , THR A:247 , HOH A:2813	BINDING SITE FOR RESIDUE SO4 A1672
7	AC7	SOFTWARE	LEU A:663 , HOH A:2796	BINDING SITE FOR RESIDUE CA A1673

(no "SS Bond" information available for 2VFQ)

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

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

(no "PROSITE Motif" information available for 2VFQ)

(no "Exon" information available for 2VFQ)

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:556
 aligned with FIBER_BPP22 | P12528 from UniProtKB/Swiss-Prot  Length:667

    Alignment length:556
                                   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      
          FIBER_BPP22   112 DQYSIEADKKFKYSVKLSDYPTLQDAASAAVDGLLIDRDYNFYGGETVDFGGKVLTIECKAKFIGDGNLIFTKLGKGSRIAGVFMESTTTPWVIKPWTDDNQWLTDAAAVVATLKQSKTDGYQPTVSDYVKFPGIETLLPPNAKGQNITSTLEIRECIGVEVHRASGLMAGFLFRGCHFCKMVDANNPSGGKDGIITFENLSGDWGKGNYVIGGRTSYGSVSSAQFLRNNGGFERDGGVIGFTSYRAGESGVKTWQGTVGSTTSRNYNLQFRDSVVIYPVWDGFDLGADTDMNPELDRPGDYPITQYPLHQLPLNHLIDNLLVRGALGVGFGMDGKGMYVSNITVEDCAGSGAYLLTHESVFTNIAIIDTNTKDFQANQIYISGACRVNGLRLIGIRSTDGQGLTIDAPNSTVSGITGMVDPSRINVANLAEEGLGNIRANSFGYDSAAIKLRIHKLSKTLDSGALYSHINGGAGSGSAYTQLTAISGSTPDAVSLKVNHKDCRGAEIPFVPDIASDDFIKDSSCFLPYWENNSTSLKALVKKPNGELVRLTLATL 667
               SCOP domains d2vfqa_ A: P22 tailspike protein                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2vfqA00 A:111-666  [code=2.160.20.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...eeehhh...hhhhhhh...eeee..eee.....eee......eeee..eee..eeeeee......eee..eee....................hhhhh...............hhhhh...hhhh..hhh......eeeeee.....eee..eee.eeeeee.....eee..eeeee.....eeee..........eee..eeee.....eeee..........eee..eee......eee...............eee..eee......eee..............................eee..eee......eeeeee..eee..eee......eeeeee..eee..eee...........eee....eee..ee............eee...eee..ee...hhh......................eeeeee...........eeeeeee........eeeeeeeee..eeeeeeeee.hhh..............hhh.....eeeeeee....eeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vfq A 111 DQYSIEADKKFKYSVKLSDYPTLQDAASAAVDGLLIDRDYNFYGGETVDFGGKVLTIECKAKFIGDGNLIFTKLGKGSRIAGVFMESTTTPWVIKPWTDDNQWLTDAAAVVATLKQSKTDGYQPTVSDYVKFPGIETLLPPNAKGQNITSTLEIRECIGVEVHRASGLMAGFLFRGCHFCKMVDANNPSGGKDGIITFENLSGDWGKGNYVIGGRTSYGSVSSAQFLRNNGGFERDGGVIGFTSYRAGESGVKTWQGTVGSTTSRNYNLQFRDSVVIYPVWDGFDLGADTDMNPELDRPGDYPITQYPLHQLPLNHLIDNLLVRGALGVGFGMDGKGMYASNITVEDCAGSGAYLLTHESVFTNIAIIDTNTKDFQANQIYISGACRVNGLRLIGIRSTDGQSLTIDAPNSTVSGITGMVDPSRINVANLAEEGLGNIRANSFGYDSAAIKLRIHKLSKTLDSGALYSHINGGAGSGSAYTQLTAISGSTPDAVSLKVNHKDCRGAEIPFVPDIASDDFIKDSSCFLPYWENNSTSLKALVKKPNGELVRLTLATL 666
                                   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       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: All beta proteins (24004)

Fold: Single-stranded right-handed beta-helix (140)

Superfamily: Pectin lyase-like (89)

Family: P22 tailspike protein (18)

Protein domain: P22 tailspike protein (18)

Salmonella phage P22 [TaxId: 10754] (18)

d2vfqa_

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 3 Solenoid (196)

Topology: Pectate Lyase C-like (105)

Homologous Superfamily: [code=2.160.20.20, no name defined] (19)

Bacteriophage p22 (Enterobacteria phage p22) (4)

2vfqA00

A:111-666

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

Asymmetric Unit(hide GO term definitions)

Chain A (FIBER_BPP22 | P12528)

molecular function
	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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
biological process
	GO:0085027	entry into host via enzymatic degradation of host anatomical structure	Penetration by symbiont of a host anatomical structure which provides a barrier to symbiont entry, mediated by symbiont degradative enzymes.
	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: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:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

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Biological Unit
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	2vfq
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	FIBER_BPP22 \| P12528
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	3.2.1.-
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1clw	TAILSPIKE PROTEIN FROM PHAGE P22, V331A MUTANT
1lkt	CRYSTAL STRUCTURE OF THE HEAD-BINDING DOMAIN OF PHAGE P22TAILSPIKE PROTEIN
1qa1	TAILSPIKE PROTEIN, MUTANT V331G
1qa2	TAILSPIKE PROTEIN, MUTANT A334V
1qa3	TAILSPIKE PROTEIN, MUTANT A334I
1qq1	TAILSPIKE PROTEIN, MUTANT E359G
1qrb	PLASTICITY AND STERIC STRAIN IN A PARALLEL BETA-HELIX:RATIONAL MUTATIONS IN P22 TAILSPIKE PROTEIN
1qrc	TAILSPIKE PROTEIN, MUTANT W391A
1tsp
1tyv	STRUCTURE OF TAILSPIKE-PROTEIN
2vfm	LOW TEMPERATURE STRUCTURE OF P22 TAILSPIKE PROTEIN FRAGMENT (109-666)
2vfn	LOW TEMPERATURE STRUCTURE OF P22 TAILSPIKE PROTEIN FRAGMENT (109-666), MUTANT V125A
2vfo	LOW TEMPERATURE STRUCTURE OF P22 TAILSPIKE PROTEIN FRAGMENT (109-666), MUTANT V125L
2vfp	LOW TEMPERATURE STRUCTURE OF P22 TAILSPIKE PROTEIN FRAGMENT (109-666), MUTANT V349L

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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