5A29 - JenaLib

Title :   FAMILY 2 PECTATE LYASE FROM VIBRIO VULNIFICUS

Authors :   R. Mclean, J. K. Hobbs, M. D. Suits, S. Tuomivaara, D. Jones, A. B. Borast D. W. Abbott

Date :   15 May 15 (Deposition) - 01 Jul 15 (Release) - 16 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Lyase, Pectin, Polysaccharide Lyase, Endolytic, Exolytic, Beta- Elimination, Ancestral Gene Resurrection, Magnesium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Mclean, J. K. Hobbs, M. D. Suits, S. T. Tuomivaara, D. Jones, A. B. Boraston, D. W. Abbott
Functional Analyses Of Resurrected And Contemporary Enzymes Illuminate An Evolutionary Path For The Emergence Of Exolysis In Polysaccharide Lyase Family 2.
J. Biol. Chem. V. 290 21231 2015
PubMed-ID: 26160170 | Reference-DOI: 10.1074/JBC.M115.664847

Compounds

Molecule 1 - EXOPOLYGALACTURONATE LYASE
	Chains	:	A
	Fragment	:	RESIDUES 19-566
	Organism Scientific	:	VIBRIO VULNIFICUS
	Organism Taxid	:	196600
	Strain	:	YJ016
	Synonym	:	PECTATE LYASE

Molecule 2 - PECTATE LYASE
	Chains	:	B
	Organism Scientific	:	VIBRIO VULNIFICUS
	Organism Taxid	:	196600
	Other Details	:	CUSTOM SYNTHESIZED, CODON OPTIMIZED CODING SEQUENCE
	Strain	:	YJ016
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Asymmetric/Biological Unit (3, 16)

No.	Name	Count	Type	Full Name
1	EDO	12	Ligand/Ion	1,2-ETHANEDIOL
2	MN	1	Ligand/Ion	MANGANESE (II) ION
3	SRT	3	Ligand/Ion	S,R MESO-TARTARIC ACID

Sites (16, 16)

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:129 , GLU A:150 , HIS A:192 , HOH A:2137 , HIS B:4 , HIS B:6	BINDING SITE FOR RESIDUE MN A 601
02	AC2	SOFTWARE	ASN A:298 , SER A:299 , ARG A:304 , TYR A:394 , HOH A:2197 , HOH A:2487 , HIS B:4 , HIS B:5 , HIS B:6	BINDING SITE FOR RESIDUE SRT B1018
03	AC3	SOFTWARE	LYS A:152 , SER A:326 , LYS A:329 , HOH A:2240 , HOH A:2321 , SER B:7 , SER B:8 , GLY B:9 , LEU B:10 , VAL B:11 , ARG B:13 , HIS B:16	BINDING SITE FOR RESIDUE SRT B1019
04	AC4	SOFTWARE	ILE A:230 , TYR A:266 , LYS A:267 , PRO A:277 , VAL A:278 , ILE A:331 , ASN A:335 , ALA A:336 , GLU A:339 , ALA A:358 , HOH A:2266	BINDING SITE FOR RESIDUE SRT A1568
05	AC5	SOFTWARE	LEU A:151 , PHE A:176 , HIS A:180 , GLY A:190 , ALA A:232 , HOH A:2152	BINDING SITE FOR RESIDUE EDO A1569
06	AC6	SOFTWARE	ARG A:418 , PHE A:467 , GLU A:471 , GLN A:474	BINDING SITE FOR RESIDUE EDO A1570
07	AC7	SOFTWARE	GLY A:190 , ARG A:191 , HIS A:192 , HOH A:2186 , HOH A:2487	BINDING SITE FOR RESIDUE EDO A1571
08	AC8	SOFTWARE	GLN A:84 , ARG A:88 , HIS A:154 , TYR A:155 , GLY A:541 , HOH A:2082 , HOH A:2089	BINDING SITE FOR RESIDUE EDO A1572
09	AC9	SOFTWARE	TYR A:508 , THR A:558 , TYR A:562 , HOH A:2488 , ARG B:13 , GLY B:14	BINDING SITE FOR RESIDUE EDO A1573
10	BC1	SOFTWARE	PHE A:160 , HOH A:2159	BINDING SITE FOR RESIDUE EDO A1574
11	BC2	SOFTWARE	GLN A:41 , ASP A:200 , LYS A:202 , ARG A:206	BINDING SITE FOR RESIDUE EDO A1575
12	BC3	SOFTWARE	ALA A:343 , ASN A:347 , ASP A:348 , ALA A:349 , ARG A:352 , HOH A:2388	BINDING SITE FOR RESIDUE EDO A1576
13	BC4	SOFTWARE	LEU A:340 , HIS A:341 , GLU A:344 , ARG A:421 , PRO A:537 , HOH A:2326 , HOH A:2384	BINDING SITE FOR RESIDUE EDO A1577
14	BC5	SOFTWARE	PHE A:204 , HIS A:205 , ARG A:206 , GLY A:254 , ALA A:257 , HOH A:2215 , HOH A:2259 , HOH A:2490	BINDING SITE FOR RESIDUE EDO A1578
15	BC6	SOFTWARE	TYR A:363 , TYR A:367 , GLU A:427 , HOH A:2393 , HOH A:2491	BINDING SITE FOR RESIDUE EDO A1579
16	BC7	SOFTWARE	SER A:443 , LYS A:451 , PRO A:452 , THR A:453 , HOH A:2412	BINDING SITE FOR RESIDUE EDO A1580

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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

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Chain A from PDB  Type:PROTEIN  Length:548
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhh............eee.......eee.....eeeeehhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.............eee.....ee................hhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhh................ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............ee.............hhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh............................................hhhhhhhhhhhh.hhhhhhhhhhhhhhh..ee.........ee.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhee..ee.......eee...hhhhhhhhhhhhhh.hhhhh..........eeee..eeeeehhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a29 A  19 ADYTEQDAMRVQAVKTYIDNVLQEGRSQIKTTPLLADGINTTTRKPVEWIYPDGRTATISNFANQQNFLRALTAMSVVTEDQRYQLEAVRITRYFMDNFIADNGLFYWGGHRFVNLDTLELEGPQNKNSVHELKNHYPYYPFLYHVDPHATERYIKAFWQAHVEDWQSLDMGRHGSYSKNYDDKVFHRPIPASLVDQSKLPIMPETKGLTFINAGSDLIYAAYQLDWLAPSANAQGSAAWGQYLMTQYKLAKHPKTGAPVYQFTSPKKREWPPQSDKDTNSKYGDRAARQFGPELGNIAREGNVLFKSNDKSIVFNNALIELHLAEQRNDAAIREQVVDALLNFYRLAYNPENGTIKPIFSDGTSIEGIPLARDGYYGPKGRVFNAHKPKTEEYLLPILRAYRLQADPELWQLAANMTHHYGWGSLGNDAKAKPTLNMQLSSVSPMTLFSAIELYQITQQPEYLEFARAAADKLVEKRFVRGYFLANPRYLNASIDAIEPLALLTLDATLKGKTAQVAPYLSGSGYIHGEFAGKENAYDTNEIYKQTR 566
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558

Chain B from PDB  Type:PROTEIN  Length:18
                                                  
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author .................. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 5a29 B   0 HHHHHHHSSGLVPRGSHA  17
                                     9

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

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